10.5061/DRYAD.ZKH189394
Percequillo, Alexandre
0000-0002-7892-8912
University of Sao Paulo
Prado, Joyce
University of Sao Paulo
Abreu, Edson
0000-0003-4547-6160
University of Sao Paulo
Dalapicolla, Jeronymo
Instituto Tecnologico Vale
Pavan, Ana Carolina
University of Sao Paulo
Chiquito, Elisandra
Universidade Federal do Espírito Santo
Brennand, Pamella
University of Sao Paulo
Steppan, Scott
Florida State University
Lemmon, Alan
Florida State University
Lemmon, Emily
Florida State University
Tempo and mode of evolution of Oryzomyine rodents (Rodentia, Cricetidae,
Sigmodontinae): a phylogenomic approach
Dryad
dataset
2021
FOS: Biological sciences
São Paulo Research Foundation
https://ror.org/02ddkpn78
09/16009-1
2021-02-28T00:00:00Z
2021-02-28T00:00:00Z
en
74618292 bytes
3
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
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 incertae sedis 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 Gallus gallus (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 Homo sapiens 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
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)