DOI: 10.5061/dryad.k3j9kd5gg
title: Dubautia haupuensis, a new species of the Hawaiian silversword alliance (Compositae--Madiinae) from Hā'upu, Kaua'i

description: Dubautia haupuensis B.G.Baldwin & K.R.Wood is newly described from
 windswept ridgelines near the summit of Hāʻupu, Kauaʻi, in the Hawaiian
 Islands, where only two clusters of plants are currently known. Based on
 molecular phylogenetic data, this highly endangered shrub of the Hawaiian
 silversword alliance belongs to a recently resolved clade of endemic
 Kauaʻi taxa, mostly from wet or bog habitats, including D.
 imbricata subsp. acronaea, D. imbricata subsp. imbricata, D. kalalauensis,
 D. kenwoodii, D. laevigata, D. syndetica, and D. waialealae. Unlike its
 close relatives and other members of Dubautia, D. haupuensis has
 the following unique combination of morphological characteristics:
 well-branched shrubs with leaves opposite, sessile, and glabrous, leaf
 venation ± parallelodromous, with 5 to 9 basal nerves, capitulescences
 densely corymbiform to paniculiform, peduncles hirsute, peduncular bracts
 lance-linear to ovate, with faces glabrous and margins ciliate, heads 7 to
 12-flowered, paleate throughout, the paleae each partially clasping a
 floret, with faces glabrous and distal margins ciliate, corolla
 tube/throat sessile-glandular, the throat dilated ≤ 2' tube width,
 and pappus ± equaling corolla, of 20 to 31 setiform to narrowly subulate,
 densely ciliate scales, the cilia &lt; 0.5 mm long. It also is
 distinguished from all other taxa of the silversword alliance by
 diagnostic nuclear ribosomal DNA nucleotide states. Six of the seven taxa
 that constitute a clade with D. haupuensis have highly restricted
 distributions on Kauaʻi and are of significant conservation concern, as
 reflected by listing most of them as Endangered by the U.S. Fish and
 Wildlife Service. Dubautia haupuensis is also exceedingly rare and in need
 of immediate conservation action to prevent its extinction. Invasive
 plants (especially melastomes), potential ungulate activity, lack of
 opportunity for outcrossing, and any mortality from stochastic events are
 major threats to the species, in addition to possible impacts of
 anthropogenic climate change.
description: The DNA sequences aligned here using MAFFT (nexus file) represent
 the non-identical nuclear ribosomal DNA sequences published by Baldwin et
 al. (2021) American Journal of Botany 108: 2015-2037 plus novel external
 and internal transcribed spacer region sequences for the newly described
 species, <em>Dubautia haupuensis</em>, which were the result
 of Sanger sequencing (using the same methods as in Baldwin et al. (2021).
 The two tree files are from a maximum likelihood (ML) analysis and a
 separate phylogenetic analysis using Bayesian inference (BI). ML analyses
 were run using IQ-TREE 1.6.12 (Nguyen et al. 2015), with nucleotide
 substitution models for combined-spacer and for 5.8S gene partitions
 selected using ModelFinder (Kalyaanamoorthy et al. 2017), as in Baldwin et
 al. (2021). BI analyses were run using MrBayes 3.2.7a (Ronquist et al.
 2012) on the CIPRES Portal (Miller et al. 2010), with model selection of
 K80+G for spacers and K80+I for 5.8S gene (20 million generations, 2 runs,
 3 hot chains + 1 cold chain, and 0.25 burnin).
