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Citation for Study 10620

Citation title: "Rate Heterogeneity, Ancestral Character State Reconstruction, and the Evolution of Limb Morphology in Lerista (Scincidae, Squamata)".

Study name: "Rate Heterogeneity, Ancestral Character State Reconstruction, and the Evolution of Limb Morphology in Lerista (Scincidae, Squamata)".

This study is part of submission 10610 (Status: Published).

Citation

Skinner A. 2010. Rate Heterogeneity, Ancestral Character State Reconstruction, and the Evolution of Limb Morphology in Lerista (Scincidae, Squamata). Systematic Biology, .

Authors

• Skinner A. (submitter)

Abstract

Rates of phenotypic evolution derive from numerous interrelated processes acting at varying spatial and temporal scales, and frequently differ substantially among lineages. Although current models employed in reconstructing ancestral character states permit independent rates for distinct types of transition (forward and reverse transitions, and transitions between different states), these rates are typically assumed to be identical for all branches in a phylogeny. In this paper, I present a general model of character evolution enabling rate heterogeneity among branches. This model is employed in assessing the extent to which the assumption of uniform transition rates affects reconstructions of ancestral limb morphology in the scincid lizard clade Lerista and, accordingly, the potential for rate variability to mislead inferences of evolutionary patterns. Permitting rate variation among branches significantly improves model fit for both the manus and pes. A constrained model in which the rate of digit acquisition is assumed to be effectively zero is strongly supported in each case; when compared with a model assuming unconstrained transition rates, this model provides a substantially better fit for the manus and a nearly identical fit for the pes. Ancestral states reconstructed assuming the constrained model imply patterns of limb evolution differing significantly from those implied by reconstructions for uniform-rate models, particularly for the pes; while ancestral states for the uniform-rate models consistently entail the reacquisition of pedal digits, those for the model incorporating among-lineage rate heterogeneity imply repeated, unreversed digit loss. These results indicate that the assumption of identical transition rates for all branches in a phylogeny may be inappropriate in modelling the evolution of phenotypic traits, and emphasise the need for careful evaluation of phylogenetic tests of Dollo's law.

Keywords

Character evolution, Dollo's law, likelihood, limb reduction, lizard, model, skink

External links

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S10620
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref19027,
  	 author = {Adam  Skinner},
  	 title = {Rate Heterogeneity, Ancestral Character State Reconstruction, and the Evolution of Limb Morphology in Lerista (Scincidae, Squamata)},
  	 year = {2010},
  	 keywords = {Character evolution, Dollo's law, likelihood, limb reduction, lizard, model, skink},
  	 doi = {},
  	 url = {http://},
  	 pmid = {},
  	 journal = {Systematic Biology},
  	 volume = {},
  	 number = {},
  	 pages = {},
  	 abstract = {Rates of phenotypic evolution derive from numerous interrelated processes acting at varying spatial and temporal scales, and frequently differ substantially among lineages.  Although current models employed in reconstructing ancestral character states permit independent rates for distinct types of transition (forward and reverse transitions, and transitions between different states), these rates are typically assumed to be identical for all branches in a phylogeny.  In this paper, I present a general model of character evolution enabling rate heterogeneity among branches.  This model is employed in assessing the extent to which the assumption of uniform transition rates affects reconstructions of ancestral limb morphology in the scincid lizard clade Lerista and, accordingly, the potential for rate variability to mislead inferences of evolutionary patterns.  Permitting rate variation among branches significantly improves model fit for both the manus and pes.  A constrained model in which the rate of digit acquisition is assumed to be effectively zero is strongly supported in each case; when compared with a model assuming unconstrained transition rates, this model provides a substantially better fit for the manus and a nearly identical fit for the pes.  Ancestral states reconstructed assuming the constrained model imply patterns of limb evolution differing significantly from those implied by reconstructions for uniform-rate models, particularly for the pes; while ancestral states for the uniform-rate models consistently entail the reacquisition of pedal digits, those for the model incorporating among-lineage rate heterogeneity imply repeated, unreversed digit loss.  These results indicate that the assumption of identical transition rates for all branches in a phylogeny may be inappropriate in modelling the evolution of phenotypic traits, and emphasise the need for careful evaluation of phylogenetic tests of Dollo's law.}
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 19027
  AU  - Skinner,Adam 
  T1  - Rate Heterogeneity, Ancestral Character State Reconstruction, and the Evolution of Limb Morphology in Lerista (Scincidae, Squamata)
  PY  - 2010
  KW  - Character evolution
  KW  - Dollo's law
  KW  - likelihood
  KW  - limb reduction
  KW  - lizard
  KW  - model
  KW  - skink
  UR  - http://dx.doi.org/
  N2  - Rates of phenotypic evolution derive from numerous interrelated processes acting at varying spatial and temporal scales, and frequently differ substantially among lineages.  Although current models employed in reconstructing ancestral character states permit independent rates for distinct types of transition (forward and reverse transitions, and transitions between different states), these rates are typically assumed to be identical for all branches in a phylogeny.  In this paper, I present a general model of character evolution enabling rate heterogeneity among branches.  This model is employed in assessing the extent to which the assumption of uniform transition rates affects reconstructions of ancestral limb morphology in the scincid lizard clade Lerista and, accordingly, the potential for rate variability to mislead inferences of evolutionary patterns.  Permitting rate variation among branches significantly improves model fit for both the manus and pes.  A constrained model in which the rate of digit acquisition is assumed to be effectively zero is strongly supported in each case; when compared with a model assuming unconstrained transition rates, this model provides a substantially better fit for the manus and a nearly identical fit for the pes.  Ancestral states reconstructed assuming the constrained model imply patterns of limb evolution differing significantly from those implied by reconstructions for uniform-rate models, particularly for the pes; while ancestral states for the uniform-rate models consistently entail the reacquisition of pedal digits, those for the model incorporating among-lineage rate heterogeneity imply repeated, unreversed digit loss.  These results indicate that the assumption of identical transition rates for all branches in a phylogeny may be inappropriate in modelling the evolution of phenotypic traits, and emphasise the need for careful evaluation of phylogenetic tests of Dollo's law.
  L3  - 
  JF  - Systematic Biology
  VL  - 
  IS  - 
  ER  -