Supplementary material: Ultraconserved elements improve the resolution of difficult nodes within the rapid radiation of neotropical sigmodontine rodents (Cricetidae: Sigmodontinae)

Sigmodontine rodents (Cricetidae, Sigmodontinae) represent the second largest muroid subfamily and the most species-rich group of New World mammals, encompassing above 410 living species and ca. 87 genera. Even with advances on the clarification of sigmodontine phylogenetic relationships that have been made recently, the phylogenetic relationships among the 11 main group of genera (i.e., tribes) remain poorly resolved, in particular among those forming the large clade Oryzomyalia. This pattern has been interpreted as consequence of a rapid radiation upon the group entrance into South America. Here, we attempted to resolve phylogenetic relationships within Sigmodontinae using target capture and high-throughput sequencing of ultraconserved elements (UCEs). We enriched and sequenced UCEs for 56 individuals and collected data from four already available genomes. Analyses of distinct data sets, based on the capture of 4,634 loci, resulted in a highly resolved phylogeny consistent across diff..., Taxon Sampling and Target Capture of UCEs
UCEs for 60 species of muroids were gathered. Of these, 53 belong to Sigmodontinae, including representatives of all sigmodontine tribes, but Wiedomyini. The other seven species belong to three of the other four subfamilies of Cricetidae, Cricetinae (2), Neotominae (1), and Tylomyinae (1), and to the families Muridae (2) and Spalacidae (1). Details of the specimens analyzed, including their taxonomic classification and museum or collection number or genome assembly are provided in Supplementary Table S1.
Data for 56 of the 60 analyzed specimens were gathered in this study as follows. Genomic DNA was extracted using the Qiagen DNeasy Tissue and Blood kit. Samples were quantified using the Qubit BR dsDNA kit (Thermo Fisher Inc). Library prep was performed using the KAPA HyperPrep Kit and 0.8-1.2ug of DNA. Libraries were enriched for UCE loci using the UCE-5Kv1 probe set (Mycroarray Inc), and sequencing was performed using Illumina Technology using..., Supplementary Material
Captions of Figures and Tables
Supplementary Figures
Supplementary Figures S1-S11
Supplementary Table S1
List of taxa included in the present study.
Supplementary Table S2
Best-fitting model for each UCE locus for the 60-species data set (with 70% taxon occupancy, 2a) and 42-genera data sets with 70% (2b) and 90% taxon occupancy (2c). Columns are abbreviated as follows: Var = variable sites; gap = gaps. BIC = Bayesian Information Criterion. Details of the data sets constructed via the 'gene shopping' procedure (2d) and the different dating analyses (2e) are provided in this Table (see also Online Appendix for details).
Supplementary Table S3
Genera and species richness of each sigmodontine tribe. Proportion of genera and species sampled per sigmodontine tribe in our 60-species data set (of which 53 are sigmodontine species).
Supplementary Table S4
Comparison of the crown age estimates for selected nodes obtained in the present study and those of selected previous ...