description: # *Dubautia haupuensis*, a new species of the Hawaiian silversword
 alliance (Compositae--Madiinae) from Hā'upu, Kaua'i
 [https://doi.org/10.5061/dryad.k3j9kd5gg](https://doi.org/10.5061/dryad.k3j9kd5gg) This submission represents the supporting molecular phylogenetic data for an accepted *Systematic Botany* manuscript by the same name. ## Description of the data and file structure The aligned DNA sequence matrix nexus file (sword_ETS_ITS_58_merge.nex) is a concatation of 18S-26S nuclear ribosomal external and internal transcribed spacer region sequences for the Hawaiian silversword alliance (*Argyroxiphium*, *Dubautia*, *Wilkesia*; Compositae--Madiinae), with two North American tarweed outgroup taxa at the top of the alignment (*Anisocarpus scabridus* and *Carlquistia muirii*). The external transcribed spacer sequences are partial at the 5' end; the internal transcribed spacer region sequences are complete. The sequences included here represent all of the DNA samples included in Baldwin et al. (2021) *American Journal of Botany* 108: 2015-2037 plus new sequences for the new-to-science *Dubautia haupuensis*, described in the *Systematic Botany* manuscript. The tree files are from analyses based on maximum likelihood (sword_ITS_ETS_merge_6_22_23.nex.treefile) and Bayesian inference (sword_7_3_23_MrBayes_consensus.tre); results of both are summarized in a highly condensed tree figure (Fig. 1) in the Systematic Botany manuscript associated with this submission, where much of the tree structure is collapsed to emphasize the most relevant clades (but not collapsed in the tree files). Maximum likelihood analyses were conducted using IQ-TREE 1.6.12 (Nguyen et al. 2015), with nucleotide substitution models for the combined-spacer and for the 5.8S gene partitions chosen by ModelFinder (Kalyaanamoorthy et al. 2017), as in Baldwin et al. (2021).  Bayesian inference analyses were conducted using MrBayes 3.2.7a (Ronquist et al. 2012) on the CIPRES Portal (Miller et al. 2010), with nucleotide substitution model selection of K80+G for the spacers and K80+I for the 5.8S gene (20 million generations; 2 runs, 3 hot chains + 1 cold chain; burnin 0.25).  Sequence names in the alignment and tree files are abbreviations of the taxon names (in letters --- first letter of genus name followed by first 2--4 letters of species epithet and ending with first letter of (any) subspecies epithet, in lower case. Apart from BW or W preceding numbers (see below), capital letters following taxon abbreviations are island abbreviations (only for the minority of taxa that occur across multiple islands): EM = East Maui; H = Hawaii/Big Island; K = Kauai; L = Lanai; M = Maui; MM = Maui and Molokai; Mo or Mol = Molokai. Numbers following taxon/island abbreviations are one of the following: (1) a unique 3--4 digit collection number identifier not preceded by any capital lettering, corresponding to a collection number of Bruce Baldwin's (details of those samples are in Baldwin et al. (2021), (2) a 1 or 2 digit number, corresponding to the number of collection samples represented by that sequence (in situations where different populations of the same taxon -- or rarely multiple taxa -- have identical sequences), in which case the identity of those samples represent all of the samples for that taxon minus any additional sample of that taxon represented by a longer collection number in the matrix (note: a single-digit number separated by an underscore from a collection number is not the number of individuals but instead a number assigned to one of multiple plants collected under that collection number), or (3) a number preceded by BW, representing a collection by someone other than Baldwin, and defined below. The additional, new sample added to this dataset that is not in Baldwin et al. (2021) is indicated as W18458_D_haupu_ETS_ITS, for *Dubautia haupuensis*, *Wood et al. 18458*. Sample crosswalk for BW samples and others (with complex names): Argyr7 = All samples of *Argyroxiphium* except *A. caliginis 660* (A_cali_660); Wgymn = *Wilkesia gymnoxiphium*; W_hobd = *Wilkesia hobdyi*; D_pal or D_pale = *Dubautia paleata* (BW714 = *Wood 12507*; BW719 = *Wood 12517*); Drail = *Dubautia raillardioides*; D_lati or Dlati = *D. latifolia*; D_laev = *Dubautia laevigata* (BW779 = *S.J. Bainbridge s.n.