Cargando…

Tip dating with fossil sites and stratigraphic sequences

Tip dating, a method of phylogenetic analysis in which fossils are included as terminals and assigned an age, is becoming increasingly widely used in evolutionary studies. Current implementations of tip dating allow fossil ages to be assigned as a point estimate, or incorporate uncertainty through t...

Descripción completa

Detalles Bibliográficos
Autores principales: King, Benedict, Rücklin, Martin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7323711/
https://www.ncbi.nlm.nih.gov/pubmed/32617191
http://dx.doi.org/10.7717/peerj.9368
_version_ 1783551821104545792
author King, Benedict
Rücklin, Martin
author_facet King, Benedict
Rücklin, Martin
author_sort King, Benedict
collection PubMed
description Tip dating, a method of phylogenetic analysis in which fossils are included as terminals and assigned an age, is becoming increasingly widely used in evolutionary studies. Current implementations of tip dating allow fossil ages to be assigned as a point estimate, or incorporate uncertainty through the use of uniform tip age priors. However, the use of tip age priors has the unwanted effect of decoupling the ages of fossils from the same fossil site. Here we introduce a new Markov Chain Monte Carlo (MCMC) proposal, which allows fossils from the same site to have linked ages, while still incorporating uncertainty in the age of the fossil site itself. We also include an extension, allowing fossil sites to be ordered in a stratigraphic column with age bounds applied only to the top and bottom of the sequence. These MCMC proposals are implemented in a new open-source BEAST2 package, palaeo. We test these new proposals on a dataset of early vertebrate fossils, concentrating on the effects on two sites with multiple acanthodian fossil taxa but wide age uncertainty, the Man On The Hill (MOTH) site from northern Canada, and the Turin Hill site from Scotland, both of Lochkovian (Early Devonian) age. The results show an increased precision of age estimates when fossils have linked tip ages compared to when ages are unlinked, and in this example leads to support for a younger age for the MOTH site compared with the Turin Hill site. There is also a minor effect on the tree topology of acanthodians. These new MCMC proposals should be widely applicable to studies that employ tip dating, particularly when the terminals are coded as individual specimens.
format Online
Article
Text
id pubmed-7323711
institution National Center for Biotechnology Information
language English
publishDate 2020
publisher PeerJ Inc.
record_format MEDLINE/PubMed
spelling pubmed-73237112020-07-01 Tip dating with fossil sites and stratigraphic sequences King, Benedict Rücklin, Martin PeerJ Evolutionary Studies Tip dating, a method of phylogenetic analysis in which fossils are included as terminals and assigned an age, is becoming increasingly widely used in evolutionary studies. Current implementations of tip dating allow fossil ages to be assigned as a point estimate, or incorporate uncertainty through the use of uniform tip age priors. However, the use of tip age priors has the unwanted effect of decoupling the ages of fossils from the same fossil site. Here we introduce a new Markov Chain Monte Carlo (MCMC) proposal, which allows fossils from the same site to have linked ages, while still incorporating uncertainty in the age of the fossil site itself. We also include an extension, allowing fossil sites to be ordered in a stratigraphic column with age bounds applied only to the top and bottom of the sequence. These MCMC proposals are implemented in a new open-source BEAST2 package, palaeo. We test these new proposals on a dataset of early vertebrate fossils, concentrating on the effects on two sites with multiple acanthodian fossil taxa but wide age uncertainty, the Man On The Hill (MOTH) site from northern Canada, and the Turin Hill site from Scotland, both of Lochkovian (Early Devonian) age. The results show an increased precision of age estimates when fossils have linked tip ages compared to when ages are unlinked, and in this example leads to support for a younger age for the MOTH site compared with the Turin Hill site. There is also a minor effect on the tree topology of acanthodians. These new MCMC proposals should be widely applicable to studies that employ tip dating, particularly when the terminals are coded as individual specimens. PeerJ Inc. 2020-06-26 /pmc/articles/PMC7323711/ /pubmed/32617191 http://dx.doi.org/10.7717/peerj.9368 Text en ©2020 King and Rücklin https://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Evolutionary Studies
King, Benedict
Rücklin, Martin
Tip dating with fossil sites and stratigraphic sequences
title Tip dating with fossil sites and stratigraphic sequences
title_full Tip dating with fossil sites and stratigraphic sequences
title_fullStr Tip dating with fossil sites and stratigraphic sequences
title_full_unstemmed Tip dating with fossil sites and stratigraphic sequences
title_short Tip dating with fossil sites and stratigraphic sequences
title_sort tip dating with fossil sites and stratigraphic sequences
topic Evolutionary Studies
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7323711/
https://www.ncbi.nlm.nih.gov/pubmed/32617191
http://dx.doi.org/10.7717/peerj.9368
work_keys_str_mv AT kingbenedict tipdatingwithfossilsitesandstratigraphicsequences
AT rucklinmartin tipdatingwithfossilsitesandstratigraphicsequences