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An Evaluation of Different Partitioning Strategies for Bayesian Estimation of Species Divergence Times.

ABSTRACT: The explosive growth of molecular sequence data has made it possible to estimate species divergence times under relaxed-clock models using genome-scale data sets with many gene loci. In order to improve both model realism and to best extract information about relative divergence times in the sequence data, it is important to account for the heterogeneity in the evolutionary process across genes or genomic regions. Partitioning is a commonly used approach to achieve those goals. We group sites that have similar evolutionary characteristics into the same partition and those with different characteristics into different partitions, and then use different models or different values of model parameters for different partitions to account for the among-partition heterogeneity. However, how to partition data in practical phylogenetic analysis, and in particular in relaxed-clock dating analysis, is more art than science. Here, we use computer simulation and real data analysis to study the impact of the partition scheme on divergence time estimation. The partition schemes had relatively minor effects on the accuracy of posterior time estimates when the prior assumptions were correct and the clock was not seriously violated, but showed large differences when the clock was seriously violated, when the fossil calibrations were in conflict or incorrect, or when the rate prior was mis-specified. Concatenation produced the widest posterior intervals with the least precision. Use of many partitions increased the precision, as predicted by the infinite-sites theory, but the posterior intervals might fail to include the true ages because of the conflicting fossil calibrations or mis-specified rate priors. We analyzed a data set of 78 plastid genes from 15 plant species with serious clock violation and showed that time estimates differed significantly among partition schemes, irrespective of the rate drift model used. Multiple and precise fossil calibrations reduced the differences among partition schemes and were important to improving the precision of divergence time estimates. While the use of many partitions is an important approach to reducing the uncertainty in posterior time estimates, we do not recommend its general use for the present, given the limitations of current models of rate drift for partitioned data and the challenges of interpreting the fossil evidence to construct accurate and informative calibrations.

SUBMITTER: Angelis K

PROVIDER: S-EPMC5790132 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature

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An Evaluation of Different Partitioning Strategies for Bayesian Estimation of Species Divergence Times.

Angelis Konstantinos K Álvarez-Carretero Sandra S Dos Reis Mario M Yang Ziheng Z

Systematic biology 20180101 1

The explosive growth of molecular sequence data has made it possible to estimate species divergence times under relaxed-clock models using genome-scale data sets with many gene loci. In order to improve both model realism and to best extract information about relative divergence times in the sequence data, it is important to account for the heterogeneity in the evolutionary process across genes or genomic regions. Partitioning is a commonly used approach to achieve those goals. We group sites th ...[more]

PMID: 29029343

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Project description:Understanding causes of biological diversity may be greatly enhanced by knowledge of divergence times. Strict and relaxed clock models are used in Bayesian estimation of divergence times. We examined whether: i) strict clock models are generally more appropriate in shallow phylogenies where rate variation is expected to be low, ii) the likelihood ratio test of the clock (LRT) reliably informs which model is appropriate for dating divergence times. Strict and relaxed models were used to analyse sequences simulated under different levels of rate variation. Published shallow phylogenies (Black bass, Primate-sucking lice, Podarcis lizards, Gallotiinae lizards, and Caprinae mammals) were also analysed to determine natural levels of rate variation relative to the performance of the different models.Strict clock analyses performed well on data simulated under the independent rates model when the standard deviation of log rate on branches, ?, was low (? 0.1), but were inappropriate when ?>0.1 (95% of rates fall within 0.0082-0.0121 subs/site/Ma when ? = 0.1, for a mean rate of 0.01). The independent rates relaxed clock model performed well at all levels of rate variation, although posterior intervals on times were significantly wider than for the strict clock. The strict clock is therefore superior when rate variation is low. The performance of a correlated rates relaxed clock model was similar to the strict clock. Increased numbers of independent loci led to slightly narrower posteriors under the relaxed clock while older root ages provided proportionately narrower posteriors. The LRT had low power for ? = 0.01-0.1, but high power for ? = 0.5-2.0. Posterior means of ?2 were useful for assessing rate variation in published datasets. Estimates of natural levels of rate variation ranged from 0.05-3.38 for different partitions. Differences in divergence times between relaxed and strict clock analyses were greater in two datasets with higher ?2 for one or more partitions, supporting the simulation results.The strict clock can be superior for trees with shallow roots because of low levels of rate variation between branches. The LRT allows robust assessment of suitability of the clock model as does examination of posteriors on ?2.

Project description:BACKGROUND:Malagasy tenrecs belong to the Afrotherian clade of placental mammals and comprise three subfamilies divided in eight genera (Tenrecinae: Tenrec, Echinops, Setifer and Hemicentetes; Oryzorictinae: Oryzorictes, Limnogale and Microgale; Geogalinae:Geogale). The diversity of their morphology and incomplete taxon sampling made it difficult until now to resolve phylogenies based on either morphology or molecular data for this group. Therefore, in order to delineate the evolutionary history of this family, phylogenetic and dating analyses were performed on a four nuclear genes dataset (ADRA2B, AR, GHR and vWF) including all Malagasy tenrec genera. Moreover, the influence of both taxon sampling and data partitioning on the accuracy of the estimated ages were assessed. RESULTS:Within Afrotheria the vast majority of the nodes received a high support, including the grouping of hyrax with sea cow and the monophyly of both Afroinsectivora (Macroscelidea + Afrosoricida) and Afroinsectiphillia (Tubulidentata + Afroinsectivora). Strongly supported relationships were also recovered among all tenrec genera, allowing us to firmly establish the grouping of Geogale with Oryzorictinae, and to confirm the previously hypothesized nesting of Limnogale within the genus Microgale. The timeline of Malagasy tenrec diversification does not reflect a fast adaptive radiation after the arrival on Madagascar, indicating that morphological specializations have appeared over the whole evolutionary history of the family, and not just in a short period after colonization. In our analysis, age estimates at the root of a clade became older with increased taxon sampling of that clade. Moreover an augmentation of data partitions resulted in older age estimates as well, whereas standard deviations increased when more extreme partition schemes were used. CONCLUSION:Our results provide as yet the best resolved gene tree comprising all Malagasy tenrec genera, and may lead to a revision of tenrec taxonomy. A timeframe of tenrec evolution built on the basis of this solid phylogenetic framework showed that morphological specializations of the tenrecs may have been affected by environmental changes caused by climatic and/or subsequent colonization events. Analyses including various taxon sampling and data partitions allow us to point out some possible pitfalls that may lead to biased results in molecular dating; however, further analyses are needed to corroborate these observations.

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An Evaluation of Different Partitioning Strategies for Bayesian Estimation of Species Divergence Times.

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An Evaluation of Different Partitioning Strategies for Bayesian Estimation of Species Divergence Times.

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