ArticleBMC evolutionary biology2012
Winding up the molecular clock in the genus Carabus (Coleoptera: Carabidae): assessment of methodological decisions on rate and node age estimation.
Article in BMC evolutionary biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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23 citing papers in PubMed.
- Article
- Article
- Molecular phylogeny of mega-diverse Carabus attests late Miocene evolution of alpine environments in the Himalayan-Tibetan Orogen.Scientific reports · 2023Article
- Dispersal ability and its consequences for population genetic differentiation and diversification.Proceedings. Biological sciences · 2022Article
- Molecular and biometric data onZooKeys · 2022Article
- HyRAD-X Exome Capture Museomics Unravels Giant Ground Beetle Evolution.Genome biology and evolution · 2021Article
- Chronological Incongruences between Mitochondrial and Nuclear Phylogenies ofLife (Basel, Switzerland) · 2021Article
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- The mitochondrial genome of the Jeju ground beetleMitochondrial DNA. Part B, Resources · 2019Article
- Pleistocene climate change and the formation of regional species pools.Proceedings. Biological sciences · 2019Article
- The role of dispersal for shaping phylogeographical structure of flightless beetles from the Andes.PeerJ · 2019Article
- The first stygobiont species of Coleoptera from Portugal, with a molecular phylogeny of theZooKeys · 2019Article
- Diatraea saccharalis history of colonization in the Americas. The case for human-mediated dispersal.PloS one · 2019Article
- Long-term population persistence of flightless weevils (Eurhoptus pyriformis) across old- and second-growth forests patches in southern Appalachia.BMC evolutionary biology · 2018Article
- A biogeographical profile of the sand cockroachEcology and evolution · 2018Article
- Transoceanic origin of microendemic and flightless New Caledonian weevils.Royal Society open science · 2017Article
- The discovery of Iberobaeniidae (Coleoptera: Elateroidea): a new family of beetles from Spain, with immatures detected by environmental DNA sequencing.Proceedings. Biological sciences · 2016Article
- Macroevolution of hyperdiverse flightless beetles reflects the complex geological history of the Sunda Arc.Scientific reports · 2016Article
- Article
- Thermal niche evolution and geographical range expansion in a species complex of western Mediterranean diving beetles.BMC evolutionary biology · 2014Article
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3 authors.
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Abstract
backgroundRates of molecular evolution are known to vary across taxa and among genes, and this requires rate calibration for each specific dataset based on external information. Calibration is sensitive to evolutionary model parameters, partitioning schemes and clock model. However, the way in which these and other analytical aspects affect both the rates and the resulting clade ages from calibrated phylogenies are not yet well understood. To investigate these aspects we have conducted calibration analyses for the genus Carabus (Coleoptera, Carabidae) on five mitochondrial and four nuclear DNA fragments with 7888 nt total length, testing different clock models and partitioning schemes to select the most suitable using Bayes Factors comparisons.
resultsWe used these data to investigate the effect of ambiguous character and outgroup inclusion on both the rates of molecular evolution and the TMRCA of Carabus. We found considerable variation in rates of molecular evolution depending on the fragment studied (ranging from 5.02% in cob to 0.26% divergence/My in LSU-A), but also on analytical conditions. Alternative choices of clock model, partitioning scheme, treatment of ambiguous characters, and outgroup inclusion resulted in rate increments ranging from 28% (HUWE1) to 1000% (LSU-B and ITS2) and increments in the TMRCA of Carabus ranging from 8.4% (cox1-A) to 540% (ITS2). Results support an origin of the genus Carabus during the Oligocene in the Eurasian continent followed by a Miocene differentiation that originated all main extant lineages.
conclusionsThe combination of several genes is proposed as the best strategy to minimise both the idiosyncratic behaviors of individual markers and the effect of analytical aspects in rate and age estimations. Our results highlight the importance of estimating rates of molecular evolution for each specific dataset, selecting for optimal clock and partitioning models as well as other methodological issues potentially affecting rate estimation.
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