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Posts tagged ‘homology’

Thoughts: Bio-ontologies with only minimal predetermined relations

Time for some reflection on this (2015) Spring’s Weekly Discussion on Phenotype ontologies – origins, theory, applications, prospects, and challenges. It gets to be a little (and intentionally) provocative (as opposed to very carefully thought out) towards the end.

We started off three months ago with Daduhl et al. 2010, who provide an inspiring vision on the subject (page 370):

“The application of ontologies to systematics has the potential to force clarification and improve communication about morphological character diversity across taxonomic domains. As a result, ontologies could extend the applicability and level of universality of characters for phylogenetic analysis and improve the knowledge of evolutionary transformations. These computable vocabularies could enable efficient computer processing of vast amounts of data and allow the exploration and aggregation of data across studies that is currently difficult to do in morphology-based phylogenetics.”

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Weekly reading: SISRS – Site Identification from Short Read Sequences

This week’s discussion will focus on a novel method to identify and separate signal from noise for Next-Generation sequencing datasets – SISRS.

Schwartz, R.S., K. Harkins, A.C. Stone & R.A. Cartwright. 2014. A composite genome approach to identify phylogenetically informative data from Next-Generation Sequencing. http://arxiv.org/abs/1305.3665

Weekly reading: Structural complexity in ancestral ontologies

Next week’s reading in our quickly ending series on coding characters and (most recently) dynamic homology.

Ramírez, M.J. & P. Michalik. 2014. Calculating structural complexity in phylogenies using ancestral ontologies. Cladistics (Early View). Available here.

Update: Wonderful paper! Love the innovative and somewhat irreverent use of ontologies specifically to address and answer a genuine systematic question complex, outside of the “Protégé paradigm” (and in fact without formal reasoning, period). Ramírez and co-authors are onto something novel and impactful.

Weekly reading: Using dynamic homology without parsimony

Dynamic homologypart 1, part2, and now, for behavioral data (not exclusively, one presumes):

Japyassú, H.F. & F.d.A. Machado. 2010. Coding behavioural data for cladistic analysis: using dynamic homology without parsimony. Cladistics 26: 625-642. Available here.

More on this soon, well, hopefully. At least we are caught up now with our weekly reading posts.

Weekly reading: A dynamic homology approach for morphological data

Following up on last week’s wide-ranging explorations of dynamic homology sensu Wheeler, this week’s original, inspiring, and overall excellent paper by Martín Ramírez applies the issue to the challenge of properly (read: parsimoniously) assigning one or two of three potentially available sclerite ‘identities’ to their homologous positions in the complex male spider pedipalps and ranging over variously simultaneous inferred clades. Complex, engaging, and well conceived material for thought and possible application.

Ramírez, M.J. 2007. Homology as a parsimony problem: a dynamic homology approach for morphological data. Cladistics 23: 588-612. Available here.

P.s.: Posted retrospectively for April 04, 2014.

Weekly reading: Dynamic homology and the likelihood criterion

Dynamic homology is an intriguing concept, though getting from the general notion of optimizing character correspondence (inapplicables, indels) and phylogeny simultaneously to a fully realized implementation is not trivial. In this week’s reading we examine a paper by Ward Wheeler who has promoted this approach with a strong emphasis on parsimony optimization.

Wheeler, W.C.  2006. Dynamic homology and the likelihood criterion. Cladistics 22: 157-170. Available here.

P.s.: Posted retrospectively for March 28, 2014.

Worthwhile reads on cladistic character coding

Some pointers to literature relevant to one of the most intellectually engaging topics I can think of in systematics – how to properly “code” cladistic characters. “Code” in quotation marks because there is more to it than a single verb or action might denote. For what it is worth, Olivier Rieppel’s (2007) “performance” paper is a must read in my assessment; he talks about the process of character “scoping”. Though practically all papers can be considered sincere (yes, that can matter) and scholarly contributions to advance the field, occasionally in an intellectual discourse setting overshadowed by too-easy dichotomies of pattern versus process, supposed methodological rigor versus eclecticism, or total evidence versus cherry picking (as I said, too easy, and no improvement here either in such a stenographic account).

Franz, N.M. 2014. Anatomy of a cladistic analysis. Cladistics 30: 294-321. pdf

I will update this listing, from time to time. My own current take is here, with corresponding WHS 2012 presentation:

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