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EXTINCTION RATES SHOULD NOT BE ESTIMATED FROM MOLECULAR PHYLOGENIES

Molecular phylogenies contain information about the tempo and mode of species diversification through time. Because extinction leaves a characteristic signature in the shape of molecular phylogenetic trees, many studies have used data from extant taxa only to infer extinction rates. This is a promis... Full description

Journal Title: Evolution 2010-06, Vol.64 (6), p.1816-1824
Main Author: Rabosky, Daniel L.
Format: Electronic Article Electronic Article
Language: English
Subjects:
Publisher: Malden, USA: Blackwell Publishing Inc
ID: ISSN: 0014-3820
Link: https://www.ncbi.nlm.nih.gov/pubmed/20030708
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title: EXTINCTION RATES SHOULD NOT BE ESTIMATED FROM MOLECULAR PHYLOGENIES
format: Article
creator:
  • Rabosky, Daniel L.
subjects:
  • Adaptation (Biology)
  • Adaptive radiation
  • Biological taxonomies
  • Cladistic analysis
  • Estimated taxes
  • Evolution
  • Extinct species
  • Extinction
  • Extinction (Biology)
  • Extinction, Biological
  • macroevolution
  • Mass extinction events
  • Models, Biological
  • Molecular biology
  • Phylogenetics
  • Phylogeny
  • Population genetics
  • Speciation
  • Species extinction
  • Statistical variance
  • Taxonomy
  • Usage
ispartof: Evolution, 2010-06, Vol.64 (6), p.1816-1824
description: Molecular phylogenies contain information about the tempo and mode of species diversification through time. Because extinction leaves a characteristic signature in the shape of molecular phylogenetic trees, many studies have used data from extant taxa only to infer extinction rates. This is a promising approach for the large number of taxa for which extinction rates cannot be estimated from the fossil record. Here, I explore the consequences of violating a common assumption made by studies of extinction from phylogenetic data. I show that when diversification rates vary among lineages, simple estimators based on the birth-death process are unable to recover true extinction rates. This is problematic for phylogenetic trees with complete taxon sampling as well as for the simpler case of clades with known age and species richness. Given the ubiquity of variation in diversification rates among lineages and clades, these results suggest that extinction rates should not be estimated in the absence of fossil data.
language: eng
source:
identifier: ISSN: 0014-3820
fulltext: no_fulltext
issn:
  • 0014-3820
  • 1558-5646
url: Link


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descriptionMolecular phylogenies contain information about the tempo and mode of species diversification through time. Because extinction leaves a characteristic signature in the shape of molecular phylogenetic trees, many studies have used data from extant taxa only to infer extinction rates. This is a promising approach for the large number of taxa for which extinction rates cannot be estimated from the fossil record. Here, I explore the consequences of violating a common assumption made by studies of extinction from phylogenetic data. I show that when diversification rates vary among lineages, simple estimators based on the birth-death process are unable to recover true extinction rates. This is problematic for phylogenetic trees with complete taxon sampling as well as for the simpler case of clades with known age and species richness. Given the ubiquity of variation in diversification rates among lineages and clades, these results suggest that extinction rates should not be estimated in the absence of fossil data.
editionReceived February 17, 2009Accepted December 3, 2009
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subjectAdaptation (Biology) ; Adaptive radiation ; Biological taxonomies ; Cladistic analysis ; Estimated taxes ; Evolution ; Extinct species ; Extinction ; Extinction (Biology) ; Extinction, Biological ; macroevolution ; Mass extinction events ; Models, Biological ; Molecular biology ; Phylogenetics ; Phylogeny ; Population genetics ; Speciation ; Species extinction ; Statistical variance ; Taxonomy ; Usage
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abstractMolecular phylogenies contain information about the tempo and mode of species diversification through time. Because extinction leaves a characteristic signature in the shape of molecular phylogenetic trees, many studies have used data from extant taxa only to infer extinction rates. This is a promising approach for the large number of taxa for which extinction rates cannot be estimated from the fossil record. Here, I explore the consequences of violating a common assumption made by studies of extinction from phylogenetic data. I show that when diversification rates vary among lineages, simple estimators based on the birth-death process are unable to recover true extinction rates. This is problematic for phylogenetic trees with complete taxon sampling as well as for the simpler case of clades with known age and species richness. Given the ubiquity of variation in diversification rates among lineages and clades, these results suggest that extinction rates should not be estimated in the absence of fossil data.
copMalden, USA
pubBlackwell Publishing Inc
pmid20030708
doi10.1111/j.1558-5646.2009.00926.x
tpages9
editionReceived February 17, 2009Accepted December 3, 2009
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