Sequence capture data support the taxonomy of Pogonolepis (Asteraceae: Gnaphalieae) and show unexpected genetic structure
Alexander N. Schmidt-Lebuhn
A *
+ Author Affiliations
- Author Affiliations
A CSIRO, Centre for Australian National Biodiversity Research, Clunies Ross Street, Canberra, ACT 2601, Australia.
Australian Systematic Botany 35(4) 317-325 https://doi.org/10.1071/SB22010
Submitted: 22 March 2022 Accepted: 7 August 2022 Published: 25 August 2022
© 2022 The Author(s) (or their employer(s)). Published by CSIRO Publishing. This is an open access article distributed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC BY-NC-ND)
Abstract
Variation in breeding systems between species of the same taxonomic group complicates the consistent application of species concepts, and perhaps even the logically consistent circumscription of species. Several genera of arid-zone ephemerals in the Angianthus clade (Asteraceae: Gnaphalieae: Gnaphaliinae) contain both outcrossing and non-outcrossing species. The latter are recognised by producing an order of magnitude fewer pollen grains per anther and an often reduced number of corolla lobes, and they are frequently more widespread than are the former. In its current taxonomy, the genus Pogonolepis comprises an otherwise morphologically indistinguishable pair of one outcrossing and one non-outcrossing species. I generated sequence capture data to test the genetic segregation of P. stricta and P. muelleriana and the utility of sequence capture data for species circumscription and diagnostics. Phylogenetic analysis showed the two species to form two specimen clades, supporting the current taxonomy. Contrary to expectations, non-outcrossing P. muelleriana exhibited lower gene concordance, in line with values expected from recombination, as well as higher heterozygosity than its outcrossing sister species. More research on the breeding system and population structure of the two species may be required to explain these results.
Keywords: Asteraceae, Australia, breeding system, Gnaphalieae, Pogonolepis, sequence capture, species delimitation, target enrichment.
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.| Conservation implications of widespread polyploidy and apomixis: a case study in the genus Pomaderris (Rhamnaceae).Crossref | GoogleScholarGoogle Scholar |
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.
| Integrative approach resolves the taxonomy of the Ozothamnus ledifolius (Asteraceae: Gnaphaliae) species complex in Tasmania, Australia.Crossref | GoogleScholarGoogle Scholar |
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)
| Crossref |
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
| hybpiper-rbgv and yang-and-smith-rbgv: containerization and additional options for assembly and paralog detection in target enrichment data.Crossref | GoogleScholarGoogle Scholar |
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
| HybPiper: extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment.Crossref | GoogleScholarGoogle Scholar |
Johnson MG, Pokorny L, Dodsworth S, Botigué 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.
| A universal probe set for targeted sequencing of 353 nuclear genes from any flowering plant designed using k-medoids clustering.Crossref | GoogleScholarGoogle Scholar |
Levin DA (1979) The nature of plant species. Science 204, 381–384.
| The nature of plant species.Crossref | GoogleScholarGoogle Scholar |
Mallet J (1995) A species definition for the modern synthesis. Trends in Ecology & Evolution 10, 294–299.
| A species definition for the modern synthesis.Crossref | GoogleScholarGoogle Scholar |
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.
| An efficient screen for reproductive pathways using mature seeds of monocots and dicots.Crossref | GoogleScholarGoogle Scholar |
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
| New targets acquired: improving locus recovery from the Angiosperms353 probe set.Crossref | GoogleScholarGoogle Scholar |
Minh BQ, Nguyen MAT, von Haeseler A (2013) Ultrafast approximation for phylogenetic bootstrap. Molecular Biology and Evolution 30, 1188–1195.
| Ultrafast approximation for phylogenetic bootstrap.Crossref | GoogleScholarGoogle Scholar |
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.
| IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era.Crossref | GoogleScholarGoogle Scholar |
Minh BQ, Hahn MW, Lanfear R (2020b) New methods to calculate concordance factors for phylogenomic datasets. Molecular Biology and Evolution 37, 2727–2733.
| New methods to calculate concordance factors for phylogenomic datasets.Crossref | GoogleScholarGoogle Scholar |
Mishler BD, Donoghue MJ (1982) Species concepts: a case for pluralism. Systematic Zoology 31, 491–504.
| Species concepts: a case for pluralism.Crossref | GoogleScholarGoogle Scholar |
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
| The hunting of the SNaRC: a snarky solution to the species problem.Crossref | GoogleScholarGoogle Scholar |
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
| HybPhaser: a workflow for the detection and phasing of hybrids in target capture data sets.Crossref | GoogleScholarGoogle Scholar |
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.
