The implications of lineage-specific rates for divergence time estimation
Rate variation adds considerable complexity to divergence time estimation in molecular phylogenies. Here, we evaluate the impact of lineage-specific rates—which we define as among-branch-rate-variation that acts consistently across the entire genome. We compare its impact to residual rates—defined a...
| Main Authors: | , , |
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| Format: | Journal article |
| Language: | English |
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Oxford University Press
2019
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| _version_ | 1826282909357572096 |
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| author | Carruthers, T Sanderson, MJ Scotland, RW |
| author_facet | Carruthers, T Sanderson, MJ Scotland, RW |
| author_sort | Carruthers, T |
| collection | OXFORD |
| description | Rate variation adds considerable complexity to divergence time estimation in molecular phylogenies. Here, we evaluate the impact of lineage-specific rates—which we define as among-branch-rate-variation that acts consistently across the entire genome. We compare its impact to residual rates—defined as among-branch-rate-variation that shows a different pattern of rate variation at each sampled locus, and gene-specific rates—defined as variation in the average rate across all branches at each sampled locus. We show that lineage-specific rates lead to erroneous divergence time estimates, regardless of how many loci are sampled. Further, we show that stronger lineage-specific rates lead to increasing error. This contrasts to residual rates and gene-specific rates, where sampling more loci significantly reduces error. If divergence times are inferred in a Bayesian framework, we highlight that error caused by lineage-specific rates significantly reduces the probability that the 95% highest posterior density includes the correct value, and leads to sensitivity to the prior. Use of a more complex rate prior—which has recently been proposed to model rate variation more accurately—does not affect these conclusions. Finally, we show that the scale of lineage-specific rates used in our simulation experiments is comparable to that of an empirical data set for the angiosperm genus Ipomoea. Taken together, our findings demonstrate that lineage-specific rates cause error in divergence time estimates, and that this error is not overcome by analyzing genomic scale multilocus data sets. |
| first_indexed | 2024-03-07T00:50:57Z |
| format | Journal article |
| id | oxford-uuid:86642c35-e147-44a5-b96a-57f4c34898ba |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T00:50:57Z |
| publishDate | 2019 |
| publisher | Oxford University Press |
| record_format | dspace |
| spelling | oxford-uuid:86642c35-e147-44a5-b96a-57f4c34898ba2022-03-26T22:03:37ZThe implications of lineage-specific rates for divergence time estimationJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:86642c35-e147-44a5-b96a-57f4c34898baEnglishSymplectic Elements at OxfordOxford University Press2019Carruthers, TSanderson, MJScotland, RWRate variation adds considerable complexity to divergence time estimation in molecular phylogenies. Here, we evaluate the impact of lineage-specific rates—which we define as among-branch-rate-variation that acts consistently across the entire genome. We compare its impact to residual rates—defined as among-branch-rate-variation that shows a different pattern of rate variation at each sampled locus, and gene-specific rates—defined as variation in the average rate across all branches at each sampled locus. We show that lineage-specific rates lead to erroneous divergence time estimates, regardless of how many loci are sampled. Further, we show that stronger lineage-specific rates lead to increasing error. This contrasts to residual rates and gene-specific rates, where sampling more loci significantly reduces error. If divergence times are inferred in a Bayesian framework, we highlight that error caused by lineage-specific rates significantly reduces the probability that the 95% highest posterior density includes the correct value, and leads to sensitivity to the prior. Use of a more complex rate prior—which has recently been proposed to model rate variation more accurately—does not affect these conclusions. Finally, we show that the scale of lineage-specific rates used in our simulation experiments is comparable to that of an empirical data set for the angiosperm genus Ipomoea. Taken together, our findings demonstrate that lineage-specific rates cause error in divergence time estimates, and that this error is not overcome by analyzing genomic scale multilocus data sets. |
| spellingShingle | Carruthers, T Sanderson, MJ Scotland, RW The implications of lineage-specific rates for divergence time estimation |
| title | The implications of lineage-specific rates for divergence time estimation |
| title_full | The implications of lineage-specific rates for divergence time estimation |
| title_fullStr | The implications of lineage-specific rates for divergence time estimation |
| title_full_unstemmed | The implications of lineage-specific rates for divergence time estimation |
| title_short | The implications of lineage-specific rates for divergence time estimation |
| title_sort | implications of lineage specific rates for divergence time estimation |
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