DOI: 10.5061/dryad.573n5tb4j
title: Phylogenomics of the Andean tetraploid clade of the American Amaryllidaceae (subfamily Amaryllidoideae): unlocking a polyploid generic radiation abetted by continental geodynamics

description: The second large clade of the endemic American Amaryllidaceae subfam.
 Amaryllidoideae constitutes the tetraploid-derived (n = 23)
 Andean-centered tribes, most of which have 46 chromosomes. Despite
 progress in resolving phylogenetic relationships of the group with nrDNA,
 certain subclades were poorly resolved or weakly supported in those
 previous studies. Sequence capture using anchored hybrid enrichment was
 employed across 95 species of the clade along with five outgroups and
 generated sequences of 524 nuclear genes and a partial plastome. Maximum
 likelihood phylogenetic analyses were conducted on concatenated
 supermatrices, and coalescent species tree analyses were run on the gene
 trees, followed by hybridization network, age diversification and
 biogeographic analyses. The four tribes Clinantheae, Eucharideae,
 Eustephieae (the first branch), and Hymenocallideae (sister to Clinanthus)
 are resolved in all analyses with 100% support. Nuclear gene supermatrix
 and species tree results were largely in concordance; however cytonuclear
 discordance was evident. Hybridization network analysis identified
 significant reticulation in Clinanthus, Hymenocallis, Stenomesson and the
 subclade of Eucharideae comprising Eucharis, Caliphruria, and Urceolina.
 Our data support a previous treatment of the latter as a single genus,
 Urceolina, with the addition of Eucrosia dodsonii. Biogeographic analysis
 and penalized likelihood age estimation suggests an origin in the central
 Andean region (north and central Peru) for the complex in the
 mid-Oligocene, with more dispersals than vicariances in its history, but
 no extinctions. The Eucharideae experienced a sudden lineage radiation ca.
 10 Mya. We tie much of the divergences in the Andean-centered lineages to
 the rise of the Andes, directly and indirectly, and suggest that the
 Amotape-Huancabamba Zone functioned as both a corrider (dispersal) and a
 barrier to migration (vicariance). Several taxonomic changes are made.
 This is the largest DNA sequence data set to be applied within
 Amaryllidaceae to date.The second large clade of the endemic American
 Amaryllidaceae subfam. Amaryllidoideae constitutes the tetraploid-derived
 (n = 23) Andean-centered tribes, most of which have 46 chromosomes.
 Despite progress in resolving phylogenetic relationships of the group with
 nrDNA, certain subclades were poorly resolved or weakly supported in those
 previous studies. Sequence capture using anchored hybrid enrichment was
 employed across 95 species of the clade along with five outgroups and
 generated sequences of 524 nuclear genes and a partial plastome. Maximum
 likelihood phylogenetic analyses were conducted on concatenated
 supermatrices, and coalescent species tree analyses were run on the gene
 trees, followed by hybridization network, age diversification and
 biogeographic analyses. The four tribes Clinantheae, Eucharideae,
 Eustephieae (the first branch), and Hymenocallideae (sister to Clinanthus)
 are resolved in all analyses with 100% support. Nuclear gene supermatrix
 and species tree results were largely in concordance; however cytonuclear
 discordance was evident. Hybridization network analysis identified
 significant reticulation in Clinanthus, Hymenocallis, Stenomesson and the
 subclade of Eucharideae comprising Eucharis, Caliphruria, and Urceolina.
 Our data support a previous treatment of the latter as a single genus,
 Urceolina, with the addition of Eucrosia dodsonii. Biogeographic analysis
 and penalized likelihood age estimation suggests an origin in the central
 Andean region (north and central Peru) for the complex in the
 mid-Oligocene, with more dispersals than vicariances in its history, but
 no extinctions. The Eucharideae experienced a sudden lineage radiation ca.
 10 Mya. We tie much of the divergences in the Andean-centered lineages to
 the rise of the Andes, directly and indirectly, and suggest that the
 Amotape-Huancabamba Zone functioned as both a corrider (dispersal) and a
 barrier to migration (vicariance). Several taxonomic changes are made.
