Biodiversity Literature Repository
Published August 25, 2022 | Version v1
Journal article Restricted

Sequence capture data support the taxonomy of Pogonolepis (Asteraceae: Gnaphalieae) and show unexpected genetic structure

Creators

Description

Schmidt-Lebuhn, Alexander N. (2022): Sequence capture data support the taxonomy of Pogonolepis (Asteraceae: Gnaphalieae) and show unexpected genetic structure. Australian Systematic Botany 35 (4): 317-325, DOI: 10.1071/SB22010, URL: http://dx.doi.org/10.1071/sb22010

Files

Restricted

The record is publicly accessible, but files are restricted to users with access.

Linked records

Additional details

Cites
Publication: 10.1007/s10592-019-01184-2 (DOI)
Publication: 10.11646/phytotaxa.358.2.2 (DOI)
Publication: 10.1007/978-94-009-4812-9_20 (DOI)
Publication: 10.1101/2021.11.08.467817 (DOI)
Publication: 10.3732/apps.1600016 (DOI)
Publication: 10.1093/sysbio/syy086 (DOI)
Publication: 10.1126/science.204.4391.381 (DOI)
Publication: 10.1016/0169-5347(95)90031-4 (DOI)
Publication: 10.1046/j.1365-313x.2000.00647.x (DOI)
Publication: 10.1002/aps3.11420 (DOI)
Publication: 10.1093/molbev/mst024 (DOI)
Publication: 10.1093/molbev/msaa106 (DOI)
Publication: 10.2307/2413371 (DOI)
Publication: 10.3998/ptpbio.16039257.0010.001 (DOI)
Publication: 10.1002/aps3.11441 (DOI)
Publication: 10.1007/s001220050586 (DOI)
Publication: 10.5962/p.292501 (DOI)
Publication: 10.1111/j.1095-8339.1973.tb02169.x (DOI)
Publication: 10.1111/j.1096-0031.2011.00367.x (DOI)
Publication: 10.1002/tax.12510 (DOI)
Publication: 10.5962/p.238385 (DOI)
Publication: 10.5962/p.184058 (DOI)
Publication: 10.5962/p.184052 (DOI)
Publication: 10.5962/p.184036 (DOI)
Publication: 10.5962/p.184026 (DOI)
Publication: 10.5962/p.184025 (DOI)
Publication: 10.1071/SB9950001 (DOI)
Publication: 10.1101/2020.10.11.335174 (DOI)
Publication: 10.5962/p.292262 (DOI)
Publication: 10.1093/molbev/msu245 (DOI)
Publication: 10.1007/978-3-319-44966-1 (DOI)
Has part
Taxonomic treatment: 10.5281/zenodo.10974471 (DOI)
Taxonomic treatment: http://treatment.plazi.org/id/052287BADD38FFF4103DF9B2FC2117DE (URL)
Figure: 10.5281/zenodo.10974465 (DOI)
Figure: 10.5281/zenodo.10974467 (DOI)
Figure: 10.5281/zenodo.10974469 (DOI)
Is source of
Dataset: https://www.gbif.org/dataset/33b90653-44a4-4906-840e-526fbf251b44 (URL)

