Imperial College London

Dr. Martin D. Brazeau

Faculty of Natural SciencesDepartment of Life Sciences (Silwood Park)

Senior Lecturer
 
 
 
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Contact

 

+44 (0)20 7594 2254m.brazeau

 
 
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Location

 

W2.2KennedySilwood Park

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Summary

 

Publications

Publication Type
Year
to

22 results found

Brazeau MD, Guillerme T, Smith MR, 2018, An algorithm for morphological phylogenetic analysis with inapplicable data., Syst Biol

Morphological data play a key role in the inference of biological relationships and evolutionary history, and are essential for the interpretation of the fossil record. The hierarchical interdependence of many morphological characters, however, complicates phylogenetic analysis. In particular, many characters only apply to a subset of terminal taxa. The widely used "reductive coding" approach treats taxa in which a character is inapplicable as though data on the character's state is simply missing (unknown). This approach has long been known to create spurious tree length estimates on certain topologies, potentially leading to erroneous results in phylogenetic searches-but no practical solution has previously been suggested. Here we present a single-character algorithm for reconstructing ancestral states in reductively coded datasets, following the theoretical guideline of minimizing homoplasy over all characters. Our algorithm uses up to three traversals to score a tree, and a fourth to fully resolve final states at each node within the tree. We use explicit criteria to resolve ambiguity in applicable/inapplicable dichotomies, and to optimize missing data. So that it can be applied to single characters, the algorithm employs local optimization; as such, the method provides a fast but approximate inference of ancestral states and tree score. The application of our method to published morphological datasets indicates that, compared to traditional methods, it identifies different trees as "optimal". As such, the use of our algorithm to handle inapplicable data will significantly alter the outcome of tree searches, modifying the inferred placement of living and fossil taxa and potentially leading to major differences in reconstructions of evolutionary history.

JOURNAL ARTICLE

Castiello M, Brazeau MD, 2018, Neurocranial anatomy of the petalichthyid placoderm Shearsbyaspis oepiki Young revealed by X-ray computed microtomography, PALAEONTOLOGY, Vol: 61, Pages: 369-389, ISSN: 0031-0239

JOURNAL ARTICLE

Brazeau MD, Friedman M, Jerve A, Atwood RCet al., 2017, A three-dimensional placoderm (stem-group gnathostome) pharyngeal skeleton and its implications for primitive gnathostome pharyngeal architecture, JOURNAL OF MORPHOLOGY, Vol: 278, Pages: 1220-1228, ISSN: 0362-2525

JOURNAL ARTICLE

Kamminga P, De Bruin PW, Geleijns J, Brazeau MDet al., 2017, X-ray computed tomography library of shark anatomy and lower jaw surface models, SCIENTIFIC DATA, Vol: 4, ISSN: 2052-4463

JOURNAL ARTICLE

Brazeau MD, de Winter V, 2015, The hyoid arch and braincase anatomy of Acanthodes support chondrichthyan affinity of 'acanthodians', PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 282, ISSN: 0962-8452

JOURNAL ARTICLE

Giles S, Coates MI, Garwood RJ, Brazeau MD, Atwood R, Johanson Z, Friedman Met al., 2015, Endoskeletal structure in Cheirolepis (Osteichthyes, Actinopterygii), An early ray-finned fish, PALAEONTOLOGY, Vol: 58, Pages: 849-870, ISSN: 0031-0239

JOURNAL ARTICLE

Brazeau MD, Friedman M, 2015, The origin and early phylogenetic history of jawed vertebrates, NATURE, Vol: 520, Pages: 490-497, ISSN: 0028-0836

JOURNAL ARTICLE

Giles S, Friedman M, Brazeau MD, 2015, Osteichthyan-like cranial conditions in an Early Devonian stem gnathostome, NATURE, Vol: 520, Pages: 82-U175, ISSN: 0028-0836

