Browsing by Author "Meudt HM"

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    A roadmap of phylogenomic methods for studying polyploid plant genera
    (John Wiley and Sons, Inc., on behalf of Botanical Society of America, 2024-04-22) Ning W; Meudt HM; Tate JA
    Phylogenetic inference of polyploid species is the first step towards understanding their patterns of diversification. In this paper, we review the challenges and limitations of inferring species relationships of polyploid plants using traditional phylogenetic sequencing approaches, as well as the mischaracterization of the species tree from single or multiple gene trees. We provide a roadmap to infer interspecific relationships among polyploid lineages by comparing and evaluating the application of current phylogenetic, phylogenomic, transcriptomic, and whole-genome approaches using different sequencing platforms. For polyploid species tree reconstruction, we assess the following criteria: (1) the amount of prior information or tools required to capture the genetic region(s) of interest; (2) the probability of recovering homeologs for polyploid species; and (3) the time efficiency of downstream data analysis. Moreover, we discuss bioinformatic pipelines that can reconstruct networks of polyploid species relationships. In summary, although current phylogenomic approaches have improved our understanding of reticulate species relationships in polyploid-rich genera, the difficulties of recovering reliable orthologous genes and sorting all homeologous copies for allopolyploids remain a challenge. In the future, assembled long-read sequencing data will assist the recovery and identification of multiple gene copies, which can be particularly useful for reconstructing the multiple independent origins of polyploids.
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    Forget-me-not phylogenomics: Improving the resolution and taxonomy of a rapid island and mountain radiation in Aotearoa New Zealand (Myosotis; Boraginaceae)
    (Elsevier Inc., 2024-11-22) Meudt HM; Pearson S; Ning W; Prebble JM; Tate JA
    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 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 Aotearoa New Zealand and Australia, which is ∼ 2-3 × 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 Angiosperms353 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.
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    Taxonomic revision of the southern hemisphere pygmy forget-me-not group (Myosotis; Boraginaceae) based on morphological, population genetic and climate-edaphic niche modelling data
    (CSIRO Publishing, 2022-05-05) Prebble JM; Symonds VV; Tate JA; Meudt HM; Wilson P
    A taxonomic revision of the southern hemisphere pygmy forget-me-not group (Myosotis L.; Boraginaceae) is presented here. Climate-edaphic niches are modelled and compared for five species in the pygmy group, namely, M. antarctica Hook.f., M. brevis de Lange & Barkla, M. drucei (L.B.Moore) de Lange & Barkla, M. pygmaea Colenso and M. glauca (G.Simpson & J.S.Thomson) de Lange & Barkla, and one unnamed putative taxon, M. "Volcanic Plateau". In this case, niche-modelling data mostly do not aid species delimitation, but morphological and genetic data provide evidence for recognising the following three species within the group: M. brevis and M. glauca (both endemic to New Zealand), and an enlarged M. antarctica (native to New Zealand, Campbell Island and Chile). Myosotis antarctica is here circumscribed to include M. antarctica sens. strict., M. drucei and M. pygmaea. The following two allopatric subspecies of M. antarctica are recognised on the basis of minor morphological differences: subsp. antarctica (formerly M. antarctica from Campbell Island and Chile, M. drucei and M. "Volcanic Plateau") and subsp. traillii Kirk (formerly known by New Zealand botanists as M. pygmaea Colenso, an illegitimate name). For all three species, which are considered Threatened or At Risk, most of their genetic variation is partitioned between rather than within populations, meaning that conserving as many populations as possible should be the priority to minimise risk of extinction.