Data from: Embracing Biodiversity: Multispecies Population Genomics of Leafless Bossiaeas Reveals Novel Taxa, Population Dynamics, and Conservation Strategies
Field | Value | Language |
dc.contributor.author | McMaster, Eilish Summer | |
dc.contributor.author | Yap, Jia-Yee Samantha | |
dc.contributor.author | McDougall, Keith L. | |
dc.contributor.author | James, Elizabeth A. | |
dc.contributor.author | Walsh, Neville | |
dc.contributor.author | Jario, Nic | |
dc.contributor.author | Peterie, Jess | |
dc.contributor.author | Rossetto, Maurizio | |
dc.date.accessioned | 2024-04-22T01:16:04Z | |
dc.date.available | 2024-04-22T01:16:04Z | |
dc.date.issued | 2024-04-22 | |
dc.identifier.uri | https://hdl.handle.net/2123/32470 | |
dc.description.abstract | Leafless Bossiaea species are a unique group of plants endemic to Australia which present intriguing challenges in taxonomy and conservation due to their morphological simplicity and often small, disjunct populations. We employed whole genome reduced representation sequencing to enhance our understanding of the population dynamics, diversity, and taxonomy of leafless Bossiaea species. Our dataset comprised 52,539 SNPs across 283 samples from seven leafless Bossiaea species, including six listed threatened species. We examined population structure, phylogenetic relationships, kinship, and gene flow within and between populations. Based on our population genomic analyses we propose recognition of the novel taxon Bossiaea vombata subsp. orientalis and a change in status from species (B. milesiae) to subspecies for B. fragrans subsp. milesiae. Additionally, we reveal extensive clonal reproduction across species and limited gene flow at distances > 1 km, shedding light on the challenges faced by these species. We advocate a coordinated approach to conservation, focusing on restoring self-sustaining populations and leveraging genetic rescue strategies. By addressing the population dynamics of multiple species simultaneously in taxonomically challenging lineages, we can make informed choices to safeguard biodiversity and evolutionary potential. | en_AU |
dc.language.iso | en | en_AU |
dc.subject | reduced representation sequencing | en_AU |
dc.subject | DArT | en_AU |
dc.subject | DArTseq | en_AU |
dc.subject | SNP data | en_AU |
dc.subject | Bossiaea | en_AU |
dc.title | Data from: Embracing Biodiversity: Multispecies Population Genomics of Leafless Bossiaeas Reveals Novel Taxa, Population Dynamics, and Conservation Strategies | en_AU |
dc.type | Dataset | en_AU |
dc.identifier.doi | 10.25910/0ca8-4b67 | |
dc.description.method | Description of the data and file structure Within the zip is DArT data, metadata, and the R script used to analyse and make plots. File structure is important, as RRtools package uses specific structure to find files. Running the R script will produce the figures and tables found in the paper. Note that the latitude and longitude measures were rounded to the nearest degree to maintain confidentiality of the specific locations of the threatened species, as per dryad guidelines. Code/Software R version 4.3.1 (2023-06-16) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Monterey 12.5.1 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0 locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 time zone: Australia/Sydney tzcode source: internal attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] tidyr_1.3.1 tanggle_1.8.0 stringr_1.5.1 SNPRelate_1.36.0 gdsfmt_1.38.0 RRtools_0.1 [7] RColorBrewer_1.1-3 ozmaps_0.4.5 openxlsx_4.2.5.2 lattice_0.22-5 heatmaply_1.5.0 viridis_0.6.5 [13] viridisLite_0.4.2 plotly_4.10.4 ggtree_3.10.0 ggthemes_5.0.0 ggpubr_0.6.0 ggrepel_0.9.5 [19] ggmap_4.0.0 ggfortify_0.4.16 ggplot2_3.4.4 geosphere_1.5-18 dplyr_1.1.4 diveRsity_1.9.90 [25] data.table_1.15.0 ComplexHeatmap_2.18.0 circlize_0.4.15 ape_5.7-1 adegenet_2.1.10 ade4_1.7-22 | en_AU |
dc.relation.other | NSW Department of Planning and Environment | |
usyd.faculty | SeS faculties schools::Faculty of Science::School of Life and Environmental Sciences | en_AU |
workflow.metadata.only | No | en_AU |
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