“Part 1” – allowing for subsequent parts (e.g., for the blue/non-blue use case; now added at end of post). The relevant OpenTree background discussion is here:
There as several interesting and generally closely overlapping issues and views here. I will pick just (or mainly) the one introduced by Jonathan Rees (November 02, 2014).
“Here’s another example I’m struggling with: there are currently a couple of species in OTT that are misclassified as crustaceans instead of molluscs. When we fix this problem, there will be an incompatible ‘change’ in the membership of Arthropoda. Does this mean that the new group should get a new identifier? – after all its identity in some sense has changed. If so, annotations and OTU mappings linked to the old id have no home in the tree. It doesn’t get a new id with the current taxonomy generator, which assumes that names are tied uniquely to taxon concepts (with some exceptions), but with a more principled system where groups are defined by membership or phylogenetic hypotheses, it might. This would have an impact on OTU mappings and annotation carryover. I don’t have a good answer to this one, but am working on ways to anchor the semantics of ids.”
I am attempting to reproduce this under varying scenarios in the Euler/X toolkit. Starting simple, then expanding. I have created an initial scenario with two phylogenetic perspectives of the Ecdysozoa (molting animals) sec. ott1 (= OpenTree Topology at time =1; the later version) versus Ecdysozoa sec. ott0 (OTT at time = 0; the earlier version. Initially, an alignment with complete taxonomic congruence.
The third and likely penultimate session in our “explore cladistic coding” series. A brief primer below; more during our discussions and practices.
Second chapter in the “let’s get some practice” series. In this week’s reading practice we will explore the interaction of alternative coding schemes and tree/optimization outcomes, both “by hand” and with WinClada and NONA. In particular, we will apply and compare simple binary, non-additive multi-state, and complex additive character coding schemes. We will assess their effects on cladogram length and on the character state optimizations along the internal cladogram nodes. We will start by learning how to code complex character state hierarchies as additive binary as well as additive multi-state characters. Please do some reading of the handout beforehand.
As part of the series on character coding and analysis, we will learn about the software DELTA during this week’s discussion (February 14, 2014). As stated on its website, “[t]he DELTA format (DEscription Language for TAxonomy) is a flexible and powerful method of recording taxonomic descriptions for computer processing”, and “[i]t was adopted as a standard for data exchange by Biodiversity Information Standards (TDWG).” Read more
This week our weekly lab discussion group shifts gears from the empiricism/realism debate to actual, and mostly still “manual” (as if hands could think), character matrix assembly, Wagner tree construction, and upward-/downward-pass parsimony-based character state optimization. Consistency and retention indices. And WinClada and NONA. Let’s see how far the first session will take us towards understanding the interaction between characters, parsimony, optimizations, and trees.
This is a developing post related to a prior entry on cladistic character coding. “Systematic philosophy”, naturally (in a historical science), is a rich topic with influential contributions from various competing philosophical schools such as empiricism or realism. Often these contributions acknowledge their heritage openly, however this is not always the case.