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The Congruence of Morphological Characters in Studies of Vertebrate Phylogeny

University of Bath, Biology & Biochemistry Department talk given on 24/03/2011 it was for a very broad audience, so you'll have to excuse my lack of any real detail ;) N.B. BEST-VIEWED IN FULLSCREEN
by

Ross Mounce

on 24 March 2011

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Transcript of The Congruence of Morphological Characters in Studies of Vertebrate Phylogeny

The Congruence of Morphological Characters in Studies of Vertebrate Phylogeny by Ross Mounce
and Matthew Wills What are morphological characters? Why would we use this to infer phylogeny? " Theory-laden abstractions of putatively homologous features that we believe may be phylogenetically informative " Morphology A.) B.) Why investigate character congruence? C.) e.g. the radius PCR ...to include Fossils to gain unique historical insight! ~ 40 MYA " The hypothesis of nonspecificity " Sokal & Sneath, 1963 a.k.a.
we're going to assume that on average characters give the same phylogenetic signal ...therefore the more characters the better! c.f. the assumption of phylogenomics:
- the more sequences the better! What's going on?
Why doesn't every character combination
give the same answer? " In empirical studies, character sets have uniformly revealed substantial incongruences. Dendrograms produced from different sets are seldom completely dissimilar, yet are never completely alike. " Farris, 1971 (trees) But... The problem remained unanswered Cladistics 'won' over phenetics

Computers enabled more characters to be analyzed and in a shorter time

PCR also enabled more characters (molecular sequences) to be analyzed 1970s to 1990s Perhaps the data will 'settle' if we have >100 characters? errr... Nope “Present practices focus on solutions to matrices rather than on character homology, and rely on algorithms and statistics rather than biology to determine relationships...

Evidence for phylogenies is presented in a manner that obscures character conflict...” Mooi & Gill (2010) Conflict: who cares? Phylogenies without Synapomorphies—A Crisis in Fish Systematics: Time to Show Some Character. Zootaxa 2450:26-40. http://www.mapress.com/zootaxa/2010/f/zt02450p040.pdf I do! Why do we still encounter unexplained & significant incongruence
between character sets? Process Heterogeneity Different Evolutionary History OR shared phylogeny
BUT
different rates of evolution

causing 'apparent' incongruence e.g. gene duplication or loss
horizontal transfer
hybridisation
recombination
deep gene divergence OR BOTH :S * * :) Molecules-only Molecules
and/or
Morphology Method (Overview) Gather multiple independent empirical morphological datasets easier said than done! 1. 2. Divide each of these into cranial
and postcranial partitions 3. Compare the congruence of these
character partitions in each case using a battery of tests some of which
take ages! (manually) Method (Detail) 1. Gathering data Mounce, R. 2010. The (continued) growth of phylogenetic information. @ The 12th Young Systematists' Forum The barriers to which are the subject of a whole talk: http://bit.ly/phylodata Method (Detail) 3. Stats & Statistical tests CI
RI
HER
CFI
%missing ILD
TILD
IRD Templeton's
KH
Winning Sites Of which we calculated many consensus tree-related subvariants * * * * * * * * * additionally inc. 1st order taxon jackknifing ILD tests Results Meta for N = alpha = 0.05 the number of datasets with significant incongruence
(p-val < 0.05 ) between cranial and postcranial partitions: ILD
TILD
IRD 19
51
23 63 High type I error rate Conclusion Meta Multiple tests, using Multiple randomisations, on Multiple datasets... of partition congruence, of morphological characters ...consistently indicate significantly more datasets to have incongruent partitions than one would expect by chance ? Evidence of process heterogeneity ? Further Work Examine the effect and interaction of possible biases in more detail: dataset A dataset B | | | Continue to encourage community to share data: e.g. Mounce et al 2011 An Open Letter in Support of Palaeontological Digital Data Archiving

Stoltzfus, A, Kumar, S, Gillespie, E, Mounce, R, Chisham, B, Cellinese, N, Pontelli, E
(in prep) MIAPA survey: Minimum Information About a Phylogenetic Analysis Continue to harvest data for re-analysis
and where necessary provide critical comment: fingers crossed!
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