Skip to content

Posts tagged ‘morphology’

Weekly reading: Mikó et al. 2012. On Dorsal Prothoracic Appendages in Treehoppers (Hemiptera: Membracidae) and the Nature of Morphological Evidence

Our next reading is a response to a 2011 article (that paper available here) interpreting the “prothoracic helmet” of treehoppers as serially homologous with wings. Mikó et al. showcase some modern techniques for visualizing morphology, such as confocal laser scanning microscopy (CLSM) and micro-computed tomography (μ-CT) to provide an alternate interpretation, and discuss the importance of having well-defined morphological concepts for interpreting complex morphological structures.

Mikó et al. 2012 is available online here.

Weekly reading: Balhoff et al. on a semantic model for wasp species description

Following Daduhl et al. and Vogt et al., our third paper in the phenotype ontologies Weekly Discussion series will dive into an applied example by Balhoff and co-authors (mainly of the Deans Lab) with a clear taxonomic emphasis. Already we have seen that different scientific orientations draw on phenotype ontologies with the expectation of reframing and solving specific problem complexes.

Daduhl et al.‘s focus was firmly within the bounds of evolutionary and phylogenetic analyses of phenotypes across broader and deeper taxonomic scales. Implementation challenges notwithstanding, there was an underlying agreement that the legacy of phenotype-centric systematic work could be appropriated towards the outlined representation and inference goals.

Vogt et al., in turn, emphasized a need for consistent, machine-processable standards with regards to phenotype syntactics, semantics, etc.; including a separation of descriptive and evolutionary/explanatory elements in our morphological terminology. This has the makings of a potentially divergent paradigm in relation to Daduhl et al.‘s program and perspective.

Another interesting development is the Phenoscape team’s exploration of homology relations in ontologies, outlined here: http://phenoscape.org/wiki/Reasoning_over_homology_statements.

In light of these different lines of research, we set ourselves two immediate questions to address:

1. What are actual applications that utilize phenotype ontologies and (optionally) reasoning for (a) multi-taxon studies with (b) an evolutionary/systematic orientation?

2. Suppose we had the “awesome ontology & reasoning” infrastructure on hand, where current technological limits no longer apply. What kinds of questions would  we ask this infrastructure to solve for us (that cannot be addressed otherwise)?

The paper for next week applies directly to these questions.

Balhoff, J.P., I. Mikó, M.J. Yoder, P.L. Mullins & A.R. Deans. 2013. A semantic model for species description applied to the ensign wasps (Hymenoptera: Evaniidae) of New Caledonia. Systematic Biology 62: 639–659. Available on-line here.

Weekly reading: Daduhl et al. on the Teleost Anatomy Ontology

Last semester’s Weekly Discussion series dealt with Next Generation Sequencing technologies and related informatics challenges and advances. A review of what we read and discussed remains pending. Meanwhile we have selected a topic for the coming Spring 2014 semester:

Phenotype ontologies – origins, theory, applications, prospects, and challenges.

As usual we will place an emphasis on the utility of ontology-centered approaches for systematics – phylogenetics, taxonomy – in particular. The series starts off with a helpful paper that covers a lot of ground and is closely aligned with the OBO Foundry community.

Dahdul, W.M., J.G. Lundberg, P.E. Midford, J.P. Balhoff, H. Lapp, T.J. Vision, M.A. Haendel, M. Westerfield & P.M. Mabee. 2010. The teleost anatomy ontology: anatomical representation for the genomics age. Systematic Biology 59: 369-383. Available on-line here.

Systematics today: Why study comparative (insect) morphology

A New Year’s post whose motivation derives in part from an engaging discussion of a paper by Wright & Hillis 2014 we had during the past Fall semester. As I recall, we concurred that the paper was adequately executed in terms of running from premises to methods to conclusions. But we also thought (well, at least some of us) that it is yet another part of an unfortunate legacy in our field that tends to separate issues of ‘generating good evidence’ from issues of ‘identifying the right method of inference’. Lots of simulations were carried out when the matrix and characters in question were taken as is and essentially invisible.

Read more

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: 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: Rieppel on the performance of morphological characters

Last week we saw that coding inapplicables is tricky; essentially one must understand the limitations of the ‘square matrix’ and utilize reductive coding in such a way that logical and biological dependencies inherent in homology assessments are not distorted by the way in which global parsimony optimization occurs. We also saw a shift from a rather clear-cut stance about the boundaries between data and inference, to a more qualified position where inferences derived from an initial matrix and analysis should caution one to re-examine ‘the evidence’. Taking this dethroning of primary observations several steps further, next week we are reading:

Rieppel, O. 2007. The performance of morphological characters in broad-scale phylogenetic analyses. Biological Journal of the Linnean Society 92: 297–308. Available here. 

Read more