JOURNAL ARTICLE

Brazeau MD, Friedman M, 2014, The characters of Palaeozoic jawed vertebrates, ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Vol: 170, Pages: 779-821, ISSN: 0024-4082

JOURNAL ARTICLE

Friedman M, Brazeau MD, 2013, PALAEONTOLOGY A jaw-dropping fossil fish, NATURE, Vol: 502, Pages: 175-177, ISSN: 0028-0836

JOURNAL ARTICLE

Brazeau MD, 2013, Taking a step back: computational problems for morphological data revisited, Annual Meeting of the Society-for-Integrative-and-Comparative-Biology (SICB), Publisher: OXFORD UNIV PRESS INC, Pages: E23-E23, ISSN: 1540-7063

CONFERENCE PAPER

Brazeau MD, 2012, A revision of the anatomy of the Early Devonian jawed vertebrate Ptomacanthus anglicus Miles, PALAEONTOLOGY, Vol: 55, Pages: 355-367, ISSN: 0031-0239

JOURNAL ARTICLE

Giles S, Brazeau MD, Atwood RC, Friedman Met al., 2012, ENDOSKELETAL ANATOMY OF THE STEM ACTINOPTERYGIAN CHEIROLEPIS REVEALED BY HIGH-RESOLUTION COMPUTED TOMOGRAPHY, 72nd Annual Meeting of the Society-of-Vertebrate-Paleontology, Publisher: TAYLOR & FRANCIS INC, Pages: 101-101, ISSN: 0272-4634

CONFERENCE PAPER

Brazeau MD, 2011, Problematic character coding methods in morphology and their effects, BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Vol: 104, Pages: 489-498, ISSN: 0024-4066

JOURNAL ARTICLE

Anderson PSL, Friedman M, Brazeau MD, Rayfield EJet al., 2011, Initial radiation of jaws demonstrated stability despite faunal and environmental change, NATURE, Vol: 476, Pages: 206-209, ISSN: 0028-0836

JOURNAL ARTICLE

Brazeau MD, 2011, Before and beyond congruence: using phylogenetic homology to infer evolutionary process, Annual Meeting of the Society-for-Integrative-and-Comparative-Biology, Publisher: OXFORD UNIV PRESS INC, Pages: E16-E16, ISSN: 1540-7063

CONFERENCE PAPER

Friedman M, Brazeau MD, 2011, Sequences, stratigraphy and scenarios: what can we say about the fossil record of the earliest tetrapods?, PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 278, Pages: 432-439, ISSN: 0962-8452

JOURNAL ARTICLE

Friedman M, Brazeau MD, 2010, A REAPPRAISAL OF THE ORIGIN AND BASAL RADIATION OF THE OSTEICHTHYES, JOURNAL OF VERTEBRATE PALEONTOLOGY, Vol: 30, Pages: 36-56, ISSN: 0272-4634

JOURNAL ARTICLE

Brazeau MD, 2009, The braincase and jaws of a Devonian 'acanthodian' and modern gnathostome origins, NATURE, Vol: 457, Pages: 305-308, ISSN: 0028-0836

JOURNAL ARTICLE

Brazeau MD, Jeffery JE, 2008, The hyomandibulae of rhizodontids (Sarcopterygii, stem-tetrapoda), JOURNAL OF MORPHOLOGY, Vol: 269, Pages: 654-665, ISSN: 0362-2525

JOURNAL ARTICLE

Brazeau MD, Ahlberg PE, 2006, Tetrapod-like middle ear architecture in a Devonian fish, NATURE, Vol: 439, Pages: 318-321, ISSN: 0028-0836

JOURNAL ARTICLE

Brazeau MD, 2005, A new genus of rhizodontid (Sarcopterygii, Tetrapodomorpha) from the Lower Carboniferous Horton Bluff Formation of Nova Scotia, and the evolution of the lower jaws in this group, CANADIAN JOURNAL OF EARTH SCIENCES, Vol: 42, Pages: 1481-1499, ISSN: 0008-4077

JOURNAL ARTICLE

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