DOI: 10.5061/dryad.4f4qrfjh6
title: Data from: Caught in the act: Incipient speciation at the southern limit of Viburnum in the Central Andes

description: 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 as V. seemenii f. minor has recently occupied the drier
 Tucuman-Bolivian forest region from Samaipata in Bolivia to Salta in
 northern Argentina. Plants in these populations form a well-supported
 clade with a distinctive genetic signature and they have evolved smaller,
 narrower leaves. We interpret this as the beginning of a within-species
 divergence process that has elsewhere in the neotropics resulted
 repeatedly in Viburnum species with a particular set of leaf ecomorphs.
 Specifically, the southern populations are in the process of evolving the
 small, glabrous, and entire leaf ecomorph that has evolved in four other
 montane areas of endemism. As predicted based on our studies of leaf
 ecomorphs in Chiapas, Mexico, these southern populations experience
 generally drier conditions, with large diurnal temperature fluctuations.
 In a central portion of the range of V. seemenii, characterized by wetter
 climatic conditions, we also document what may be the initial
 differentiation of the leaf ecomorph with larger, pubescent, and toothy
 leaves. The emergence of these ecomorphs thus appears to be driven by
 adaptation to subtly different climatic conditions in separate geographic
 regions, as opposed to parapatric differentiation along elevational
 gradients as suggested by Viburnum species distributions in other parts of
 the neotropics.
description: 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 <em>V.
 incarum</em>, 29 as <em>V. seemenii</em>, 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
 reference-guided method. For this purpose, we used the draft reference
 genome of <em>V. lautum </em>(Donoghue et al. 2022). We
 discarded paralog reads that mapped to multiple locations in the
 reference.
description: Ipyrad is needed to open HDF5 files
description: # 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)