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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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Mean rates of molecular evolution and TMRCA of Carabus based on non-coding gene fragments. Rates are given in substitutions per site per million years per lineage, and TMRCA of Carabus in millions of years before present. Different clock models, ambiguous character and outgroup inclusion/exclusion were considered.
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Figure 6: Mean rates of molecular evolution and TMRCA of Carabus based on non-coding gene fragments. Rates are given in substitutions per site per million years per lineage, and TMRCA of Carabus in millions of years before present. Different clock models, ambiguous character and outgroup inclusion/exclusion were considered.

Mentions: The effect of gapped characters on rate and node age estimation was assessed in all gene fragments showing sequence length variation (Figure 6). In the case of ribosomal genes, the exclusion of gapped positions (nogaps option in Gblocks) had a noticeable effect lowering the estimates of evolutionary rates and ingroup age, up to three-fold, for the most variable gene fragments, hence with gappier alignments (ITS2 and LSU-B). These gene fragments diminished by 50 and 90% of aligned nucleotide positions, respectively, with a dramatic loss of phylogenetic information and great oscillations in the estimated parameters. Expectedly, more length-conserved fragments (LSU-A and rrnL) were only slightly affected by character culling in Gblocks, with 27 and 1% of character loss, respectively, under the most conservative nogaps treatment, and consequently showed lower variation, particularly in estimation of evolutionary rates. Less restrictive character culling approaches (allgaps option in Gblocks) preserved more characters to be used for branch length estimation and produced intermediate results, still with significant effects on rate estimation for highly variable markers, but not so much for that of the TMRCA of Carabus in the case of ITS2 and LSU-B data. The estimated mean node age in these cases was affected to a higher extent by outgroup inclusion/exclusion and by the clock model.


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)

Mean rates of molecular evolution and TMRCA of Carabus based on non-coding gene fragments. Rates are given in substitutions per site per million years per lineage, and TMRCA of Carabus in millions of years before present. Different clock models, ambiguous character and outgroup inclusion/exclusion were considered.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 6: Mean rates of molecular evolution and TMRCA of Carabus based on non-coding gene fragments. Rates are given in substitutions per site per million years per lineage, and TMRCA of Carabus in millions of years before present. Different clock models, ambiguous character and outgroup inclusion/exclusion were considered.
Mentions: The effect of gapped characters on rate and node age estimation was assessed in all gene fragments showing sequence length variation (Figure 6). In the case of ribosomal genes, the exclusion of gapped positions (nogaps option in Gblocks) had a noticeable effect lowering the estimates of evolutionary rates and ingroup age, up to three-fold, for the most variable gene fragments, hence with gappier alignments (ITS2 and LSU-B). These gene fragments diminished by 50 and 90% of aligned nucleotide positions, respectively, with a dramatic loss of phylogenetic information and great oscillations in the estimated parameters. Expectedly, more length-conserved fragments (LSU-A and rrnL) were only slightly affected by character culling in Gblocks, with 27 and 1% of character loss, respectively, under the most conservative nogaps treatment, and consequently showed lower variation, particularly in estimation of evolutionary rates. Less restrictive character culling approaches (allgaps option in Gblocks) preserved more characters to be used for branch length estimation and produced intermediate results, still with significant effects on rate estimation for highly variable markers, but not so much for that of the TMRCA of Carabus in the case of ITS2 and LSU-B data. The estimated mean node age in these cases was affected to a higher extent by outgroup inclusion/exclusion and by the clock model.

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