DOI: 10.5061/dryad.v41ns1s53
title: Data from: Forget-me-not phylogenomics: Improving the resolution and taxonomy of a rapid island and mountain radiation in Aotearoa New Zealand (Myosotis; Boraginaceae)

description: Island and mountain systems represent natural laboratories for studies of
 species radiations, but they often present several challenges for
 phylogenetic inference and species delimitation. The southern hemisphere
 forget-me-nots (Myosotis, Boraginaceae) comprise a geologically recent
 radiation centred in Aotearoa New Zealand, a mountainous archipelago, with
 about 50 species that are morphologically and ecologically divergent but
 lack genetic variation sufficient to resolve phylogenetic relationships
 and species boundaries using standard DNA Sanger sequencing markers,
 AFLPs, or microsatellites. Many of these Myosotis species are
 geographically restricted in alpine areas, uncommon or threatened, have
 polyploid and dysploid genomes, and are of high taxonomic and conservation
 priority. Here we present phylogenomic analyses using target-capture of
 Angiosperms353 baits, and genome skimming of whole plastomes and nrDNA, to
 improve resolution of the radiation, explore biogeographic and
 morphological patterns within it, and address specific taxonomic questions
 for each species. Our comprehensive sampling includes over 300 individuals
 representing nearly all species from New Zealand and Australia, which is
 ~2–3x more taxon sampling and ~80–120× more molecular data than previously
 published for Myosotis. Exploration of different data filtering,
 curation and analyses (coalescent vs. concatenation) improved the
 resolution of the Angiosmperms353 tree, which despite short backbone
 branches with low support values, showed taxonomic and geographic
 patterns, including multiple switches between ebracteate and bracteate
 inflorescences and multiple expansions within New Zealand from Te
 Waipounamu South Island to Te Ika-a-Māui North Island, Rakiura Stewart
 Island, subantarctic islands, and Australia. Some of these patterns were
 also seen in the genome skimming datasets, and comparison of the three
 datasets was useful for improving our understanding of the taxonomy and
 resolution of this radiation. Although this phylogenomic study does not
 fully overcome all of the challenges regarding species delimitation of
 this rapid island and mountain species radiation, it nevertheless makes an
 important contribution to an integrative taxonomic revision of the
 southern hemisphere species of Myosotis.
description: Total DNA was extracted from silica-dried material of 332
 individuals of New Zealand and Australian Myosotis (Boraginaceae) and
 outgroups using a modified CTAB protocol, and genomic libraries were
 prepared. The Standard Protocol for the myBaits Hybiridzation Capture for
 Targeted NGS Manual was followed using the Angiosperms353 bait set.
 Libraries were pooled and sequenced on Illumina MiSeq and HiSeq.
 Preliminary analyses of a 329-loci x 329-individual dataset was conducted,
 including observing all 329 Angiosperms353 gene alignments and gene trees.
 After filtering, concatenated (IQTree) phylogenetic analyses and species
 tree analyses (ASTRAL) were conducted on the Angiosperms353 alignments
 representing 25-loci-single-copy and 56-loci-single-copy datasets, as well
 as the final 322-loci dataset (each with 291 individuals). Genome skim
 sequencing was also undertaken on 259 of the genomic libraries, from which
 whole plastomes and the nuclear ribosomal DNA tandem repeat cluster was
 extracted and aligned for separate phylogenetic analyses in IQTree. We
 wish to acknowledge the use of New Zealand eScience Infrastructure (NeSI;
 https://www.nesi.org.nz) high performance computing facilities, consulting support, and training services as part of this research. New Zealand's national facilities are provided by NeSI and funded jointly by NeSI's collaborator institutions and through the Ministry of Business, Innovation & Employment's Research Infrastructure programme.
