Two new species of Aphyllon from northeastern Mexico: Sequence alignments and phylogenetic trees
Data files
Oct 31, 2023 version files 125.16 KB
Abstract
Plants originally identified as Aphyllon ludovicianum that occur near Monterrey, Nuevo Leon, and Cuatro Ciénegas Bolson, Coahuila, Mexico, were found to not align with the protologue of that species, the close relative A. multiflorum, or any other species of Aphyllon. Following a detailed study of floral morphology, geographic range, host species, and phylogenetic position using dry herbarium specimens, field study and georeferenced color photographs, we propose the new binomials Aphyllon spectabile for the plants from Nuevo Leon and Aphyllon gypsophilum for the plants from Coahuila, Mexico. This increases the taxonomic diversity of Aphyllon to 27 species plus ten additional subspecies. Gymnosperma glutinosum and two species of Xanthisma were reported for the first time as a host species for the genus Aphyllon. We also provide an updated key to Aphyllon in Mexico.
README: Two new species of Aphyllon from northeastern Mexico: Sequence alignments and phylogenetic trees
https://doi.org/10.5061/dryad.bzkh189gc
Description of the data and file structure
Aphyllon sequence data stored as a FASTA sequence alignment, a text-based format, in two files:
ludo_clade_cpDNA_2023_08_22.fasta – Three concatenated plastid genes from 38 samples.
ludo_clade_nrDNA_2023_08_22.fasta – Concatenated internal and external transcribed spacers of the nuclear ribosomal cistron (ITS and ETS) from 40 samples.
FASTA files contain one or more sequences begins with a greater-than character (">") followed by a description of the sequence (all in a single line). The next line immediately following the description line is the sequence representation, with one letter per nucleic acid (A, T, C, G) , or inferred gap (–). Positions in which the nucleic acid is uncertain are represented by several other letters.
Phylogenetic trees of the Aphyllon ludovicianum complex inferred using maximum likelihiood stored in Newick format, a text-based format, with nodes labels with bootstrap support. Tip names include the binomial followed by the collector/collection number and herbarium/accession number of the original sample, if available.
ludo_clade_cpDNA_2023-08-22.tre
ludo_clade_nrDNA_2023-08-22.tre
Sharing/Access information
Individual sequences are also available on GenBank: https://www.ncbi.nlm.nih.gov/nucleotide/
Methods
Most data was obtained from previously published DNA sequences (Schneider et al. 2016), however a few new samples were added as follows: DNA was extracted using a DNeasy Plant Pro kit, genes of interest amplified using polymerase chain reaction using primers and methods from Schneider et al. 2016. Dideoxy (Sanger) sequencing was performed in forward and reverse directions. Raw sequence chromatograms were inspected for quality and trimmed, then aligned with existing nuclear ribosomal and concatenated plastid sequence alignments from Schneider et al. (2016) using the MUSCLE plugin for Geneious 9.1.8.