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 (~ 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.