DOI: 10.5061/dryad.hmgqnk9x7
title: Phylogenomics of sigmodontine rodents (Cricetidae: Sigmodontinae): Cloud forests and Pliocene extinction explain the timing and spread of an iconic South American radiation

description: 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 (~ 10.46 million
 years ago [mya]) with two waves of increased lineage generation and
 biogeographic transition rates, the first of which occurred following a
 four-million-year lag after the invasion. The timing and location of this
 initial radiation (6.61 - 5.78 mya, Oryzomyalia) coincided with the spread
 of montane cloud forest along the Andean cordillera during the Late
 Miocene Cooling. We propose a scenario where sigmodontines did not spread
 throughout the continent until the Mid-Pliocene Faunal Turnover (4.5 – 3.0
 mya), a period of high extinction of South American mammals. A
 comprehensive classification for the subfamily (including two new Linnaean
 tribes) is provided that incorporates these new results.
description: # 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 generated using the *Rodent418loci* probe set
 (Bangs and Steppan, 2021), of which 13 were generated from a previous
 study across rodents (Bangs and Steppan, 2021). The remaining 39 samples
 were from an AHE study focused on the tribe Oryzomyini using the
 *Vertebrate518loci* probe set (Percequillo et al., 2021), that overlapped
 for 176 loci. All files are labeled as “Probe set, locus number,” for
 example, “L315.fas” or “R005.fas,” etc… “R” refers to loci from the
 *Rodent418loci* set and “L” refers to loci from the *Vertebrate518loci*
 set. The numbers refer to the locus numbers in the respective AHE
 projects, or to the targeted genes RAG1 and IRBP. ## Access information
 Data was derived from the following sources: * Original newly generated
 filtered reads (using *Rodent418loci* probe set) are available from NCBI
 Short Read Archive, BioProject accession number PRJNA1273194; sample
 accession numbers SAMN48939036- SAMN48939191. *  The remaining 39 samples
 were from an AHE study focused on the tribe Oryzomyini using the
 *Vertebrate518loci* probe set (Percequillo et al., 2021), that overlapped
 for 176 loci.