Phylogenomics of sigmodontine rodents (Cricetidae: Sigmodontinae): Cloud forests and Pliocene extinction explain the timing and spread of an iconic South American radiation

Studies of biotic radiations following geographic invasions often overlook the potential role of subsequent climatic, biotic, and geologic triggers, instead focusing largely on the earliest stage of an invasion. The rodent subfamily Sigmodontinae, a clade of over 500 species that radiated throughout South America as an early participant in the Great American Biotic Interchange, is a prominant example. Here, we place the timing and transitions of this radiation in context of changing climatic, biotic, and geologic factors by reconstructing the biogeography of the radiation. To accomplish this, we generated new sequence data using the Rodent418loci Anchored Hybrid Enrichment (AHE) set for 180 specimens and combined them with published AHE data to produce a phylogeny that includes over 80% of the genera and 40% of the known species (including all incertae sedis taxa), and a fossil-calibrated chronogram. Our results indicate a single invasion of South America at the base of Sigmodontinae (~..., , # Phylogenomics of sigmodontine rodents (Cricetidae: Sigmodontinae): Cloud forests and Pliocene extinction explain the timing and spread of an iconic South American radiation

Dataset DOI: [10.5061/dryad.hmgqnk9x7](10.5061/dryad.hmgqnk9x7)

## Description of the data and file structure

### Files and variables

#### File: sigmo_reference.fasta

**Description:** The file “sigmo_reference.fasta” is the quasi-reference generated using sequences from four Cricetidae samples (*Cricetulus griseus, Microtus ochrogaster, Peromyscus leucopus, and* Phyllotis xanthopygus) from Bangs and Steppan (2021). The reference sequence was a majority-rule consensus of the four samples for all 418 loci.

#### File: AHE_Alignments.zip

**Description:** A zip file for the folder of alignments for each of the 415 loci successfully sequenced for all samples using the *Rodent418loci* Anchored Hybrid Enrichment set (Bangs and Steppan, 2021). Of the 219 samples, 180 had Anchored Hybrid Enrichment (AHE) libraries gen...,