Skip to main content
Dryad logo

Data from: Plastome and nuclear phylogenies of dwarf mistletoes (Arceuthobium: Viscaceae)

Citation

Schneider, Adam (2021), Data from: Plastome and nuclear phylogenies of dwarf mistletoes (Arceuthobium: Viscaceae), Dryad, Dataset, 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