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Multi-Model Approaches to Phylogenetics: Implications for Idealization

Watkins, Aja (2021) Multi-Model Approaches to Phylogenetics: Implications for Idealization. [Preprint]

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Abstract

Phylogenetic models traditionally represent the history of life as having a strictly-branching tree structure. However, it is becoming increasingly clear that the history of life is often not strictly-branching; lateral gene transfer, endosymbiosis, and hybridization, for example, can all produce lateral branching events. There is thus motivation to allow phylogenetic models to have a reticulate structure. One proposal involves the reconciliation of genealogical discordance. Briefly, this method involves using patterns of disagreement -- discordance -- between trees of different genes to add lateral branching events to phylogenetic trees of taxa, and to estimate the most likely cause of these events. I use this practice to argue for: (1) a need for expanded accounts of multiple-models idealization, (2) a distinction between automatic and manual de-idealization, and (3) recognition that idealization may serve the meso-level aims of science in a different way than hitherto acknowledged.


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Item Type: Preprint
Creators:
CreatorsEmailORCID
Watkins, Ajaajawatki@bu.edu0000-0003-0171-8738
Keywords: phylogenetics, idealization, genealogical discordance, lateral gene transfer, hybridization
Subjects: Specific Sciences > Biology > Systematics
General Issues > Models and Idealization
Depositing User: Aja Watkins
Date Deposited: 13 Sep 2021 21:41
Last Modified: 13 Sep 2021 21:41
Item ID: 19560
Subjects: Specific Sciences > Biology > Systematics
General Issues > Models and Idealization
Date: 2021
URI: https://philsci-archive.pitt.edu/id/eprint/19560

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