| Main role of self-pollination rate on reproductive allocations in pseudogamous apomicts.Crossref | GoogleScholarGoogle Scholar |
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.
| Phenetic analyses of Ozothamnus hookeri (Asteraceae), with the recognition of a new species, O. cupressoides.Crossref | GoogleScholarGoogle Scholar |
Richards AJ (1973) The origin of Taraxacum agamospecies. Botanical Journal of the Linnean Society 66, 189–211.
| The origin of Taraxacum agamospecies.Crossref | GoogleScholarGoogle Scholar |
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.
| Fallacies and false premises: a critical assessment of the arguments for the recognition of paraphyletic taxa in botany.Crossref | GoogleScholarGoogle Scholar |
Schmidt-Lebuhn AN, Bovill J (2021) Phylogenomic data reveal four major clades of Australian Gnaphalieae (Asteraceae. TAXON 70, 1020–1034.
| Phylogenomic data reveal four major clades of Australian Gnaphalieae (Asteraceae.Crossref | GoogleScholarGoogle Scholar |
Short PS (1983) A revision of Angianthus Wendl., sensu lato (Compositae: Inuleae: Gnaphaliinae), 1. Muelleria 5, 143–183.
| A revision of Angianthus Wendl., sensu lato (Compositae: Inuleae: Gnaphaliinae), 1.Crossref | GoogleScholarGoogle Scholar |
Short PS (1985) A revision of Actinobole Fenzl ex Endl. (Compositae: Inuleae: Gnaphaliinae). Muelleria 6, 9–22.
| A revision of Actinobole Fenzl ex Endl. (Compositae: Inuleae: Gnaphaliinae).Crossref | GoogleScholarGoogle Scholar |
Short PS (1986) A revision of Pogonolepis (Compositae: Inuleae: Gnaphaliinae). Muelleria 6, 237–253.
| A revision of Pogonolepis (Compositae: Inuleae: Gnaphaliinae).Crossref | GoogleScholarGoogle Scholar |
Short PS (1989) A revision of Podotheca Cass. (Asteraceae: Inuleae: Gnaphaliinae). Muelleria 7, 39–56.
| A revision of Podotheca Cass. (Asteraceae: Inuleae: Gnaphaliinae).Crossref | GoogleScholarGoogle Scholar |
Short PS (1990a) A revision of the genus Chthonocephalus Steetz (Asteraceae: Inuleae: Gnaphaliinae). Muelleria 7, 225–238.
| A revision of the genus Chthonocephalus Steetz (Asteraceae: Inuleae: Gnaphaliinae).Crossref | GoogleScholarGoogle Scholar |
Short PS (1990b) A revision of Trichanthodium Sond. & F.Muell. ex Sond. (Asteraceae: Inuleae: Gnaphaliinae). Muelleria 7, 213–224.
| A revision of Trichanthodium Sond. & F.Muell. ex Sond. (Asteraceae: Inuleae: Gnaphaliinae).Crossref | GoogleScholarGoogle Scholar |
Short PS (1990c) New taxa and new combinations in Australian Gnaphaliinae (Inuleae: Asteraceae). Muelleria 7, 239–252.
| New taxa and new combinations in Australian Gnaphaliinae (Inuleae: Asteraceae).Crossref | GoogleScholarGoogle Scholar |
Short PS (1995) A revision of Millotia (Asteraceae-Gnaphalieae). Australian Systematic Botany 8, 1–47.
| A revision of Millotia (Asteraceae-Gnaphalieae).Crossref | GoogleScholarGoogle Scholar |
Short PS (2000) Notes on Myriocephalus Benth. s. lat. (Asteraceae: Gnaphalieae). Australian Systematic Botany 13, 729–738.
| Notes on Myriocephalus Benth. s. lat. (Asteraceae: Gnaphalieae).Crossref | GoogleScholarGoogle Scholar |
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
| On the potential of Angiosperms353 for population genomics.Crossref | GoogleScholarGoogle Scholar |
Walsh NG (2015) Elevation of rank for Leucochrysum albicans var. tricolor (Asteraceae: Gnaphalieae). Muelleria 34, 11–13.
| Elevation of rank for Leucochrysum albicans var. tricolor (Asteraceae: Gnaphalieae).Crossref | GoogleScholarGoogle Scholar |
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.
| Orthology inference in nonmodel organisms using transcriptomes and low-coverage genomes: improving accuracy and matrix occupancy for phylogenomics.Crossref | GoogleScholarGoogle Scholar |
Zachos FE (2016) ‘Species Concepts in Biology.’ (Springer International Publishing)
| Crossref |
