The modern molecular clock

Bromham, Lindell; Penny, David

doi:10.1038/nrg1020

Cited by 557 publications

(465 citation statements)

References 68 publications

(105 reference statements)

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“…In practice, this typically means that the hypotheses being tested should have dates separated by hundreds of thousands to millions of years. It is the responsibility of the researcher to fully report uncertainty associated with time estimates (Bromham and Penny, 2003;Graur and Martin, 2004;Parham, 2012). Uncertainty associated with fossil ages and strata can be easily incorporated as priors in Bayesian phylogenetic analyses (e.g., Drummond et al, 2006).…”

Section: Discussionmentioning

confidence: 99%

The emerging field of geogenomics: Constraining geological problems with genetic data

Baker

Fritz

Dick³

et al. 2014

Earth-Science Reviews

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The development of a genomics-derived discipline within geology is timely, as a result of major advances in acquiring and processing geologically relevant genetic data. This paper articulates the emerging field of "geogenomics," which involves the use of large-scale genetic data to constrain geological hypotheses. The paper introduces geogenomics and discusses how hypotheses can be addressed through collaboration between geologists and evolutionary biologists. As an example, geogenomic methods are applied to evaluate competing hypotheses regarding the timing of the Andean uplift, the closure of the Isthmus of Panama, the onset of trans-Amazon drainage, and Quaternary climate variation in the Neotropics.

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Section: Discussionmentioning

confidence: 99%

The emerging field of geogenomics: Constraining geological problems with genetic data

Baker

Fritz

Dick³

et al. 2014

Earth-Science Reviews

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“…Straka, 2004). This necessarily results in highly reduced long-term gross metabolic rates and longer effective generation times in these taxa, and hence it is probable that their rates of molecular evolution differ from those of other arthropods that lack such prolonged dormant stages (for a review of factors affecting rates of molecular evolution, see Bromham and Penny, 2003).…”

Section: Introductionmentioning

confidence: 99%

Molecular phylogeny of the Notostraca

Korn

Rabet

Ghate³

et al. 2013

Molecular Phylogenetics and Evolution

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a b s t r a c tWe used a combined analysis of one nuclear (28S rDNA) and three mitochondrial markers (COI, 12S rDNA, 16S rDNA) to infer the molecular phylogeny of the Notostraca, represented by samples from the six continents that are inhabited by this group of branchiopod crustaceans. Our results confirm the monophyly of both extant notostracan genera Triops and Lepidurus with good support in model based and maximum parsimony analyses. We used branchiopod fossils as a calibration to infer divergence times among notostracan lineages and accounted for rate heterogeneity among lineages by applying relaxed-clock models. Our divergence date estimates indicate an initial diversification into the genera Triops and Lepidurus in the Mesozoic, most likely at a minimum age of 152.3-233.5 Ma, i.e., in the Triassic or Jurassic. Implications for the interpretation of fossils and the evolution of notostracan morphology are discussed. We further use the divergence date estimates to formulate a biogeographic hypothesis that explains distributions of extant lineages predominantly by overland dispersal routes. We identified an additional hitherto unrecognised highly diverged lineage within Lepidurus apus lubbocki and three additional previously unknown major lineages within Triops. Within T. granarius we found deep differentiation, with representatives distributed among three major phylogenetic lineages. One of these major lineages comprises T. cancriformis, the T. mauritanicus species group and two hitherto unrecognised T. granarius lineages. Samples that were morphologically identified as T. granarius diverged from the most basal nodes within this major lineage, and divergence dates suggested an approximate age of 23.7-49.6 Ma for T. cancriformis, indicating the need for a taxonomic revision of Triassic and Permian fossils that are currently attributed to the extant T. cancriformis. We thus elevate T. cancriformis minor to full species status as Triops minor Trusheim, 1938 and include in this species the additional Upper Triassic samples that were attributed to T. cancriformis. We further elevate T. cancriformis permiensis to full species status as Triops permiensis Gand et al., 1997.

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“…It should be stressed here, as by Bromham and Penny (2003), that lineage-specific variation in rate of molecular evolution can complicate molecular dating, because a calibration rate estimated from one lineage may not be an accurate representation of the rate in other lineages. Also, estimation of divergence time is generally more difficult than reconstruction of a phylogenetic tree, because no gene would evolve at a constant rate (Glazko and Nei, 2003).…”

Section: Introductionmentioning

confidence: 99%