 This is the largest DNA sequence data set to be applied within
 Amaryllidaceae to date.
description: This dataset represents the results of various phylogenetic
 analyses of genomic data collected from 100 species of the monocot family
 Amaryllidaceae (subfamily Amarylidoideae). The data were generated with
 sequence capture using anchored hybrid enrichment, employed across 95
 species of the tetraploid Andean clade along with five outgroups (100 taxa
 in total). This generated sequences of 524 nuclear genes and a partial
 plastome. The fastq files from the sequencing are deposited in  Sequence
 Read Archive (SRA) database of The National Center for Biotechnology
 Information NCBI) as <strong>Bioproject
 PRJNA635412</strong>,<strong>SRA Accessions numbers
 SAMN15066108 – SAMN15066207</strong>. These will not be publicly
 available until our paper is published. Files deposited with
 <strong>DRYAD </strong>are as follows: –
 Individual gene alignments in fasta format (gnes are named):
 <strong>All_Nuclear_Genes.zip</strong> –
 Input files and results from <strong>RAxML</strong> thorough
 analyses (best tree and bootstrap) of concatenated supermatrices of
 nuclear loci, coding + flanking regions (AndeanSuperMatrix_RAxML_wholeAll;
 input: andean_whole_supermatrix_sorted.fasta,
 andean_whole_supermatrix_partition.txt); coding regions only (Andean RAxML
 All Coding_only; input: andean_coding_supermatrix_sorted.fasta,
 andean_coding_supermatrix_partition.txt), loci with 70% taxon coverage
 (input: supermatrix_over70.fasta, supermatrix_over70.partition.txt); loci
 with 90% taxon coverage (Andean whole RAxML_90 per cent; input:
 supermatrix90percent.fasta, supermatrix90percent.part), and partial
 plastome [Andean_Plastome_RAxML, Large Single Copy (LSC) and Inverted
 Repeat (IR) regions (input: Andean_LSC&IRtrim.fasta,
 Andean_LSC&IRtrim.part.txt)]. Archived as
 <strong>RAxML.zip</strong>. The two input files are all that
 is required to run RAxML. – Gene trees for use in
 species tree estimation with the program
 <strong>ASTRAL-III</strong> (ASTRAL Analyses/gene
 trees/): andean_coding, andean_whole, loci70percent, loci90percent;
 bootstrap and Local Posterior Probablility (LPP) tree files from the
 various ASTRAL-III analyses (ASTRAL Analyses/). Archived as
 <strong>ASTRAL analyses.zip</strong>. –
 Infile (90pcAndeanMLsupermatrix), R scripts
 (Andean_chronos_script3_EG.NEW.txt, Andean_lamda cycle_script5.txt), and
 relaxed and correlated trees from the divergence dating analysis with
 <strong>APE </strong>in <strong>R v.4.0</strong>
 (time_calibrated_tree_3_correlated.tre,
 time_calibrated_tree_3_relaxed.tre). Archived as
 <strong>ape.zip</strong>. – Infiles, model
 test results, and results of biogeographic analyses (Nuclear supermatrix
 tree DIVAlike+J/, Plastome super matrix BAYSAREA+J) using
 <strong>BioGeoBears</strong> as implemented in
 <strong>RASP v. 4.2</strong>. Archived as
 <strong>RASP.zip</strong>. – Infiles
 (Clinantheae 99pc supermatrix.nex, Eucharideae99pcsupermatrix.nex,
 Hymenocallis99pcsupermatrix.nex) for hybridization network analyses with
 <strong>Splitstree v.4.15.1</strong>. Archived as
 <strong>Splitstree v.4.15.1</strong>. –
 Infile (time_calibrated_tree_3_relaxed.tre) and results for BAMM (Bayesian
 Analysis of Macroevolutionary Mixtures) of the tetraplid Andean clade.
 Archived as <strong>BAMM.zip</strong>.
      
description: In order to use the components of the data set, the user would
 need to download and learn to use the following programs: RAxML or use it
 on the CIPRES Portal (http://www.phylo.org/), RASP 4.2, Splitstree 4.15.1, R, APE (install within R), BAMM (install in R), and ASTRAL-III. All .tre files can be visualized in all programs that can process treefiles. We use FigTree.