References

  • Chen SH, Guja LK, Schmidt-Lebuhn AN (2019) Conservation implications of widespread polyploidy and apomixis: a case study in the genus Pomaderris (Rhamnaceae). Conservation Genetics 20, 917-926. doi:10.1007/s10592-019-01184-2
  • De Salas MF, Schmidt-Lebuhn AN (2018) Integrative approach resolves the taxonomy of the Ozothamnus ledifolius (Asteraceae: Gnaphaliae) species complex in Tasmania, Australia. Phytotaxa 358, 117-138. doi:10.11646/phytotaxa.358.2.2
  • Hamrick JL, Loveless MD (1986) The influence of seed dispersal mechanisms on the genetic structure of plant populations. In 'Frugivores Seed Dispersal. Tasks for Vegetation Science'. (Eds A Estrada, TH Fleming) Vol. 15, pp. 211-223. (Springer Netherlands: Dordrecht, Netherlands) doi:10.1007/978-94-009-4812-9_20
  • Hennig W (1966) 'Phylogenetic Systematics.' (University of Illinois: Urbana, IL, USA)
  • Jackson C, McLay T, Schmidt-Lebuhn AN (2021) hybpiper-rbgv and yang-and-smith-rbgv: containerization and additional options for assembly and paralog detection in target enrichment data. BioRxiv doi:10.1101/2021.11.08.467817
  • Johnson MG, Gardner EM, Liu Y, Medina R, Goffinet B, Shaw AJ, Zerega NJC, Wickett NJ (2016) HybPiper: extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment. Applications in Plant Sciences 4, 1600016. doi:10.3732/apps.1600016
  • Johnson MG, Pokorny L, Dodsworth S, Botigue LR, Cowan RS, Devault A, Eiserhardt WL, Epitawalage N, Forest F, Kim JT, Leebens-Mack JH, Leitch IJ, Maurin O, Soltis DE, Soltis PS, Wong GK, Baker WJ, Wickett NJ (2019) A universal probe set for targeted sequencing of 353 nuclear genes from any flowering plant designed using k-medoids clustering. Systematic Biology 68, 594-606. doi:10.1093/sysbio/ syy086
  • Levin DA (1979) The nature of plant species. Science 204, 381-384. doi:10.1126/science.204.4391.381
  • Mallet J (1995) A species definition for the modern synthesis. Trends in Ecology & Evolution 10, 294-299. doi:10.1016/0169-5347(95) 90031-4
  • Matzk F, Meister A, Schubert I (2001) An efficient screen for reproductive pathways using mature seeds of monocots and dicots. The Plant Journal 21, 97-108. doi:10.1046/j.1365-313x.2000.00647.x
  • Mayr E (1970) 'Populations, species, and evolution.' (Harvard University Press: Cambridge, MA, USA)
  • McLay TGB, Birch JL, Gunn BF, Ning W, Tate JA, Nauheimer L, Joyce EM, Simpson L, Schmidt-Lebuhn AN, Baker WJ, Forest F, Jackson CJ (2021) New targets acquired: improving locus recovery from the Angiosperms353 probe set. Applications in Plant Sciences 9, e11420. doi:10.1002/aps3.11420
  • Minh BQ, Nguyen MAT, von Haeseler A (2013) Ultrafast approximation for phylogenetic bootstrap. Molecular Biology and Evolution 30, 1188-1195. doi:10.1093/molbev/mst024
  • Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, Lanfear R (2020a) IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Molecular Biology and Evolution 37, 1530-1534. doi:10.1093/ molbev/msaa015
  • Minh BQ, Hahn MW, Lanfear R (2020b) New methods to calculate concordance factors for phylogenomic datasets. Molecular Biology and Evolution 37, 2727-2733. doi:10.1093/molbev/msaa106
  • Mishler BD, Donoghue MJ (1982) Species concepts: a case for pluralism. Systematic Zoology 31, 491-504. doi:10.2307/2413371
  • Mishler BD, Wilkins JS (2018) The hunting of the SNaRC: a snarky solution to the species problem. Philosophy, Theory, and Practice in Biology 10, 1. doi:10.3998/ptpbio.16039257.0010.001
