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Winding up the molecular clock in the genus Carabus (Coleoptera: Carabidae): assessment of methodological decisions on rate and node age estimation.

Andújar C, Serrano J, Gómez-Zurita J - BMC Evol. Biol. (2012)

Bottom Line: 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).The 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Departamento de Zoología y Antropología Física, Facultad de Veterinaria, Universidad de Murcia, 30071 Murcia, Spain. candujar@um.es

ABSTRACT

Background: Rates 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.

Results: We 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.

Conclusions: The 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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Ultrametric time-calibrated trees obtained with BEAST for each individual (left) and combined datasets (right) of Carabus. Trees obtained with the ingroup dataset (including only Carabus species) and locus-specific optimal parameters. Nodes represented by black-filled circles received posterior probabilities (pp) higher than 0.9, bars represent 95% HPD intervals for node ages in Ma. The 95% HPD intervals of the TMRCA of Carabus are shaded in grey. Pie charts represent support (black, pp ≥ 0.95; dark grey, pp ≥ 0.85; light grey, pp ≥ 0.50; white, node not recovered) in MrBayes (outgroup dataset) and BEAST (outgroup and ingroup datasets) for calibration nodes A, B and C, for the different gene fragments: cox1-A (1), cox1-B (2), cob (3), nd5 (4), rrnL (5), LSU-A (6), LSU-B (7), ITS2 (8), HUWE1 (9), MIT (10), NUC (11) and MIT-NUC (12).
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Figure 2: Ultrametric time-calibrated trees obtained with BEAST for each individual (left) and combined datasets (right) of Carabus. Trees obtained with the ingroup dataset (including only Carabus species) and locus-specific optimal parameters. Nodes represented by black-filled circles received posterior probabilities (pp) higher than 0.9, bars represent 95% HPD intervals for node ages in Ma. The 95% HPD intervals of the TMRCA of Carabus are shaded in grey. Pie charts represent support (black, pp ≥ 0.95; dark grey, pp ≥ 0.85; light grey, pp ≥ 0.50; white, node not recovered) in MrBayes (outgroup dataset) and BEAST (outgroup and ingroup datasets) for calibration nodes A, B and C, for the different gene fragments: cox1-A (1), cox1-B (2), cob (3), nd5 (4), rrnL (5), LSU-A (6), LSU-B (7), ITS2 (8), HUWE1 (9), MIT (10), NUC (11) and MIT-NUC (12).

Mentions: For the mitochondrial dataset only two of the 34 specimens lacked one of the five sequenced fragments. In the case of nuclear genes six specimens lacked a single gene fragment, three lacked two loci and only one, within the outgroup taxa, lacked three fragments. Thus, completeness of the data matrices is very high and the effect of missing data is expected to be low. Bayesian phylogenetic analyses for the concatenated datasets resulted in the recovery of focal nodes A, B and C with posterior probability of 1.0 in all instances. Node A--split between Carabus (Macrothorax) rugosus and C. (M.) morbillosus--was found with a posterior probability (pp) higher than 0.95 for all individual DNA fragments except for LSU-B (pp = 0.74) and LSU-A (pp < 0.5). Node B--split of Carabus (Mesocarabus) riffensis from European Mesocarabus--appeared highly supported (pp > 0.95) for most individual DNA fragments, except for ITS2 (pp = 0.9), LSU-A (pp = 0.67), cox1-A and cob (pp < 0.5). Finally, node C--split between the subgenera Eurycarabus and Nesaeocarabus--was recovered for all individual fragments, although with pp < 0.85 in nd5, rrnl and LSU-B. Figure 2 shows support of nodes A, B and C as obtained with MrBayes and BEAST analyses.


Winding up the molecular clock in the genus Carabus (Coleoptera: Carabidae): assessment of methodological decisions on rate and node age estimation.

Andújar C, Serrano J, Gómez-Zurita J - BMC Evol. Biol. (2012)

Ultrametric time-calibrated trees obtained with BEAST for each individual (left) and combined datasets (right) of Carabus. Trees obtained with the ingroup dataset (including only Carabus species) and locus-specific optimal parameters. Nodes represented by black-filled circles received posterior probabilities (pp) higher than 0.9, bars represent 95% HPD intervals for node ages in Ma. The 95% HPD intervals of the TMRCA of Carabus are shaded in grey. Pie charts represent support (black, pp ≥ 0.95; dark grey, pp ≥ 0.85; light grey, pp ≥ 0.50; white, node not recovered) in MrBayes (outgroup dataset) and BEAST (outgroup and ingroup datasets) for calibration nodes A, B and C, for the different gene fragments: cox1-A (1), cox1-B (2), cob (3), nd5 (4), rrnL (5), LSU-A (6), LSU-B (7), ITS2 (8), HUWE1 (9), MIT (10), NUC (11) and MIT-NUC (12).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3368785&req=5

Figure 2: Ultrametric time-calibrated trees obtained with BEAST for each individual (left) and combined datasets (right) of Carabus. Trees obtained with the ingroup dataset (including only Carabus species) and locus-specific optimal parameters. Nodes represented by black-filled circles received posterior probabilities (pp) higher than 0.9, bars represent 95% HPD intervals for node ages in Ma. The 95% HPD intervals of the TMRCA of Carabus are shaded in grey. Pie charts represent support (black, pp ≥ 0.95; dark grey, pp ≥ 0.85; light grey, pp ≥ 0.50; white, node not recovered) in MrBayes (outgroup dataset) and BEAST (outgroup and ingroup datasets) for calibration nodes A, B and C, for the different gene fragments: cox1-A (1), cox1-B (2), cob (3), nd5 (4), rrnL (5), LSU-A (6), LSU-B (7), ITS2 (8), HUWE1 (9), MIT (10), NUC (11) and MIT-NUC (12).
Mentions: For the mitochondrial dataset only two of the 34 specimens lacked one of the five sequenced fragments. In the case of nuclear genes six specimens lacked a single gene fragment, three lacked two loci and only one, within the outgroup taxa, lacked three fragments. Thus, completeness of the data matrices is very high and the effect of missing data is expected to be low. Bayesian phylogenetic analyses for the concatenated datasets resulted in the recovery of focal nodes A, B and C with posterior probability of 1.0 in all instances. Node A--split between Carabus (Macrothorax) rugosus and C. (M.) morbillosus--was found with a posterior probability (pp) higher than 0.95 for all individual DNA fragments except for LSU-B (pp = 0.74) and LSU-A (pp < 0.5). Node B--split of Carabus (Mesocarabus) riffensis from European Mesocarabus--appeared highly supported (pp > 0.95) for most individual DNA fragments, except for ITS2 (pp = 0.9), LSU-A (pp = 0.67), cox1-A and cob (pp < 0.5). Finally, node C--split between the subgenera Eurycarabus and Nesaeocarabus--was recovered for all individual fragments, although with pp < 0.85 in nd5, rrnl and LSU-B. Figure 2 shows support of nodes A, B and C as obtained with MrBayes and BEAST analyses.

Bottom Line: 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).The 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Departamento de Zoología y Antropología Física, Facultad de Veterinaria, Universidad de Murcia, 30071 Murcia, Spain. candujar@um.es

ABSTRACT

Background: Rates 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.

Results: We 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.

Conclusions: The 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.

Show MeSH
Related in: MedlinePlus