*, 26 Jan 2008); D_kenw = *Dubautia kenwoodii* (BW215 = *Wood 1004*); D_haupu = *Dubautia haupuensis*; D_imbi or Dimbi = *Dubautia imbricata* subsp. *imbricata*; Dimba = *Dubautia* *imbricata* subsp. *acronaea*; Dkala or D_kal = *Dubautia kalalauensis* (BW774 = *S.J. Bainbridge s.n*., 26 Jan 2008); Dsynd or D_synd = *Dubautia syndetica* (BW155 = *Morden et al. 1383*); Dwle or D_wle = *Dubautia waialealae* (BW723 = *Wood 12526*); Dplam = *Dubautia plantaginea* subsp. *magnifolia*; Dpla, D_pl, or Dplan = *Dubautia plantaginea* subsp. *plantaginea* or *Dubautia plantaginea* subsp. *humilis* (in DplaWM4, together with 3 samples of *D. p.* subsp. *plantaginea* -- *Oppenheimer H110801*; *Oppenheimer & Perlman H100702*; *Wood 11567*); Dmicr = *Dubautia microcephala*; Dknuk = *Dubautia knudsenii* subsp. *knudsenii*, D_knun or Dknun = *Dubautia knudsenii* subsp. *nagatae*; Dknnf = *Dubautia knudsenii* subsp. *nagatae* (*Baldwin et al. 1500*; *Wood 12183*; *Carr 1322*) and *Dubautia knudsenii* subsp. *filiformis*; Dpauc = *Dubautia pauciflorula*; Dlaxh or D_laxh = *Dubautia laxa* subsp. *hirsuta*; Dlaxb = *Dubautia laxa* subsp. *bryanii*; Dlaxl, D_laxl, or D_lax = *Dubautia laxa* subsp. *laxa*; Dher2she4 = *Dubautia herbstobatae* and *Dubautia sherffiana*; DEMMo = *Dubautia carrii*, *Dubautia menziesii*, *Dubautia platyphylla* (except next entry), *Dubautia reticulata*, and *Dubautia waianapanapaensis*; Dplat520Ec4 & 5 = *Dubautia platyphylla* *Baldwin 520* clones 4 & 5; Dhana = *Dubautia hanaulaensis*; Dlinarb14 = *Dubautia arborea*, *Dubautia linearis* subsp. *linearis*, and *Dubautia linearis* subsp. *hillebrandii*; Dcilg2 = *Dubautia ciliolata* subsp. *glutinosa* (*Baldwin 659* & *Baldwin et al. 1511-1*); Dcilcg3 = *Dubautia ciliolata* subsp. *ciliolata* and *Dubautia ciliolata* subsp. *glutinosa* (*Baldwin et al. 1513*); D_scab, Dscab, Dsca, or D_sc = *Dubautia scabra* (BW457 = *Welton & Haus 1081*; BW791 = *Wood 12699*; BW964 = *Oppenheimer H110803*); Dscal or D_sca_l = *Dubautia scabra*; subsp. *leiophylla*; Dscas = *Dubautia scabra* subsp. *scabra*; DscalEM2a = *Wood 12590* & *12692*; DscalEM2b = *Baldwin & Bainbridge 778*, and *Oppenheimer H70910*; DscaEM2 = *Oppenheimer H71004* & *H71010*; DscalMoL3 = *Baldwin & Bainbridge 1267*, *Wood 11366*, and *Perlman 5074*; DscasH3 = *Baldwin 526*, *530*, and *Baldwin et al. 1509*). ## References * Baldwin, B. G., K. R. Wood, and W. A. Freyman.  2021.  Directionally biased habitat shifts and biogeographically informative cytonuclear discordance in the Hawaiian silversword alliance (Compositae).  *American Journal of Botany* 108: 2015–2037. * Kalyaanamoorthy, S., B. Q. Minh, T. K. F Wong, A. von Haeseler, and L. S. Jermiin.  2017.  ModelFinder: Fast model selection for accurate phylogenetic estimates.  *Nature Methods* 14: 587–589. * Miller, M. A., W. Pfeiffer, and T. Schwartz.  2010.  Creating the CIPRES Science Gateway for inference of large phylogenetic trees.  Pp. 1–8 in *Proceedings of the Gateway Computing Environments Workshop (GCE), 14 Nov. 2010, New Orleans, Louisiana*. * Nguyen, L.-T., H. A. Schmidt, A. von Haeseler, and B. Q. Minh.  2015.  IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies. *Molecular Biology and Evolution* 32: 268–274. * Ronquist, F., M. Teslenko, P. van der Mark, D. L. Ayres, A. Darling, S. Höhna, B. Larget, L. Liu, and M. A. Suchard, and J. P. Huelsenbeck.  2012.  MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space.  *Systematic Biology* 61: 539–542.