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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 combined data. Rates are given in substitutions per site per million years per lineage, and TMRCA of Carabus in millions of years before present. Different partitioning schemes, clock models and outgroup inclusion/exclusion were considered.
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Figure 5: Mean rates of molecular evolution and TMRCA of Carabus based on combined data. Rates are given in substitutions per site per million years per lineage, and TMRCA of Carabus in millions of years before present. Different partitioning schemes, clock models and outgroup inclusion/exclusion were considered.

Mentions: Data partitioning affected protein coding gene fragments (partitioning by codon positions) and concatenated datasets (partitioning by gene and by codon positions). A general trend was observed whereby the average values for the evolutionary rates and the estimated ingroup age increased with the number of partitions considered, both for individual markers (Wilcoxon signed rank test on mean rate, P < 0.01 for all partitioning treatment comparisons; Wilcoxon signed rank test on median TMRCA of Carabus, P < 0.01 for all comparisons) and their concatenation (Wilcoxon signed rank test on mean rate: P < 0.01 for all comparisons except for comparison of partitioning G-2P vs. G-3P, P = 0.058; Wilcoxon signed rank test on median TMRCA of Carabus: comparison of NP vs. G-1P, P = 0.151; G-1P vs. G-2P, P < 0.01; G-2P vs. G-3P, P = 0.016). This trend was found irrespective of the clock model enforced (Figures 4 and 5), and it was particularly exacerbated in the case of the rate estimated for nd5 and the entire dataset, which tripled its value compared to non-partitioned data when three partitions where considered, without remarkable effects on the estimation of the ingroup age. On the other hand, the coding region of the HUWE1 gene fragment showed invariable rates and estimated ingroup age independently of the partitioning strategy employed. Values for mean rates and TMRCA of Carabus and their associated 95% HPD intervals for each analysis are provided in Additional file 1: Tables S4 and S5, respectively.


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 combined data. Rates are given in substitutions per site per million years per lineage, and TMRCA of Carabus in millions of years before present. Different partitioning schemes, clock models 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 5: Mean rates of molecular evolution and TMRCA of Carabus based on combined data. Rates are given in substitutions per site per million years per lineage, and TMRCA of Carabus in millions of years before present. Different partitioning schemes, clock models and outgroup inclusion/exclusion were considered.
Mentions: Data partitioning affected protein coding gene fragments (partitioning by codon positions) and concatenated datasets (partitioning by gene and by codon positions). A general trend was observed whereby the average values for the evolutionary rates and the estimated ingroup age increased with the number of partitions considered, both for individual markers (Wilcoxon signed rank test on mean rate, P < 0.01 for all partitioning treatment comparisons; Wilcoxon signed rank test on median TMRCA of Carabus, P < 0.01 for all comparisons) and their concatenation (Wilcoxon signed rank test on mean rate: P < 0.01 for all comparisons except for comparison of partitioning G-2P vs. G-3P, P = 0.058; Wilcoxon signed rank test on median TMRCA of Carabus: comparison of NP vs. G-1P, P = 0.151; G-1P vs. G-2P, P < 0.01; G-2P vs. G-3P, P = 0.016). This trend was found irrespective of the clock model enforced (Figures 4 and 5), and it was particularly exacerbated in the case of the rate estimated for nd5 and the entire dataset, which tripled its value compared to non-partitioned data when three partitions where considered, without remarkable effects on the estimation of the ingroup age. On the other hand, the coding region of the HUWE1 gene fragment showed invariable rates and estimated ingroup age independently of the partitioning strategy employed. Values for mean rates and TMRCA of Carabus and their associated 95% HPD intervals for each analysis are provided in Additional file 1: Tables S4 and S5, respectively.

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