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: 9.11). 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.

    • "The BSP for clade B suggested constant population size through time followed by a slight decline and a further rise that seems to continue until present (Fig. 5). Based on the COI divergence rate of 3.54 % My -1 (Papadopoulou et al., 2010), the expansion started approximately 28,000 years ago. "
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    ABSTRACT: The evolutionary history of invasive species within their native range may involve key processes that allow them to colonize new habitats. Therefore, phylogeographic studies of invasive species within their native ranges are useful to understand invasion biology in an evolutionary context. Here we integrated classical and Bayesian phylogeographic methods using mitochondrial and nuclear DNA markers with a paleodistribution modeling approach, to infer the phylogeographic history of the invasive ant Wasmannia auropunctata across its native distribution in South America. We discuss our results in the context of the recent establishment of this mostly tropical species in the Mediterranean region. Our Bayesian phylogeographic analysis suggests that the common ancestor of the two main clades of W. auropunctata occurred in central Brazil during the Pliocene. Clade A would have differentiated northward and clade B southward, followed by a secondary contact beginning about 380,000 years ago in central South America. There were differences in the most suitable habitats among clades when considering three distinct climatic periods, suggesting that genetic differentiation was accompanied by changes in niche requirements, clade A being a tropical lineage and clade B a subtropical and temperate lineage. Only clade B reached more southern latitudes, with a colder climate than that of northern South America. This is concordant with the adaptation of this originally tropical ant species to temperate climates prior to its successful establishment in the Mediterranean region. This study highlights the usefulness of exploring the evolutionary history of invasive species within their native ranges to better understand biological invasions. This article is protected by copyright. All rights reserved.
    No preview · Article · Jan 2016 · Journal of Evolutionary Biology
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    • "The earliest findings were obtained in genetic studies of carnivores (Wayne et al. 1991), humans (Howell et al. 2003) and birds (Garc ıa-Moreno 2004). Subsequent large-scale, data-rich analyses of mitochondrial DNA have revealed time-dependent biases in rate estimates from a broad cross section of taxa (Fig. 1), including insects (Papadopoulou et al. 2010; Ho & Lo 2013), primates and birds (Ho et al. 2005; Subramanian et al. 2009), fish (Genner et al. 2007; Burridge et al. 2008) and amniotes (Molak & Ho 2015). A number of investigations of mitochondrial genome evolution within species have yielded evidence of timedependent rate estimates. "
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    ABSTRACT: We are writing in response to a recent critique by Emerson & Hickerson (2015), who challenge the evidence of a time-dependent bias in molecular rate estimates. This bias takes the form of a negative relationship between inferred evolutionary rates and the ages of the calibrations on which these estimates are based. Here, we present a summary of the evidence obtained from a broad range of taxa that supports a time-dependent bias in rate estimates, with a consideration of the potential causes of these observed trends. We also describe recent progress in improving the reliability of evolutionary rate estimation and respond to the concerns raised by Emerson & Hickerson (2015) about the validity of rates estimated from time-structured sequence data. In doing so, we hope to dispel some misconceptions and to highlight several research directions that will improve our understanding of time-dependent biases in rate estimates.
    Preview · Article · Dec 2015
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    • "Images of caudiculatus and compressicauda syntypes and their labels: Antoine Mantilleri, © MNHN. NA substitution rate of distantly related Tenebrionidae (Papadopoulou et al. 2010). The obtained dates of the Trichalophus cladogenesis (Fig. 4) are comparable to those of the sympatric and similarly high-altitude and flightless weevil genus Niphadomimus Zherikhin, 1987 (Grebennikov 2014a). "

    Full-text · Article · Dec 2015 · Bonn Zoological Bulletin
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