When the Map Fails the Territory: Hidden State Models, Complex Traits and the Evolution of Bird Migration

Phylogenetic comparative methods often rely on simplifying complex biological traits into discrete categories, potentially obscuring evolutionary patterns and generally limiting inferences. This dissertation confronts this ``map versus territory" problem by developing and evaluating methodological approaches that integrate known and unknown trait complexity into macroevolutionary analyses. To establish the statistical power of discrete methods in detecting trait complexity, I first demonstrate the utility of structured hidden Markov models (SHMMs) for identifying underlying continuous architectures, like threshold traits, within simulated and empirical discrete datasets (Chapter ref{ch:1}). Taking bird migration as an example of a hard-to-measure complex trait, I then develop new continuous metrics of bird movement from large-scale community science (eBird) data, using entropy-based measures and phylogenetically aligned component analysis (PACA) to reveal a multi-dimensional structure of evolutionarily relevant combinations of traits, representing underlying movement behavior in North American birds (Chapter ref{ch:2}). Next, I fit SHMMs informed by this structure to global and North American bird phylogenies, testing hypotheses about how migration may have evolved, while accounting for classification ambiguity (Chapter ref{ch:3}). I show that models incorporating hidden states that imitate the structure from Chapter ref{ch:2} were often preferred over generalized hidden Markov models and standard Markov models, suggesting that migration both contains hidden complexity and evolves along specific pathways. Overall, this dissertation provides a methodological framework for integrating continuous data and theoretical knowledge into discrete trait analyses, demonstrating a more holistic treatment of how to treat complex discretized traits like avian migration in phylogenetic comparative methods.

Name thesis:degree_name

Doctor of Philosophy

Level thesis:degree_level

doctoral

Discipline thesis:degree_discipline

Biological Sciences

Department dc:contributor.department

Biological Sciences

Grantor dc:publisher

Virginia Tech

Year dc:date.issued

2025

Author dc:creator

• Bone, Nicholas Jordan

Chair dc:contributor.committeechair

• Uyeda, Josef C.

Committee members dc:contributor.committeemember

• Sewall, Kendra
• McGlothlin, Joel W.
• Kindsvater, Holly

• Bird Migration
• Evolution
• Phylogenetic Comparative Methods
• Hidden Markov Models
• Complex Traits

Statement dc:rights

• Creative Commons Attribution 4.0 International

Licence dc:rights.uri

• http://creativecommons.org/licenses/by/4.0/

Language dc:language.iso

en

Dc Identifier Other

vt_gsexam:43459

OAI identifier oai:identifier

oai:vtechworks.lib.vt.edu:10919/133150