The comparative analysis of lineage-pair traits

For many questions in ecology and evolution, the most relevant data to consider are attributes of lineage pairs. Comparative tests for causal relationships among traits like ‘diet niche overlap’, ‘divergence time’, and ‘strength of reproductive isolation (RI)’ – measured for pairwise combinations of related species or populations – have led to several groundbreaking insights, but the correct statistical approach for these analyses has never been clear. Lineage-pair traits are non-independent, but unlike the expected covariance among species’ traits, which is captured by a phylogenetic covariance matrix arising from a given model, the expected covariance among lineage-pair traits has not been explicitly formulated. Analyses of pairwise-defined data have thus employed untested workarounds for non-independence rather than direct models of lineage-pair covariance, with consequences that are unexplored. Here, we consider how evolutionary relatedness among taxa translates into non-independenc..., , , # Data from: The comparative analysis of lineage-pair traits

[https://doi.org/10.5061/dryad.q83bk3jt7](https://doi.org/10.5061/dryad.q83bk3jt7)

## Description of the data and file structure

This folder contains code and data files for conducting the analyses in Anderson et al., *Systematic Biology*, 10.1093/sysbio/syaf061.

Data files include raw data files as in the formats in which they were downloaded as well as the analysis-ready files that were created from the raw files. Code for converting raw data to analysis-ready formats is given in anderson.etal.datawrangling.R.

### Files and variables

#### File: andersonetal.analysis.data.and.code.zip

**Description:** Within this zip file, find the following: 

Downloaded Data Files:

1. full_scaled_4d.tree: Drosophila tree from Kim et al. 2024 PLoS Biology
2. birds_pulidoSC2016_MaxCladeCredTree.txt: All-birds phylogeny from Pulido-Santacruz and Weir 2016 Evolution.
3. bouvoir_price.xls: Avian hybridization data from Price and Bouvier ...,