  • Nauheimer L, Weigner N, Joyce E, Crayn D, Clarke C, Nargar K (2021) HybPhaser: a workflow for the detection and phasing of hybrids in target capture data sets. Applications in Plant Sciences 9, e11441. doi:10.1002/aps3.11441
  • Noirot M, Couvet D, Hamon S (1997) Main role of self-pollination rate on reproductive allocations in pseudogamous apomicts. Theoretical and Applied Genetics 95, 479-483. doi:10.1007/s001220050586
  • Ohlsen DJ, Puttock CF, Walsh NG (2010) Phenetic analyses of Ozothamnus hookeri (Asteraceae), with the recognition of a new species, O. cupressoides. Muelleria 28, 110-121. doi:10.5962/p.292501
  • Richards AJ (1973) The origin of Taraxacum agamospecies. Botanical Journal of the Linnean Society 66, 189-211. doi:10.1111/j.1095- 8339.1973.tb02169.x
  • Schmidt-Lebuhn AN (2012) Fallacies and false premises: a critical assessment of the arguments for the recognition of paraphyletic taxa in botany. Cladistics 28, 174-187. doi:10.1111/j.1096-0031. 2011.00367.x
  • Schmidt-Lebuhn AN, Bovill J (2021) Phylogenomic data reveal four major clades of Australian Gnaphalieae (Asteraceae. TAXON 70, 1020-1034. doi:10.1002/tax.12510
  • Short PS (1983) A revision of Angianthus Wendl., sensu lato (Compositae: Inuleae: Gnaphaliinae), 1. Muelleria 5, 143-183. doi:10.5962/p.238385
  • Short PS (1985) A revision of Actinobole Fenzl ex Endl. (Compositae: Inuleae: Gnaphaliinae). Muelleria 6, 9-22. doi:10.5962/p.184058
  • Short PS (1986) A revision of Pogonolepis (Compositae: Inuleae: Gnaphaliinae). Muelleria 6, 237-253. doi:10.5962/p.184052
  • Short PS (1989) A revision of Podotheca Cass. (Asteraceae: Inuleae: Gnaphaliinae). Muelleria 7, 39-56. doi:10.5962/p.184036
  • Short PS (1990a) A revision of the genus Chthonocephalus Steetz (Asteraceae: Inuleae: Gnaphaliinae). Muelleria 7, 225-238. doi:10.5962/p.184026
  • Short PS (1990b) A revision of Trichanthodium Sond. & F.Muell. ex Sond. (Asteraceae: Inuleae: Gnaphaliinae). Muelleria 7, 213-224. doi:10.5962/p.184025
  • Short PS (1990c) New taxa and new combinations in Australian Gnaphaliinae (Inuleae:Asteraceae). Muelleria 7, 239-252. doi:10.5962/ p.184027
  • Short PS (1995) A revision of Millotia (Asteraceae-Gnaphalieae). Australian Systematic Botany 8, 1-47. doi:10.1071/SB9950001
  • Short PS (2000) Notes on Myriocephalus Benth. s. lat. (Asteraceae: Gnaphalieae). Australian Systematic Botany 13, 729-738. doi:10.1071/ SB99019
  • Short PS (2015) Notes concerning the classification of species included in Calocephalus R. Br. s.lat. and Gnephosis Cass. s.lat. (Asteraceae: Gnaphalieae), with descriptions of new genera and species. Journal of the Adelaide Botanic Gardens 29, 147-220.
  • Slimp M, Williams LD, Hale H, Johnson MG (2020) On the potential of Angiosperms353 for population genomics. BioRxiv doi:10.1101/ 2020.10.11.335174
  • Walsh NG (2015) Elevation of rank for Leucochrysum albicans var. tricolor (Asteraceae: Gnaphalieae). Muelleria 34, 11-13. doi:10.5962/p.292262
  • Wilson PG (1989) A revision of the genus Hyalosperma (Asteraceae: Inuleae: Gnaphaliinae). Nuytsia 7, 75-101.
  • Yang Y, Smith SA (2014) Orthology inference in nonmodel organisms using transcriptomes and low-coverage genomes: improving accuracy and matrix occupancy for phylogenomics. Molecular Biology and Evolution 31, 3081-3092. doi:10.1093/molbev/msu245
  • Zachos FE (2016) 'Species Concepts in Biology.' (Springer International Publishing) doi:10.1007/978-3-319-44966-1