DOI: 10.5061/dryad.zkh189394
title: Tempo and mode of evolution of Oryzomyine rodents (Rodentia, Cricetidae, Sigmodontinae): a phylogenomic approach

description: The tribe Oryzomyini is an impressive group of rodents, comprising 30
 extant genera and an estimated 147 species. Recent remarkable advances in
 the understanding of the diversity, taxonomy and systematics of the tribe
 have mostly derived from analyses of single or few genetic markers.
 However, the evolutionary history and biogeography of Oryzomyini, its
 origin and diversification across the Neotropics, remain unrevealed. Here
 we use a multi-locus dataset (over 400 loci) obtained through anchored
 phylogenomics to provide a genome-wide phylogenetic hypothesis for
 Oryzomyini and to investigate the tempo and mode of its evolution. Species
 tree and supermatrix analyses produced topologies with strong support for
 most branches, with all genera confirmed as monophyletic, a
 result that previous studies failed to obtain. Our analyses also
 corroborated the monophyly and phylogenetic relationship of three main
 clades of Oryzomyini (B, C and D). The origin of the
 tribe is estimated to be in the Miocene (8.93–5.38 million years ago). The
 cladogenetic events leading to the four main clades occurred during the
 late Miocene and early Pliocene and most speciation events in the
 Pleistocene. Geographic range estimates suggested an east of
 Andes origin for the ancestor of oryzomyines, most likely in
 the Boreal Brazilian region, which includes the north bank of Rio
 Amazonas and the Guiana Shield. Oryzomyini rodents are an autochthonous
 South America radiation, that colonized areas and dominions of this
 continent mainly by dispersal events. The evolutionary history of the
 tribe is deeply associated with the Andean cordillera and the landscape
 history of Amazon basin.
description: We selected 25 genera and 50 species of the tribe Oryzomyini,
 representing a fairly comprehensive sampling of generic diversity that
 includes 83% of the extant genera, and an evenly distributed sampling of
 species, with about 34% of known species included. We also included 10
 species of other Sigmodontinae as outgroups (Table S1, Supplementary
 Material), representing five tribes, Akodontini, Phyllotini, Sigmodontini,
 Thomasomyini and Wiedomyini, as well as two <i>incertae
 sedis</i> lineages. We improved the vertebrate
 Anchored Hybrid Enrichment (AHE) target loci of Lemmon et al (2012) for
 optimal use in mammals. We first identified the genomic coordinates in the
 human genome (hg19) corresponding to the coordinates of the extended
 anchor regions of <i>Gallus gallus</i> (galGal4) obtained by
 Prum et al. (2015) using the UCSC liftover tool
 (http://genome.ucsc.edu/cgi-bin/hgLiftOver). The corresponding genomic
 sequences were then extracted and aligned using MAFFT v7.023b to that of
 the regions used by Prum et al (2015) for probe design. After inspecting
 the alignments and masking any misaligned regions in Geneious R9
 (Biomatters Ltd.), 120 bp probes were tiled uniformly across the human
 sequences at 1.5x density: conserved regions targeted for AHE enrichment
 were identified using alignments across divergent species. Once the
 alignments were constructed/improved and the conserved regions were
 identified, probe sequences of length of 120bp were generated by sliding a
 window across the human sequence from the alignment. A new probe was
 generated starting every 90bp in the sequences.
 Sequence data were generated and analyzed at the Florida State
 University Center for Anchored Phylogenomics (www.anchoredphylogeny.com). Extracted DNA was quantified using Qubit and run on gels to assess initial DNA quality. Approximately 500ng of input DNA was sheared to 200-500bp fragments using a Covaris ultrasonicator. Indexing Illumina library preparations were performed on a Beckman Coulter FxP liquid-handling robot. Libraries were then pooled in groups of 16 samples and enriched using an enrichment kit produced by Agilent technologies that contained the probes described above. Enriched libraries were pooled for sequence on two HiSeq 2500 lanes, using a paired-end 150bp protocol with 8bp (single) indexing. Sequencing was performed at the Translational Laboratory in the College of Medicine at Florida State University. Reads passing the Illumina CASAVA high-chastity filter were demultiplexed using the 8-bp indexes (with no mismatches tolerated). Overlapping read pairs were merged using the Bayesian approach developed by Rokita et al (2012). Adapters were removed and sequencing errors in overlapping regions were corrected during the process. Reads were assembled using the quasi-de novo approach described by Hamilton et al (2016), with <i>Homo sapiens</i> serving as the reference during assembly. Consensus sequences were called from assembly clusters containing at least 100 reads. Orthology among consensus sequences for each locus was determined using a neighbor-joining approach that utilized alignment free pairwise distances computed using the % of shared kmers (short sequences), with one sequence per individual being allowed in each orthologous group. Putative orthologous sets containing more than 50% of the individuals were utilized downstream as independent loci. Sequences were aligned using MAFFT v7.023b. Prum, R.O., Berv, J.S., Dornburg, A., Field, D.J., Townsend, J.P., Lemmon, E.M., Lemmon, A.R., 2015. A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature 526, 569–573. https://doi.org/10.1038/nature15697 Lemmon, A.R., Emme, S.A., Lemmon, E.M., 2012. Anchored hybrid enrichment for massively high-throughput phylogenomics. Syst. Biol. 61, 727–744. https://doi.org/https://doi.org/10.1093/sysbio/sys049 Hamilton, C.A., Lemmon, A.R., Lemmon, E.M., Bond, J.E., 2016. Expanding anchored hybrid enrichment to resolve both deep and shallow relationships within the spider tree of life. BMC Evol. Biol. 16, 1–20. https://doi.org/10.1186/s12862-016-0769-y
description: We are uploading three folders:  Alignments
 (with four folders: Astral, BioGeoBears, Divergence times and RAxML and
 IQ-Tree) Probes
 Final_Raw reads_oryzomyini (with five folders: Clade B, Clade C,
 Clade D, Scolomys and Outgroup; each folder contains the raw reads, by
 specimen included in the analysis)