Supplementary materials for: Phylogenomics, lineage diversification rates, and the evolution of diadromy in clupeiformes (anchovies, herrings, sardines, and relatives)

Migration independently evolved numerous times in animals, with a myriad of ecological and evolutionary implications. In fishes, perhaps the most extreme form of migration is diadromy, the migration between marine and freshwater environments. Key and longstanding questions are: how many times has diadromy evolved in fishes, how frequently do diadromous clades give rise to non-diadromous species, and does diadromy influence lineage diversification rates? Many diadromous fishes have large geographic ranges with constituent populations that use isolated freshwater habitats. This may limit gene flow among some populations, increasing the likelihood of speciation in diadromous lineages relative to non-diadromous lineages. Alternatively, diadromy may reduce lineage diversification rates if migration is associated with enhanced dispersal capacity that facilitates gene flow within and between populations. Clupeiformes (herrings, sardines, shads and anchovies) is a model clade for testing hypoth..., , , # Supplementary materials for: Phylogenomics, lineage diversification rates, and the evolution of diadromy in clupeiformes (anchovies, herrings, sardines, and relatives)

[https://doi.org/10.5061/dryad.47d7wm3h8](https://doi.org/10.5061/dryad.47d7wm3h8)

Supplementary materials associated with manuscript.

### Description of the data and file structure

In supplementary alignments and tree files, taxon names were not changed to reflect updated taxonomy to maintain continuity throughout the bioinformatics pipeline. However, taxon names in these files can easily be associated with final species assignments because the tips names in the supplementary tree files contain the tissue numbers associated with each individual. The tissue numbers are provided in Supplementary Table S1 along with the final species assignment.

**Files associated with the Full Exon-Capture Dataset:**\
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**File name:** ASTRAL_03Dec2020_IQTREEGeneTreesSpeciesTree.tre\
**Description:** This file contains a species tre...