description: # Data from: Forget -me-not phylogenomics: Improving the resolution and
 taxonomy of a rapid island and mountain radiation in Aotearoa New Zealand
 (*Myosotis*; Boraginaceae)
 [https://doi.org/10.5061/dryad.v41ns1s53](https://doi.org/10.5061/dryad.v41ns1s53) ## File list Myosotis_A353_329loci_individual_alignments_trees_2024.zip (subfolder containing 330 files) Myosotis_A353_n291_322loci_bs20_astral_2024.treefile Myosotis_A353_n291_56loci_bs20_astral_2024.treefile Myosotis_A353_n291_25loci_bs20_astral_2024.treefile Myosotis_A353_n291_25loci_IQconcat25_2024.treefile Myosotis_nDNA_n259_aln_trim_2024.fasta Myosotis_nDNA_n259_aln_IQTree_2024.fasta Myosotis_plastome_n259_aln_trim_2024.fasta Myosotis_plastome_n259_IQTree_2024.treefile ## File descriptions Myosotis_A353_329loci_individual_alignments_trees_2024.zip - subfolder containing 329 individual Angiosperms353 gene alignments and one treefile containing 329 gene trees for 329 New Zealand and Australian Myosotis individuals and outgroups. The gene alignments are numbered with 4 digit numbers starting with 4, 5, 6 or 7, and the gene trees are labeled 1 to 329 and are in the same numerical order as the gene trees. These alignments and trees were examined by eye (using software Geneious and FigTree) to categorise loci as single-copy or multi-copy, and were subsequently filtered to the three final Angiosperms353 datasets of 291 individuals and either 322 loci, 56 loci or 25 loci. Myosotis_A353_n291_322loci_bs20_astral_2024.treefile - final ASTRAL species tree of 322 Angiosperms353 loci for 291 New Zealand and Australian Myosotis individuals and outgroup M. discolor Myosotis_A353_n291_56loci_bs20_astral_2024.treefile - ASTRAL species tree of 56 putative single-copy Angiosperms353 loci for 291 New Zealand and Australian Myosotis individuals and outgroup M. discolor Myosotis_A353_n291_25loci_bs20_astral_2024.treefile - IQtree concatenated phylogenetic tree of 25 putative single-copy Angiosperms353 loci for 291 New Zealand and Australian Myosotis individuals and outgroup M. discolor Myosotis_A353_n291_25loci_IQconcat25_2024.treefile - ASTRAL species tree of 25 putative single-copy Angiosperms353 loci for 291 New Zealand and Australian Myosotis individuals and outgroup M. discolor Myosotis_nDNA_n259_aln_trim_2024.fasta - final trimmed nrDNA alignment of 259 individuals of New Zealand and Australian Myosotis and outgroups Myosotis_nDNA_n259_aln_IQTree_2024.fasta - IQtree phylogenetic tree of nrDNA alignment of 259 individuals of New Zealand and Australian Myosotis and outgroups Myosotis_plastome_B_aln_trim_2024.fasta - final trimmed whole plastome alignment of 259 individuals of New Zealand and Australian Myosotis and outgroups (one copy of inverted repeat only retained) Myosotis_plastome_B_n259_IQTree_2024.treefile - IQtree phylogenetic tree of plastome alignment of 259 individuals of New Zealand and Australian Myosotis and outgroups (one copy of inverted repeat only retained) Sample abbreviations can be found in the Supplementary Information in the published article, especially Table S1. Sample names (for example anan_NV_Maki) comprise the following: 1) the first four letters of the species name or tag name (or for subspecies the first two letters of the species name and the first two letters of the subspecies name); 2) a two-letter country/region abbreviation, and 3) a four-letter geographic locality abbreviation (the first four letters of the location). ## Sharing and access information The original Illumina reads data, and the plastome and nrDNA sequences, are available on the NCBI BioProject PRJNA1125924. Comments and requests should be addressed to Heidi Meudt: [heidim@tepapa.govt.nz](mailto:heidim@tepapa.govt.nz). Please let me know if you use these datasets and whether there are any resulting publications from them. Thanks! ## Code Please see [https://github.com/SofiePearson/Myosotis](https://github.com/SofiePearson/Myosotis) for scripts.