Estimating the rate of evolution of the rate of molecular evolution

Thorne, Jeffrey L.; Kishino, Hirohisa; Painter, Ian

doi:10.1093/oxfordjournals.molbev.a025892

Cited by 1,201 publications

(1,153 citation statements)

References 22 publications

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“…Additionally, a Bayesian dating method was used to infer divergence time estimates and associated confidence intervals (Kishino et al, 2001). The procedure outlined in Rutschmann (2005) was followed, which involves the use of three programs: Baseml (PAML3.15; Yang, 1997), Estbranches (Thorne et al, 1998), and Multidivtime (Thorne and Kishino, 2002). Model parameters (base frequencies, transition/transversion ratio, and alpha shape parameter of the gamma distribution accounting for among-site rate heterogeneity) were estimated using the most complex substitution model implemented in Baseml, F84+G.…”

Section: Molecular-clock Analysesmentioning

confidence: 99%

Δ6-Desaturase sequence evidence for explosive Pliocene radiations within the adaptive radiation of Macaronesian Echium (Boraginaceae)

Garcı́a-Maroto

Mañas-Fernández

Garrido-Cárdenas

et al. 2009

Molecular Phylogenetics and Evolution

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a b s t r a c tThe oceanic islands of Macaronesia provide an ideal temporal and spatial context to test hypotheses of plant evolution using a novel set of phylogenetic markers, D 6 -desaturase sequences. In contrast to the limited resolution of standard molecular markers (nrDNA and plastid sequences), the D 6 -desaturase sequence phylogeny of Echium unequivocally reconstructs its active colonization across islands and archipelagos (Madeira, the Canary Islands, and Cape Verde), as well as its subsequent geographical and ecological speciation. Molecular-clock estimates using penalized likelihood and Bayesian inference reveal two radiation processes coincident with two dramatic climatic changes recorded in the region: the advent of the cold Canarian sea current (ca. 4 Ma) and the establishment of a strong seasonality in the Pleistocene (1.8 Ma). Though Echium had available all the diversity of present-day Macaronesian environments (xeric and mesic scrub, laurisilva, pine forest, and subalpine habitats) in the Miocene, evolutionary divergence appears to have been triggered by an extension of fluctuating xeric and mesic habitats with the advent of Pliocene conditions. These Echium radiations not only fulfill traditional predictions of adaptive radiation (i.e., common ancestry, rapid speciation, and phenotype-environment correlation), but also, uniquely among Macaronesian species, trait utility of woodiness. A Pliocene transition from annuality to a bush or tree-like condition occurred in early Echium lineages. Maintenance of woodiness in major lineages, and reversal to an herbaceous condition by three independent events, is reported for the first time in plants of oceanic islands.

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Section: Molecular-clock Analysesmentioning

confidence: 99%

Δ6-Desaturase sequence evidence for explosive Pliocene radiations within the adaptive radiation of Macaronesian Echium (Boraginaceae)

Garcı́a-Maroto

Mañas-Fernández

Garrido-Cárdenas

et al. 2009

Molecular Phylogenetics and Evolution

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“…Second, we used Ludwig et al's (2001) phylogeny among extant acipenseriform species to estimate the divergence time among these groups using mitochondrial cytochrome b gene sequences data retrieved from GenBank (Table 2-including inferred ploidy levels of acipenseriforms). Bayesian approaches (Thorne et al, 1998;Thorne and Kishino, 2002), one of the relaxed molecular clock methods, were used for the two dating analyses, the setting for Bayesian approaches were as follows.…”

Section: Sequence Analysis and Molecular Datingmentioning

confidence: 99%

“…Divergence times were determined using a Bayesian approach that incorporates variation of rates of evolution among genes and among lineages (Thorne et al, 1998;Thorne and Kishino, 2002), which were estimated with MULTIDIVTIME program (available from J. Thorne). This parametric approach relaxes the assumption of a strict Table 2 Twenty-four mitochondrial cytochrome b gene sequences used for dating the divergence time of acipenseriform species retrieved from GenBank for the second dating analysis a Nine distribution areas were coded from A to I according to the analysis of Bemis and Kynard (1997) (Yang, 1994) along with their variance-covariance matrix.…”

Section: Sequence Analysis and Molecular Datingmentioning

confidence: 99%

Age and biogeography of major clades in sturgeons and paddlefishes (Pisces: Acipenseriformes)

Peng

Ludwig

Wang

et al. 2007

Molecular Phylogenetics and Evolution

145

119

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“…At first we applied a global clock to a linearized tree as described in Michaux et al (2001). Secondly, we imposed a relaxed clock which allows for a heterogenous substitution rate according to Thorne et al (1998). Both methods already produced overlapping results (Michaux et al, 2001;Steppan et al, 2004).…”

Section: Molecular Clocks and Divergence Timementioning

confidence: 99%

Molecular phylogeny of the Cricetinae subfamily based on the mitochondrial cytochrome b and 12S rRNA genes and the nuclear vWF gene

Neumann

Michaux

Lebedev

et al. 2006

Molecular Phylogenetics and Evolution

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Despite some popularity of hamsters as pets and laboratory animals there is no reliable phylogeny of the subfamily Cricetinae available so far. Contradicting views exist not only about the actual number of species but also concerning the validity of several genera. We used partial DNA sequences of two mitochondrial (cytochrome b, 12S rRNA) and one partial nuclear gene (von Willebrand Factor exon 28) to provide a first gene tree of the Cricetinae based on 15 taxa comprising six genera. According to our data, Palaearctic hamsters fall into three distinct phylogenetic groups: Phodopus, Mesocricetus, and Cricetus-related species which evolved during the late Miocene about 7-12 MY ago. Surprisingly, the genus Phodopus, which was previously thought to have appeared during the Pleistocene, forms the oldest clade. The largest number of extant hamster genera is found in a group of Cricetus-related hamsters. The genus Cricetulus itself proved to be not truly monophyletic with Cricetulus migratorius appearing more closely related to Tscherskia, Cricetus, and Allocricetulus. We propose to place the species within a new monotypic genus. Molecular clock calculations are not always in line with the dating of fossil records. DNA based divergence time estimates as well as taxonomic relationships demand a reevaluation of morphological characters previously used to identify fossils and extant hamsters.

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Estimating the rate of evolution of the rate of molecular evolution

Cited by 1,201 publications

References 22 publications

Δ6-Desaturase sequence evidence for explosive Pliocene radiations within the adaptive radiation of Macaronesian Echium (Boraginaceae)

Δ6-Desaturase sequence evidence for explosive Pliocene radiations within the adaptive radiation of Macaronesian Echium (Boraginaceae)

Age and biogeography of major clades in sturgeons and paddlefishes (Pisces: Acipenseriformes)

Molecular phylogeny of the Cricetinae subfamily based on the mitochondrial cytochrome b and 12S rRNA genes and the nuclear vWF gene

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