Skip to content

Posts tagged ‘alignment’

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.

Alignment of two classifications of the Monotremata

Echidnas, platypus – monotremes are amazing. They are also subject of an exploratory project to align two highly influential classifications of mammals using the Euler/X toolkit. Of course we are talking about:

  1. Mammal Species of the World, 3rd Edition. 2005.
  2. Mammal Species of the World, 2nd Edition. 1993. [not or no longer available on-line; which relates to our project’s aims.]

The respective 1993 & 2005 monotreme classifications were authored by Colin Groves. Thanks to MSW Editor DeeAnn Reeder for enthusiasm and support. Below is an abbreviated representation of how we aligned the two classifications. Most critically, in 1998 Zaglossus sec. Flannery & Groves (1998) was revised, and a new species (concept) Z. attenboroughi was added. Let us see what else changed..

Read more

Using the Euler/X toolkit to align taxonomies – introductory notes

Most recent update: July 15, 2014 (minor editing updates; link to video).

Our group is involved in promoting concept taxonomy. Here are some preliminary, and evolving, step-by-step instructions on how to employ the Euler/X toolkit to align two taxonomies or phylogenies. A short video is also available here.

Read more

Initial alignment of two weevil classifications with the Euler toolkit

Linked here is an interim result of my attempt to align two influential weevil classifications by Thompson (1992) and Alonso-Zarazaga & Lyal (1999) with the Euler/X toolkit. For additional information see this link.

Update, February 18, 2014: Here is another alignment of two phylogenetic classifications of weevil families and subfamilies, according to Kuschel (1995) and Marvaldi & Morrone (2002).

  • Kuschel, G. 1995. A phylogenetic classification of Curculionoidea to families and subfamilies. Memoirs of the Entomological Society of Washington 14: 5-33.
  • Marvaldi, A.E. & J.J. Morrone. 2000. Phylogenetic systematics of weevils (Coleoptera: Curculionoidea): a reappraisal based on larval and adult morphology. Insect Systematics & Evolution 31: 43-58.