DOI: 10.5061/dryad.ffbg79crx
title: Data from: Plastome and nuclear phylogenies of dwarf mistletoes (Arceuthobium: Viscaceae)

description: Dwarf mistletoes are a group of morphologically-reduced aerial shoot
 parasites of Pinaceae and Cupressaceae found in the northern hemisphere
 and equatorial east Africa. Though diagnosable by a suite of morphological
 traits, phylogenetic knowledge of species relationships has been limited
 to studies employing either comprehensive sampling of one or two genes, or
 more sequence data but limited taxonomic sampling. We used genome skimming
 data to assemble 3kb of the nuclear ribosomal cistron and up to 45kb of
 the plastome to clarify the phylogenetic root of the genus, species
 monophyly, and relationships among infraspecific taxa. Genomic
 differentiation among taxa was variable; however, we found strong support
 for reciprocally monophyletic New World and Old World lineages and
 congruent nrDNA and plastome topologies at the species level and below,
 and most taxonomic sections and at the species level and below. Plastome
 gene content was stable across the genus with minimal pseudogenization or
 loss, with the notable exception of cemA. These findings form the basis of
 our re-evaluation of historical biogeographical hypotheses, species and
 subspecies-level taxonomy, and plastome evolution in Arceuthobium. More
 broadly, this work provides a foundation for future clade-focused
 comparative and biosystematics studies of Arceuthobium.
description: Campylopoda_cpDNA.tre Maximum likelihood
 Newick tree
 of <em>Arceuthobium</em> sect. <em>Campylopoda </em>with bootstrap values at node. Inferred using an expanded plastome dataset. Campylopoda_nr_cpDNA.tre Maximum likelihood Newick tree of <em>Arceuthobium</em> sect. <em>Campylopoda </em>with bootstrap values at nodes. Inferred using an expanded plastome dataset. Campylopoda_nr_cpDNA.pdf Maximum likelihood tree of <em>Arceuthobium</em> sect. <em>Campylopoda </em>with bootstrap values at nodes. Inferred using an expanded plastome dataset (portable document format)<i>.</i> Contig1.fasta Multiple sequence alignment of plastome Contig 1. Includes the following genes from the large single copy region (' denotes reverse complement): <i>rps18– rps<sup> </sup>20’<sup> </sup>– clpP’–psbB – psbT –psbN’ – psbH.</i> Contig2.fasta Multiple sequence alignment of plastome Contig 2. Includes the following genes or pseudogenes from the large single copy region (' denotes reverse complement): <i>ycf4 –cemA<sup>ψ </sup>– petA – psbJ’ – psbL’.</i> Contig3.fasta Multiple sequence alignment of plastome Contig 3. Includes the following genes from the large single copy region (' denotes reverse complement): <i>atpB’ – rbcL ­– accD</i><i>.</i> Contig4.fasta Multiple sequence alignment of plastome Contig 4. Includes the following genes or pseudogenes from the inverted repeat region:<em> </em><i>rn16 –trnA<sup>UGCψ</sup> – rrn23</i><i>.</i> Contig5.fasta Multiple sequence alignment of plastome Contig 5. Includes the following genes or pseudogenes from the inverted repeat region (' denotes reverse complement):<em> </em><i>rps19’ – rpl2’ – rpl23’ – trnM<sup>CAU</sup>’ – ycf2 – trnL<sup>CAA</sup>’– ndhB<sup>ψ</sup> – rps7’.</i> Contig6.fasta Multiple sequence alignment of plastome Contig 6<em> </em>for section <em>Campylopoda</em>. Includes the following genes or pseudogenes (' denotes reverse complement):<em> </em><i>ycf3</i>’<i>– trnS<sup>GGA</sup>– rps4’­– atpB’ – rbcL ­– accD – psaI ­– ycf4 –cemA<sup>ψ </sup>– petA – psbJ’ – psbL’</i> – <i>psbF’ – psbE’ ­– petG – trnW<sup>CCA</sup>’ – trnP<sup>UUG</sup>’ – psaJ – rps18– rps<sup> </sup>20’<sup> </sup>– clpP’–psbB – psbT –psbN’ – psbH</i> – <i>petB</i> – <i>petD – rps11’ – rpl36’­­ – rps8’ – rpl14’ – rpl16’.</i> cpDNA.tre nrDNA.fasta Multiple sequence alignment of nuclear ribosomal DNA for <em>Arceuthobium</em><i>.</i> nrDNA.tre Maximum likelihood Newick tree of <em>Arceuthobium</em> with bootstrap values at nodes. Inferred using nuclear ribosomal DNA. nrDNA_Nickrent.tre Maximum likelihood Newick tree of <em>Arceuthobium</em> with bootstrap values at nodes. Inferred using nuclear ribosomal DNA and additional ITS samples published by Nickrent et al. (2004)<i>.</i> nrDNA_Nickrent.fasta Multiple sequence alignment of nuclear ribosomal DNA for <em>Arceuthobium</em> including additional ITS samples published by Nickent et al. (2004)<i>.</i> Partitioning_Schemes.pdf Partitioning schemes and substitution models used in each maximum likelihood analysis (portable document format)<i>.</i> <strong>Viscaceae_Amphorogynaceae_cp.tre</strong> Re-analysis of Viscaceae and Amphorogynaceae sequences published by Nickrent et al. (2019) using only plastid loci (<i>rbcL</i> + <i>accD</i> + <i>matK</i>) to illustrate discordance with ITS-only generic relationships inferred by Maul et al. (2019). Exemplars of <i>Arceuthobium abietis-religiosae </i>(UC1544844) and<i> A. nigrum</i> (UC2056905) also added to allow the inference of the <i>Arceuthobium </i>crown node<i>.</i> Two specimens of Nanodeaceae (<i>Mida salicifolia</i> and <i>Nondea muscoca)</i> used as an outgroup. Likelihood analysis performed using RAxML-HPC v8.2.12 on XSEDE with 1000 bootstrap replicates and otherwise default settings<i>.</i> Voucher_Table.csv Voucher specimens, hosts, and GenBank accession numbers for newly generated sequence data. (Appendix 1 in comma-separated values format)<i>.</i> <strong>Voucher_Table.pdf</strong> Voucher specimens, hosts, and GenBank accession numbers for newly generated sequence data. (Appendix 1 in portable document format)<i>.</i> <strong>Voucher_Table.xls</strong> Voucher specimens, hosts, and GenBank accession numbers for newly generated sequence data. (Appendix 1 in Excel format).