Data from: Plastome and nuclear phylogenies of dwarf mistletoes (Arceuthobium: Viscaceae)
Cite this dataset
Schneider, Adam (2021). Data from: Plastome and nuclear phylogenies of dwarf mistletoes (Arceuthobium: Viscaceae) [Dataset]. Dryad. https://doi.org/10.5061/dryad.ffbg79crx
Abstract
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.
Usage notes
Campylopoda_cpDNA.tre
Maximum likelihood Newick tree of Arceuthobium sect. Campylopoda with bootstrap values at node. Inferred using an expanded plastome dataset.
Campylopoda_nr_cpDNA.tre
Maximum likelihood Newick tree of Arceuthobium sect. Campylopoda with bootstrap values at nodes. Inferred using an expanded plastome dataset.
Campylopoda_nr_cpDNA.pdf
Maximum likelihood tree of Arceuthobium sect. Campylopoda with bootstrap values at nodes. Inferred using an expanded plastome dataset (portable document format).
Contig1.fasta
Multiple sequence alignment of plastome Contig 1. Includes the following genes from the large single copy region (' denotes reverse complement): rps18– rps 20’ – clpP’–psbB – psbT –psbN’ – psbH.
Contig2.fasta
Multiple sequence alignment of plastome Contig 2. Includes the following genes or pseudogenes from the large single copy region (' denotes reverse complement): ycf4 –cemAψ – petA – psbJ’ – psbL’.
Contig3.fasta
Multiple sequence alignment of plastome Contig 3. Includes the following genes from the large single copy region (' denotes reverse complement): atpB’ – rbcL – accD.
Contig4.fasta
Multiple sequence alignment of plastome Contig 4. Includes the following genes or pseudogenes from the inverted repeat region: rn16 –trnAUGCψ – rrn23.
Contig5.fasta
Multiple sequence alignment of plastome Contig 5. Includes the following genes or pseudogenes from the inverted repeat region (' denotes reverse complement): rps19’ – rpl2’ – rpl23’ – trnMCAU’ – ycf2 – trnLCAA’– ndhBψ – rps7’.
Contig6.fasta
Multiple sequence alignment of plastome Contig 6 for section Campylopoda. Includes the following genes or pseudogenes (' denotes reverse complement): ycf3’– trnSGGA– rps4’– atpB’ – rbcL – accD – psaI – ycf4 –cemAψ – petA – psbJ’ – psbL’ – psbF’ – psbE’ – petG – trnWCCA’ – trnPUUG’ – psaJ – rps18– rps 20’ – clpP’–psbB – psbT –psbN’ – psbH – petB – petD – rps11’ – rpl36’ – rps8’ – rpl14’ – rpl16’.
cpDNA.tre
nrDNA.fasta
Multiple sequence alignment of nuclear ribosomal DNA for Arceuthobium.
nrDNA.tre
Maximum likelihood Newick tree of Arceuthobium with bootstrap values at nodes. Inferred using nuclear ribosomal DNA.
nrDNA_Nickrent.tre
Maximum likelihood Newick tree of Arceuthobium with bootstrap values at nodes. Inferred using nuclear ribosomal DNA and additional ITS samples published by Nickrent et al. (2004).
nrDNA_Nickrent.fasta
Multiple sequence alignment of nuclear ribosomal DNA for Arceuthobium including additional ITS samples published by Nickent et al. (2004).
Partitioning_Schemes.pdf
Partitioning schemes and substitution models used in each maximum likelihood analysis (portable document format).
Viscaceae_Amphorogynaceae_cp.tre
Re-analysis of Viscaceae and Amphorogynaceae sequences published by Nickrent et al. (2019) using only plastid loci (rbcL + accD + matK) to illustrate discordance with ITS-only generic relationships inferred by Maul et al. (2019). Exemplars of Arceuthobium abietis-religiosae (UC1544844) and A. nigrum (UC2056905) also added to allow the inference of the Arceuthobium crown node. Two specimens of Nanodeaceae (Mida salicifolia and Nondea muscoca) used as an outgroup. Likelihood analysis performed using RAxML-HPC v8.2.12 on XSEDE with 1000 bootstrap replicates and otherwise default settings.
Voucher_Table.csv
Voucher specimens, hosts, and GenBank accession numbers for newly generated sequence data. (Appendix 1 in comma-separated values format).
Voucher_Table.pdf
Voucher specimens, hosts, and GenBank accession numbers for newly generated sequence data. (Appendix 1 in portable document format).
Voucher_Table.xls
Voucher specimens, hosts, and GenBank accession numbers for newly generated sequence data. (Appendix 1 in Excel format).
Funding
National Science Foundation, Award: #DEB-1601504
California Native Plant Society, East Bay Chapter
California Native Plant Society, East Bay Chapter