On Phylogenetic Tests of Irreversible Evolution

@inproceedings{Goldberg2008OnPT,
  title={On Phylogenetic Tests of Irreversible Evolution},
  author={Emma Elizabeth Goldberg and Boris Igi{\'c}},
  booktitle={Evolution; international journal of organic evolution},
  year={2008}
}
Abstract “Dollo's law” states that, following loss, a complex trait cannot reevolve in an identical manner. Although the law has previously fallen into disrepute, it has only recently been challenged with statistical phylogenetic methods. We employ simulation studies of an irreversible binary character to show that rejections of Dollo's law based on likelihood-ratio tests of transition rate constraints or on reconstructions of ancestral states are frequently incorrect. We identify two major… 
Ancestral state reconstructions require biological evidence to test evolutionary hypotheses: A case study examining the evolution of reproductive mode in squamate reptiles.
TLDR
It is concluded that the first squamates were oviparous, that frequent transitions to viviparity have occurred, and that reversals to oviparity in vivIParous lineages either have not occurred or are exceedingly rare.
Model inadequacy and mistaken inferences of trait-dependent speciation.
TLDR
It is shown that for many empirical phylogenies, characters simulated in the absence of state-dependent diversification exhibit an even higher Type I error rate, indicating that the method is susceptible to additional, unknown model inadequacies.
DOLLO'S LAW AND THE IRREVERSIBILITY OF DIGIT LOSS IN BACHIA
TLDR
It is shown that phylogenetic analyses should incorporate evolutionary mechanisms including constraints, variation, and selection, not only for correct phylogenetic reconstruction, but also for correct evolutionary inference.
Experimental systematics: sensitivity of cladistic methods to polarization and character ordering schemes
TLDR
The results of simulations of the evolution of phenotypic traits under a Brownian motion model are presented to characterize differences in sensitivity between parsimony and 3ta to outgroup branch length, which affects the reliability of ancestral character state estimates, (2) character state ordering scheme, and (3) ingroup branch lengths that reflect the geological age of studied taxa.
Macroevolutionary analysis of discrete traits with rate heterogeneity
TLDR
The method is applied to an empirical dataset of mimetic coloration in snakes and finds elevated rates of trait evolution in two clades of harmless snakes that are broadly sympatric with dangerously venomous New World coral snakes, recapitulating an earlier analysis of the same dataset.
Tempo and mode of fl ower color evolution 1
TLDR
With the exception of fl oral symmetry, which has been well studied, many basic macroevolutionary questions about the tempo, directionality, and mode of angiosperm trait evolution have yet to be answered.
A NOVEL COMPARATIVE METHOD FOR IDENTIFYING SHIFTS IN THE RATE OF CHARACTER EVOLUTION ON TREES
TLDR
A Bayesian approach for identifying complex patterns in the evolution of continuous traits, which uses reversible‐jump Markov chain Monte Carlo sampling and performs well in recovering simulated rate shifts and simulated rates for datasets nearing the size typical for comparative phylogenetic study.
Probabilistic phylogenetic inference in the fossil record: Current and future applications
TLDR
Future goals of paleosystematists include incorporating these and other “nuisance” parameters so that, ultimately, the authors' tests of phylogeny are really tests of evolutionary histories.
Is self-fertilization an evolutionary dead end?
TLDR
Theoretical investigations, genetic data and applications of new phylogenetic methods provide indirect support for an association of selfing with negative diversification rates, and suggestions for research programs that aim to provide a richer understanding of mating system evolution and seriously challenge Stebbins' venerable hypothesis are made.
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 92 REFERENCES
Ancient polymorphism reveals unidirectional breeding system shifts
  • B. Igić, L. Bohs, J. Kohn
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 2006
TLDR
This study shows in a statistical framework that a particular character transition is irreversible, consistent with Dollo's law, and argues that current phylogenetic methods of reconstruction are potentially inadequate in cases where ancestral state information is inferred by using only the phylogeny and the distribution of character states in extant taxa.
Some Limitations of Ancestral Character-State Reconstruction When Testing Evolutionary Hypotheses
TLDR
It is argued that hypotheses of irreversible evolution (e.g., Dollo’s law; Dollo, 1893) are particularly difŽcult to test by using ancestral character state reconstruction.
THE RECONSTRUCTION OF ANCESTRAL CHARACTER STATES
TLDR
The problem of error in the phylogenetic reconstruction of ancestral character states is explored by developing the model of Frumhoff and Reeve (1994), and a hypothesis of parallelism is shown to rely on assumptions of low rates of change in at least two phylogenetically inherited characters.
LIKELIHOOD OF ANCESTOR STATES IN ADAPTIVE RADIATION
TLDR
It is concluded that measures of uncertainty are useful and should always be provided, despite simplistic assumptions about the probabilistic models that underlie them, and if uncertainty is too high, reconstruction should be abandoned.
EXAMINING TWO STANDARD ASSUMPTIONS OF ANCESTRAL RECONSTRUCTIONS: REPEATED LOSS OF DICHROMATISM IN DABBLING DUCKS (ANATINI)
  • K. Omland
  • Biology
    Evolution; international journal of organic evolution
  • 1997
TLDR
Character state mapping reconstructs monochromatic ancestors for the genus Anas as well as most of its main clades and cautions against the uncritical use of unordered parsimony as the sole criterion for inferring ancestral states.
TESTING HYPOTHESES ABOUT ECOLOGICAL SPECIALIZATION USING PHYLOGENETIC TREES
TLDR
The consequences of the fact that transition rates inferred by ML are affected not only by the distribution, but also by the frequency, of character states are explored, which shows that models with no transitions in one direction are usually strongly rejected.
TESTING HYPOTHESES ABOUT ECOLOGICAL SPECIALIZATION USING PHYLOGENETIC TREES
TLDR
The consequences of the fact that transition rates inferred by ML are affected not only by the distribution, but also by the frequency, of character states are explored, to strengthen inferences regarding character evolution.
Estimating a binary character's effect on speciation and extinction.
TLDR
This work describes how to calculate the probability that a group of extant species would have evolved as observed, given a particular model of the character's effect, under a simple model of evolution (the "BiSSE model, binary-state speciation and extinction).
Reevolution of sexuality breaks Dollo's law
TLDR
Oribatid mites are presented as a unique model system to explore the evolutionary significance of parthenogenetic and sexual reproduction and phylogenetic analyses of this study and model-based reconstruction of ancestral states of reproduction imply that Crotoniidae have reevolved sexuality from parthensogenetic ancestors within one of those clusters.
The Role of Subjectivity in Reconstructing Ancestral Character States : A Bayesian Approach to Unknown Rates , States , and Transformation Asymmetries
The synthesis of data from ecology and systematics makes possible, at least in principle, the reconstruction of features of extinct ancestors. The reliability of such reconstructions, however, is a
...
1
2
3
4
5
...