Article

Revisiting the insect mitochondrial molecular clock: the mid-Aegean Trench calibration.

Department of Entomology, Natural History Museum, London, United Kingdom.
Molecular Biology and Evolution (Impact Factor: 14.31). 02/2010; 27(7):1659-72. DOI: 10.1093/molbev/msq051
Source: PubMed

ABSTRACT Phylogenetic trees in insects are frequently dated by applying a "standard" mitochondrial DNA (mtDNA) clock estimated at 2.3% My(-1), but despite its wide use reliable calibration points have been lacking. Here, we used a well-established biogeographic barrier, the mid-Aegean trench separating the western and eastern Aegean archipelago, to estimate substitution rates in tenebrionid beetles. Cytochrome oxidase I (cox1) for six codistributed genera across 28 islands (444 individuals) on both sides of the mid-Aegean trench revealed 60 independently coalescing entities delimited with a mixed Yule-coalescent model. One representative per entity was used for phylogenetic analysis of mitochondrial (cox1, 16S rRNA) and nuclear (Mp20, 28S rRNA) genes. Six nodes marked geographically congruent east-west splits whose separation was largely contemporaneous and likely to reflect the formation of the mid-Aegean trench at 9-12 Mya. Based on these "known" dates, a divergence rate of 3.54% My(-1) for the cox1 gene (2.69% when combined with the 16S rRNA gene) was obtained under the preferred partitioning scheme and substitution model selected using Bayes factors. An extensive survey suggests that discrepancies in mtDNA substitution rates in the entomological literature can be attributed to the use of different substitution models, the use of different mitochondrial gene regions, mixing of intraspecific with interspecific data, and not accounting for variance in coalescent times or postseparation gene flow. Different treatments of these factors in the literature confound estimates of mtDNA substitution rates in opposing directions and obscure lineage-specific differences in rates when comparing data from various sources.

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    • "Isthmus of Panama: The appearance of this narrow land mass about 2.8 myr ago divided ancestral Atlantic and Pacific populations of tropical marine organisms (Knowlton and Weigt 1998; Marko 2002) and provided a corridor for the dispersal of North American terrestrial species into South America (Stehli and Webb 1985). Sardinia-Corsica: Ketmaier et al. 2003; Mattoccia et al. 2011 Strait of Gibraltar: Marino et al. 2011; Dong et al. 2012; Yu et al. 2013 Aegean Sea: Beerli et al. 1996; Papadopoulou et al. 2010 Volcanic island: Croucher et al. 2012; Mello and Schrago 2012 Japan Archipelago land bridges: Hope et al. 2010 Fossils: Calibration of nodes in phylogenetic tree with the first appearance of a taxon in the fossil record The first appearance of a taxon in the fossil record establishes the latest date for the origin of the taxon. These anchor points in phylogeny may underestimate the timing of a node. "
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    ABSTRACT: Sequence mismatch analysis (MMA) and Bayesian skyline plots (BSP) are commonly used to reconstruct historical demography. A survey of 173 research articles (2009-2014), which included estimates of historical population sizes from mtDNA or cpDNA, shows a widespread genetic signature of demographic or spatial population expansion in species of all major taxonomic groups. Associating these expansions with climatic events can provide insights into the origins of lineage diversity, range expansions (or contractions), and speciation. However, several variables can introduce error into reconstructions of demographic history, including levels of sequence polymorphism, sampling scheme, sample size, natural selection, and estimates of mutation rate. Most researchers use substitution rates estimated from divergences in phylogenetic trees dated with fossils, or geological events. Recent studies show that molecular clocks calibrated with phylogenetic divergences can overestimate the timings of population-level events by an order of magnitude. Overestimates disconnect historical population reconstructions from climatic history and confound our understanding of the factors influencing genetic variability. If mismatch distributions and BSPs largely reflect demographic history, the widespread signature of population expansion in vertebrate, invertebrate, and plant populations appears to reflect responses to postglacial climate warming. © The American Genetic Association 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
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    • "In both species, we used coalescent-based approaches to estimate the time of divergence between East Asia and other populations, which would indicate a minimum time of presence of these species on the European continent (as they are thought to have colonized Eurasia from North America), assuming the observed differentiation has started to occur in Eurasia. For both species, we assessed divergence times by calibrating the COI molecular clock rate with the widely used substitution rate in insect of 0.0115 substitutions/site/my/lineage (Brower 1994) because of its proximity with the arithmetic mean retrieved from the literature on Coleoptera (0.0114) (0.0075, Farrell 2001; 0.008, Sota & Hayashi 2007; 0.0125, Caccone & Sbordoni 2001 and 0.0177, Papadopoulou et al. 2010). Divergence time estimates were obtained with BEAST for COI data in both species. "
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    • "In both species, we used coalescent-based approaches to estimate the time of divergence between East Asia and other populations, which would indicate a minimum time of presence of these species on the European continent (as they are thought to have colonized Eurasia from North America), assuming the observed differentiation has started to occur in Eurasia. For both species, we assessed divergence times by calibrating the COI molecular clock rate with the widely used substitution rate in insect of 0.0115 substitutions/site/my/lineage (Brower 1994) because of its proximity with the arithmetic mean retrieved from the literature on Coleoptera (0.0114) (0.0075, Farrell 2001; 0.008, Sota & Hayashi 2007; 0.0125, Caccone & Sbordoni 2001 and 0.0177, Papadopoulou et al. 2010). Divergence time estimates were obtained with BEAST for COI data in both species. "
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