DOI: 10.5061/dryad.0k6djh9wd
title: Leprocaulon beechingii (Leprocaulaceae), a new species from the southern Appalachian Mountains of eastern North America

description: Leprocaulon beechingii is described as new to science based on collections
 from exposed rock outcrops in the southern Appalachian Mountains in
 eastern North America. Taxonomic placement in Leprocaulon, and
 delimitation from other members of the genus with usnic acid, is supported
 by molecular phylogenetic analyses of ITS and mtSSU sequence data. The
 species is readily recognized by its occurrence on non-calcareous rocks,
 normandinoides-type placodioid thallus, and the production of usnic acid
 and zeorin.
description: Initial BLAST searches of the sequences of the new taxon against
 the NCBI nucleotide collection revealed a close match to existing
 reference sequence of <i>Leprocaulon</i> Nyl. (ITS, e value
 0.0, % identity 89.17% to KC184096; mtSSU e value 0.0, % identity 96.36%
 to KJ66426) Taxon sampling for the present study was based on Lendemer and
 Hodkinson (2013) which utilized ITS and mtSSU sequence data. As such, data
 for these loci were assembled for the Leprocaulaceae based on the sampling
 of Lendemer and Hodkinson (2013), with representatives of Caliciaceae
 selected as the outgroup (<i>Dirinaria applanata </i>(Fée)
 D.D. Awasthi<i>, Pyxine sorediata </i>(Ach.) Mont.<i>,
 P. subcinerea </i>Stirt.), and then expanded as follows: 1)
 sequences of <i>Leprocaulon calcicola </i>Earl.-Benn., Orange,
 Hitch & M. Powell were included based on Orange et al. (2017); 2)
 newly generated ITS and mtSSU sequences from one specimen of the
 potentially new species were included; 3) sequences of <i>L.
 nicholsiae</i> Lendemer & E. Tripp were included based on
 Tripp & Lendemer (in press.), 4) a newly generated sequences
 <i>L. nicholsiae </i>Lendemer & E. Tripp<i>
 </i>(11, ITS), <i>L. knudsenii</i> Lendemer &
 B.P. Hodkinson (2, ITS), and an apparently undescribed
 <i>Leprocaulon</i> species from Chile (3, ITS) were
 included. One alignment was prepared for ITS and one
 for mtSSU, each was then subjected to auto-alignment using the MAFFT
 online interface and then manually adjusted with Mesquite 3.04 (Maddison
 & Maddison 2015). Ambiguously aligned regions were defined as an
 exclusion set in Mesquite. Each dataset was then prepared for maximum
 likelihood (ML) analyses by transforming uncertainties and polymorphisms
 to missing data, manually deleting the ambiguously aligned regions, and
 exporting the alignment as a PHYLIP file. Each resulting PHYLIP file was
 then input to ML analyses in RAxML 8.2.10 (Stamatakis 2006) with 500
 bootstrap replicates, implementing the most complex nucleotide
 substitution model in that program (GTRGAMMA). The resulting topologies
 with ML-bootstrap values were visualized in FigTree (Rambaut 2017). As no
 conflict (defined following Mason-Gamer & Kellogg 1996) was
 detected between the two datasets, the alignments were concatenated and
 the combined alignment subjected to ML analyses as outlined above but with
 the two loci partitioned and the model GTRGAMMA applied to each partition.
 The results of the combined analyses were also visualized in
 FigTree.
description: This dataset includes the following: 1) The
 single locus DNA alignment for nrITS (NEXUS format) 2)
 The single locus DNA alignment for mtSSU (NEXUS format)
 3) The concatened alignment for both loci (PHYLIP format) and the
 partitions file for this alignment. 4) A table
 crossreferencing voucher data, isolate numbers, and NCBI accession
 numbers.