Phylogenomics of sigmodontine rodents (Cricetidae: Sigmodontinae): Cloud forests and Pliocene extinction explain the timing and spread of an iconic South American radiation
Data files
Oct 22, 2025 version files 6.73 MB
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AHE_Alignments.zip
6.18 MB
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README.md
2.15 KB
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sigmo_reference.fasta
547.91 KB
Abstract
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.
Dataset DOI: 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.