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The evolution of methods for establishing evolutionary timescales.

Donoghue PC, Yang Z - Philos. Trans. R. Soc. Lond., B, Biol. Sci. (2016)

Bottom Line: While the molecular clock can be used to extend the time estimates from fossil species to lineages not represented in the fossil record, fossils are the only source of information concerning absolute (geological) times in molecular dating analysis.While node-calibrations are often constructed by a crude assessment of the fossil evidence and thus involves arbitrariness, tip-calibrations may be too sensitive to the prior on divergence times or the branching process and influenced unduly affected by well-known problems of morphological character evolution, such as environmental influence on morphological phenotypes, correlation among traits, and convergent evolution in disparate species.We discuss the utility of time information from fossils in phylogeny estimation and the search for ancestors in the fossil record.This article is part of the themed issue 'Dating species divergences using rocks and clocks'.

View Article: PubMed Central - PubMed

Affiliation: School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK phil.donoghue@bristol.ac.uk.

No MeSH data available.


Tip-calibration relies upon a molecular sequence alignment from living species, a morphological character set for living and fossil species, and a prior topology (a); total-evidence dating co-estimates topology and timescale. Branch lengths are estimated in a Bayesian MCMC approach based on both data types for living lineages and based on morphological data alone for the extinct lineages; these are calibrated to time based on the age of the fossil species (b). The divergence time estimates and inferred rates of molecular and morphological evolution are based on a consensus of the MCMC analysis (c). (Online version in colour.)
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RSTB20160020F3: Tip-calibration relies upon a molecular sequence alignment from living species, a morphological character set for living and fossil species, and a prior topology (a); total-evidence dating co-estimates topology and timescale. Branch lengths are estimated in a Bayesian MCMC approach based on both data types for living lineages and based on morphological data alone for the extinct lineages; these are calibrated to time based on the age of the fossil species (b). The divergence time estimates and inferred rates of molecular and morphological evolution are based on a consensus of the MCMC analysis (c). (Online version in colour.)

Mentions: The desire to overcome inconsistency between specified and effective node-calibrations is one of the motivations behind the development of alternative approaches to calibrating molecular clocks through the integration of morphological data and tip-calibration methods that include fossil species as terminal taxa among their extant relatives [16,74] (figureĀ 3). Tip-calibration is often considered synonymous with the so-called total-evidence dating approach that also facilitates the simultaneous estimation of time and topology [16]. However, because these two approaches can be employed separately, we will first consider tip-calibration before going on to appraise total-evidence dating.Figure 3.


The evolution of methods for establishing evolutionary timescales.

Donoghue PC, Yang Z - Philos. Trans. R. Soc. Lond., B, Biol. Sci. (2016)

Tip-calibration relies upon a molecular sequence alignment from living species, a morphological character set for living and fossil species, and a prior topology (a); total-evidence dating co-estimates topology and timescale. Branch lengths are estimated in a Bayesian MCMC approach based on both data types for living lineages and based on morphological data alone for the extinct lineages; these are calibrated to time based on the age of the fossil species (b). The divergence time estimates and inferred rates of molecular and morphological evolution are based on a consensus of the MCMC analysis (c). (Online version in colour.)
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4920342&req=5

RSTB20160020F3: Tip-calibration relies upon a molecular sequence alignment from living species, a morphological character set for living and fossil species, and a prior topology (a); total-evidence dating co-estimates topology and timescale. Branch lengths are estimated in a Bayesian MCMC approach based on both data types for living lineages and based on morphological data alone for the extinct lineages; these are calibrated to time based on the age of the fossil species (b). The divergence time estimates and inferred rates of molecular and morphological evolution are based on a consensus of the MCMC analysis (c). (Online version in colour.)
Mentions: The desire to overcome inconsistency between specified and effective node-calibrations is one of the motivations behind the development of alternative approaches to calibrating molecular clocks through the integration of morphological data and tip-calibration methods that include fossil species as terminal taxa among their extant relatives [16,74] (figureĀ 3). Tip-calibration is often considered synonymous with the so-called total-evidence dating approach that also facilitates the simultaneous estimation of time and topology [16]. However, because these two approaches can be employed separately, we will first consider tip-calibration before going on to appraise total-evidence dating.Figure 3.

Bottom Line: While the molecular clock can be used to extend the time estimates from fossil species to lineages not represented in the fossil record, fossils are the only source of information concerning absolute (geological) times in molecular dating analysis.While node-calibrations are often constructed by a crude assessment of the fossil evidence and thus involves arbitrariness, tip-calibrations may be too sensitive to the prior on divergence times or the branching process and influenced unduly affected by well-known problems of morphological character evolution, such as environmental influence on morphological phenotypes, correlation among traits, and convergent evolution in disparate species.We discuss the utility of time information from fossils in phylogeny estimation and the search for ancestors in the fossil record.This article is part of the themed issue 'Dating species divergences using rocks and clocks'.

View Article: PubMed Central - PubMed

Affiliation: School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK phil.donoghue@bristol.ac.uk.

No MeSH data available.