Caught in the act: Incipient speciation at the southern limit of Viburnum in the Central Andes

A fundamental objective of evolutionary biology is to understand the origin of independently evolving species. Phylogenetic studies of species radiations rarely are able to document ongoing speciation; instead, modes of speciation, entailing geographic separation and/or ecological differentiation, are posited retrospectively. The Oreinotinus clade of Viburnum has radiated recently from north to south through the cloud forests of Mexico and Central America to the Central Andes. Our analyses support a hypothesis of incipient speciation in Oreinotinus at the southern edge of its geographic range, from central Peru to northern Argentina. Although several species and infraspecific taxa of have been recognized in this area, multiple lines of evidence and analytical approaches (including analyses of phylogenetic relationships, genetic structure, leaf morphology, and climatic envelopes) favor the recognition of just a single species, V. seemenii. We show that what has previously been recognized..., We collected leaf tissues from herbarium samples or from our own recent collections of these plants from central Peru to southern Bolivia. We included five samples previously classified as V. incarum, 29 as V. seemenii, and 13 as “New Name 2”. Whenever possible multiple individuals per population were included, and all collections were deposited in the Yale Herbarium (YU) except for three specimens located in NY and MO (Appendix 1). Total DNA was extracted from leaf tissues using DNeasy plant extraction kits (Qiagen Inc., Hilden, Germany).
RAD-seq data were generated by Floragenex Inc. (Eugene, Oregon) by digesting genomic DNA with the PstI restriction enzyme, followed by sonication and size selection at 400 bp. Samples were ligated with 10bp barcodes for multiplexing. Then samples were pooled and sequenced on Illumina HiSeq 2500 or 4000 to produce 100bp SE reads.
Samples were demultiplexed and assembled into orthologous loci with ipyrad v.0.9.85 (Eaton and Overcast 2020) using a refere..., Ipyrad is needed to open HDF5 files, # Data from: Caught in the act: Incipient speciation at the southern limit of Viburnum in the Central Andes

In this repository, we are storing the following:

HDF5 file of the assembly produced by ipyrad of our RADseq reads (bolivia_history.seqs.hdf5)
HDF5 files with the SNPs found in item 1 (bolivia_history.snps.hdf5)
Phylip file containing the final alignment used for the tree reconstruction (10-bolivia-initial_mcov0.25_rcov0.1_ALLscaff_SelectiveSampling.phy)

HDF5 files were produced by ipyrad software (https://ipyrad.readthedocs.io/en/master/) which is a organized database that contains not only the DNA sequence, but also additional information used by this software for further analysis. As cross compatible file, we provide a Phylip version of the final alignment.

For additional reproducibility material (scripts, notebooks) check: [https://github.com/camayal/southern-oreinotinus](https://github.com/camayal/southern-oreinotinus)