AMNIOTE PHYLOGENY AND THE IMPORTANCE OF FOSSILS

@article{Gauthier1988AMNIOTEPA,
  title={AMNIOTE PHYLOGENY AND THE IMPORTANCE OF FOSSILS},
  author={Jacques A. Gauthier and Arnold G. Kluge and Timothy B Rowe},
  journal={Cladistics},
  year={1988},
  volume={4}
}
Abstract— Several prominent cladists have questioned the importance of fossils in phylogenctic inference, and it is becoming increasingly popular to simply fit extinct forms, if they are considered at all, to a cladogram of Recent taxa. Gardiner's (1982) and Løvtrup's (1985) study of amniote phylogeny exemplifies this differential treatment, and we focused on that group of organisms to test the proposition that fossils cannot overturn a theory of relationships based only on the Recent biota… 
Fossils, Topologies, Missing Data, and the Higher Level Phylogeny of Eutherian Mammals
TLDR
The assertion that fossils only play a secondary role in phylogenetic reconstruction has been countered by cladistic studies that incorporate both fossil and extant taxa, and the tendency for fossils to preserve characters lost in living taxa suggests a pivotal role for fossils in many current and pending studies.
The limitations of molecular systematics: a palaeobotanical perspective
TLDR
In a recent issue of Molecular Evolution and Systematics, Chaw & al. (1997) presented a phylogeny of modern seed plants based on comparisons of rRNA sequences, which is concerned with an apparent misunderstanding of fundamental phylogenetic concepts in their interpretations of the published trees, as well as their assessments of competing character evolution hypotheses.
In quest for a phylogeny of Mesozoic mammals
TLDR
A phylogeny of all major groups of Mesozoic mammals based on phylogenetic analyses of 46 taxa and 275 osteological and dental characters, using parsimony methods is proposed, suggesting that the “obtuse−angle symmetrodonts” are paraphyletic, and that they lack reliable and unambiguous synapomorphies.
CLADISTIC CLASSIFICATION OF AMNIOTA: A RESPONSE TO GAUTHIER ET AL.
  • H. Loconte
  • Biology
    Cladistics : the international journal of the Willi Hennig Society
  • 1990
TLDR
Gauthier et al. (1988) proposed a means of distinguishing stem lineages from their respective monophyla by developing a hierarchical nomenclature for the fossil record, in contrast to the plesion concept.
The evolutionary position of turtles revised
Abstract. Consensus on the evolutionary position of turtles within the amniote phylogeny has eluded evolutionary biologists for more than a century. This phylogenetic problem has remained unsolved
The Importance of Even Highly Incomplete Fossil Taxa in Reconstructing the Phylogenetic Relationships of the Tetraodontiformes (Acanthomorpha: Pisces)1
TLDR
Adding incomplete fossil taxa of tetraodontiforms may help to correctly establish relationships among lineages that have experienced high degrees of morphological diversification by allowing for a reinterpretation of homologous and homoplastic features, increasing the resolution rather than decreasing it.
Assembling the Squamate Tree of Life: Perspectives from the Phenotype and the Fossil Record
TLDR
This study relied on traditionally prepared specimens as well as high-resolution computed tomography scans that afforded unprecendented access to the cranial anatomy of Squamata to provide an unparalleled sample of the phenotype enabling it to more fully explore the extreme incongruences between molecular and morphological topologies for the squamate tree of life.
Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria)
TLDR
Next-generation sequencing is used to obtain seven new transcriptomes from the blood, liver, or jaws of four turtles, a caiman, a lizard, and a lungfish, and provide a phylogenetic framework and timescale with which to interpret the evolution of the peculiar morphological, developmental, and molecular features of turtles within the amniotes.
Death is on Our Side: Paleontological Data Drastically Modify Phylogenetic Hypotheses
TLDR
Predictive models are developed that demonstrate that the possession of distinctive character state combinations is the primary predictor of the degree of induced topological change, and that the relative impact of taxa (fossil and extant) can be predicted to some extent before any analysis.
Palaeomorphology: fossils and the inference of cladistic relationships
TLDR
Comparisons of real and simulated data sets show that no ap riori decisions can be made about amounts of missing data and most properties of cladograms, and both simulated and real data sets demonstrate that even highly incomplete taxa can impact on relationships.
...
...

References

SHOWING 1-10 OF 463 REFERENCES
The Contribution of Paleontology to Teleostean Phylogeny
TLDR
The main body of the paper is a historical review of paleontological methods, as practiced by workers on fossil teleosts, with the aim of identifying failures and successes, and of suggesting what contributions to phylogeny can and cannot be expected from paleontologists and their material.
FOSSILS, PHYLOGENY, AND TAXONOMIC RATES OF EVOLUTION
TLDR
The significance of much of the published study on taxonomic rates is moot until fossil data for these rates are broadly compared with cladistic hypotheses, and following the basic techniques applied by Simpson (1944), many workers have recognized three categories of taxonomic rate.
Evolution of metatherian and eutherian (mammalian) characters: a review based on cladistic methodology
TLDR
There is no special relationship between monotremes and marsupials, and there is no justification for placing them in a group Marsupionta; in a cladistic framework these are sister-groups.
Lungfish neural characters and their bearing on sarcopterygian phylogeny
TLDR
Neural synapomorphies corroborate the phylogenetic hypotheses that actinistians, amphibians, and dipnoans are each monophyletic taxa and that lepidosirenid apomorphies may have arisen by paedomorphosis.
Paedomorphosis and the evolution of the Dipnoi
TLDR
The data suggest that paedomorphosis played a pervasive role in the evolution of lungfishes and give further evidence for the evolutionary importance of heterochrony.
Alisphenoid equivalents in placentals, marsupials, monotremes and fossils
TLDR
The ossification pattern of living mammals indicates the possibility of close affinity between ‘therian’ and ‘non-therian' mammals.
On the Classification of the Reptilia
TLDR
How profoundly the modern classification of the Amniota has been affected by the recognition of these points in the phylogenetic relationships of the various orders of Eeptilia is pointed out.
Dissorophoid relationships and ontogeny, and the origin of the Lissamphibia
  • J. Bolt
  • Biology, Environmental Science
  • 1977
TLDR
A three-stage dentitional ontogenetic sequence for Doleserpeton and Tersomius is proposed, in which the third (adult) phase is similar to the adult of most other labyrinthodonts, the second (juvenile) phase resembles the adult condition in lissamphibians whereas the hypothetical first (larval)phase resembles the larvae of salamanders and oviparous caecilians.
Classification and phylogeny of the diapsid reptiles
  • M. Benton
  • Environmental Science, Geography
  • 1985
TLDR
A cladistic analysis of skull and skeletal characters of all described Permo-Triassic diapsid reptiles suggests some significant rearrangements to commonly held views of the Diapsida.
...
...