Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record
The branching times of molecular phylogenies allow us to infer speciation and extinction dynamics even when fossils are absent. Troublingly, phylogenetic approaches usually return estimates of zero extinction, conflicting with fossil evidence. Phylogenies and fossils do agree, however, that there ar...
Published in: | Proceedings of the Royal Society B: Biological Sciences |
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Online Access: | https://hdl.handle.net/11370/f25254e8-67df-4c5f-8710-cda7f8858553 https://research.rug.nl/en/publications/f25254e8-67df-4c5f-8710-cda7f8858553 https://doi.org/10.1098/rspb.2011.1439 |
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ftunigroningenpu:oai:pure.rug.nl:publications/f25254e8-67df-4c5f-8710-cda7f8858553 2024-09-09T20:04:07+00:00 Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record Etienne, Rampal S. Haegeman, Bart Stadler, Tanja Aze, Tracy Pearson, Paul N. Purvis, Andy Phillimore, Albert B. 2012-04-07 https://hdl.handle.net/11370/f25254e8-67df-4c5f-8710-cda7f8858553 https://research.rug.nl/en/publications/f25254e8-67df-4c5f-8710-cda7f8858553 https://doi.org/10.1098/rspb.2011.1439 eng eng https://research.rug.nl/en/publications/f25254e8-67df-4c5f-8710-cda7f8858553 info:eu-repo/semantics/closedAccess Etienne , R S , Haegeman , B , Stadler , T , Aze , T , Pearson , P N , Purvis , A & Phillimore , A B 2012 , ' Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record ' , Proceedings of the Royal Society of London. Series B, Biological Sciences , vol. 279 , no. 1732 , pp. 1300-1309 . https://doi.org/10.1098/rspb.2011.1439 birth-death model diversification missing species BIRTH-DEATH-MODELS EVOLUTIONARY RADIATIONS EXTINCTION RATES DIVERSIFICATION RATES SPECIES-DIVERSITY DYNAMICS SPECIATION ACCUMULATION BUTTERFLIES PATTERNS article 2012 ftunigroningenpu https://doi.org/10.1098/rspb.2011.1439 2024-06-17T15:56:51Z The branching times of molecular phylogenies allow us to infer speciation and extinction dynamics even when fossils are absent. Troublingly, phylogenetic approaches usually return estimates of zero extinction, conflicting with fossil evidence. Phylogenies and fossils do agree, however, that there are often limits to diversity. Here, we present a general approach to evaluate the likelihood of a phylogeny under a model that accommodates diversity-dependence and extinction. We find, by likelihood maximization, that extinction is estimated most precisely if the rate of increase in the number of lineages in the phylogeny saturates towards the present or first decreases and then increases. We demonstrate the utility and limits of our approach by applying it to the phylogenies for two cases where a fossil record exists (Cetacea and Cenozoic macroperforate planktonic foraminifera) and to three radiations lacking fossil evidence (Dendroica, Plethodon and Heliconius). We propose that the diversity-dependence model with extinction be used as the standard model for macro-evolutionary dynamics because of its biological realism and flexibility. Article in Journal/Newspaper Planktonic foraminifera University of Groningen research database Proceedings of the Royal Society B: Biological Sciences 279 1732 1300 1309 |
institution |
Open Polar |
collection |
University of Groningen research database |
op_collection_id |
ftunigroningenpu |
language |
English |
topic |
birth-death model diversification missing species BIRTH-DEATH-MODELS EVOLUTIONARY RADIATIONS EXTINCTION RATES DIVERSIFICATION RATES SPECIES-DIVERSITY DYNAMICS SPECIATION ACCUMULATION BUTTERFLIES PATTERNS |
spellingShingle |
birth-death model diversification missing species BIRTH-DEATH-MODELS EVOLUTIONARY RADIATIONS EXTINCTION RATES DIVERSIFICATION RATES SPECIES-DIVERSITY DYNAMICS SPECIATION ACCUMULATION BUTTERFLIES PATTERNS Etienne, Rampal S. Haegeman, Bart Stadler, Tanja Aze, Tracy Pearson, Paul N. Purvis, Andy Phillimore, Albert B. Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record |
topic_facet |
birth-death model diversification missing species BIRTH-DEATH-MODELS EVOLUTIONARY RADIATIONS EXTINCTION RATES DIVERSIFICATION RATES SPECIES-DIVERSITY DYNAMICS SPECIATION ACCUMULATION BUTTERFLIES PATTERNS |
description |
The branching times of molecular phylogenies allow us to infer speciation and extinction dynamics even when fossils are absent. Troublingly, phylogenetic approaches usually return estimates of zero extinction, conflicting with fossil evidence. Phylogenies and fossils do agree, however, that there are often limits to diversity. Here, we present a general approach to evaluate the likelihood of a phylogeny under a model that accommodates diversity-dependence and extinction. We find, by likelihood maximization, that extinction is estimated most precisely if the rate of increase in the number of lineages in the phylogeny saturates towards the present or first decreases and then increases. We demonstrate the utility and limits of our approach by applying it to the phylogenies for two cases where a fossil record exists (Cetacea and Cenozoic macroperforate planktonic foraminifera) and to three radiations lacking fossil evidence (Dendroica, Plethodon and Heliconius). We propose that the diversity-dependence model with extinction be used as the standard model for macro-evolutionary dynamics because of its biological realism and flexibility. |
format |
Article in Journal/Newspaper |
author |
Etienne, Rampal S. Haegeman, Bart Stadler, Tanja Aze, Tracy Pearson, Paul N. Purvis, Andy Phillimore, Albert B. |
author_facet |
Etienne, Rampal S. Haegeman, Bart Stadler, Tanja Aze, Tracy Pearson, Paul N. Purvis, Andy Phillimore, Albert B. |
author_sort |
Etienne, Rampal S. |
title |
Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record |
title_short |
Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record |
title_full |
Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record |
title_fullStr |
Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record |
title_full_unstemmed |
Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record |
title_sort |
diversity-dependence brings molecular phylogenies closer to agreement with the fossil record |
publishDate |
2012 |
url |
https://hdl.handle.net/11370/f25254e8-67df-4c5f-8710-cda7f8858553 https://research.rug.nl/en/publications/f25254e8-67df-4c5f-8710-cda7f8858553 https://doi.org/10.1098/rspb.2011.1439 |
genre |
Planktonic foraminifera |
genre_facet |
Planktonic foraminifera |
op_source |
Etienne , R S , Haegeman , B , Stadler , T , Aze , T , Pearson , P N , Purvis , A & Phillimore , A B 2012 , ' Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record ' , Proceedings of the Royal Society of London. Series B, Biological Sciences , vol. 279 , no. 1732 , pp. 1300-1309 . https://doi.org/10.1098/rspb.2011.1439 |
op_relation |
https://research.rug.nl/en/publications/f25254e8-67df-4c5f-8710-cda7f8858553 |
op_rights |
info:eu-repo/semantics/closedAccess |
op_doi |
https://doi.org/10.1098/rspb.2011.1439 |
container_title |
Proceedings of the Royal Society B: Biological Sciences |
container_volume |
279 |
container_issue |
1732 |
container_start_page |
1300 |
op_container_end_page |
1309 |
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1809936176133439488 |