Register      Login
Australian Systematic Botany Australian Systematic Botany Society
Taxonomy, biogeography and evolution of plants
RESEARCH ARTICLE (Open Access)

Resolution of the Eremophila tietkensii (Scrophulariaceae) species complex based on congruence between morphological and molecular pattern analyses

Amy L. Curtis https://orcid.org/0000-0001-9028-5879 A B * , Pauline F. Grierson https://orcid.org/0000-0003-2135-0272 B , Jacqueline Batley https://orcid.org/0000-0002-5391-5824 B , Jeremy Naaykens C , Rachael M. Fowler https://orcid.org/0000-0002-8953-7036 D , Anita Severn-Ellis https://orcid.org/0000-0003-3077-9441 B and Kevin R. Thiele https://orcid.org/0000-0002-6658-6636 A B
+ Author Affiliations
- Author Affiliations

A Western Australian Herbarium, Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre, WA 6983, Australia.

B School of Biological Sciences, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia.

C Rio Tinto Iron Ore, 152–158 St Georges Terrace, Perth, WA 6000, Australia.

D School of BioSciences, The University of Melbourne, Parkville, Vic. 3010, Australia.

* Correspondence to: amy.curtis@dbca.wa.gov.au

Handling Editor: David Williams

Australian Systematic Botany 35(1) 1-18 https://doi.org/10.1071/SB21005
Submitted: 12 February 2021  Accepted: 17 November 2021   Published: 2 March 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

Eremophila R.Br. comprises at least 238 species endemic to Australia, with many more having not yet been formally described. Three putative new taxa, namely, E. sp. Hamersley Range (K. Walker KW 136), E. sp. Calvert Range (A. A. Burbidge 738) and E. sp. Rudall River (P. G. Wilson 10512), were segregated from a broadly defined E. tietkensii F.Muell. & Tate by J. Hurter at the Western Australian Herbarium in 2012. Both E. sp. Hamersley Range and E. sp. Rudall River are listed as being of conservation concern in Western Australia, the former occurring in the Pilbara region in areas of prospective interest for mining development. We sought to determine whether these phrase-named entities should be formally described as new species, using multivariate analyses of morphometric and molecular data derived from specimens in the Western Australia Herbarium. Eremophila sp. Rudall River could not be adequately separated from E. tietkensii by either morphological or molecular data, and is here included within that species. By contrast, E. sp. Hamersley Range and E. sp. Calvert Range are clearly morphologically and genetically distinct. We thus describe them here as the new species E. naaykensii A.L.Curtis & K.R.Thiele and E. hurteri A.L.Curtis & K.R.Thiele. The recognition of these taxa will help inform their conservation prioritisation and subsequent management.

Keywords: congruence, ddRADseq, Eremophila, herbarium sampling, morphology, Pilbara, taxonomy, Western Australia.


References

Anderson BM, Barrett MD, Krauss SL, Thiele K (2016) Untangling a species complex of arid zone grasses (Triodia) reveals patterns congruent with co-occurring animals. Molecular Phylogenetics and Evolution 101, 142–162.
Untangling a species complex of arid zone grasses (Triodia) reveals patterns congruent with co-occurring animals.Crossref | GoogleScholarGoogle Scholar | 27179699PubMed |

Andrews S (2010) FastQC: a quality control tool for high throughput sequence data. Available at https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ [Verified 15 May 2020]

Bakker FT, Lei D, Yu J, Mohammadin S, Wei Z, van de Kerke S, Gravendeel B, Nieuwenhuis M, Staats M, Alquezar-Planas DE, Holmer R (2016) Herbarium genomics: Plastome sequence assembly from a range of herbarium specimens using an Iterative Organelle Genome Assembly pipeline. Biological Journal of the Linnean Society. Linnean Society of London 117, 33–43.
Herbarium genomics: Plastome sequence assembly from a range of herbarium specimens using an Iterative Organelle Genome Assembly pipeline.Crossref | GoogleScholarGoogle Scholar |

Beck JB, Semple JC (2015) Next‐generation sampling: pairing genomics with herbarium specimens provides species‐level signal in Solidago (Asteraceae). Applications in Plant Sciences 3, 1500014
Next‐generation sampling: pairing genomics with herbarium specimens provides species‐level signal in Solidago (Asteraceae).Crossref | GoogleScholarGoogle Scholar |

Bilton TP, McEwan JC, Clarke SM, Brauning R, van Stijn TC, Rowe SJ, Dodds KG (2018) Linkage disequilibrium estimation in low coverage high-throughput sequencing data. Genetics 209, 389–400.
Linkage disequilibrium estimation in low coverage high-throughput sequencing data.Crossref | GoogleScholarGoogle Scholar | 29588288PubMed |

Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120.
Trimmomatic: a flexible trimmer for Illumina sequence data.Crossref | GoogleScholarGoogle Scholar | 24695404PubMed |

Brown A, Buirchell B (2011) ‘A field guide to the Eremophilas of Western Australia.’ (Simon Nevill Publications: York, WA, Australia)

Brown AP, Davis RW (2016) Eremophila buirchellii and E. calcicola (Scrophulariaceae), two new species from Western Australia. Nuytsia 27, 211–216.

Buirchell BJ, Brown AP (2016) New species of Eremophila (Scrophulariaceae): thirteen geographically restricted species from Western Australia. Nuytsia 27, 253–283.

Burgman M, Maslin BR, Andrewartha D, Keatley MR, Boek C, McCarthy M (2000) Inferring threat from scientific collections: power tests and an application to Western Australian Acacia Species. In ‘Quantitative Methods for Conservation Biology’. (Eds S Ferson, M Burgman) pp. 7–26. (Springer New York: New York, NY, USA)

Byrne M, Coates DJ, Macdonald BM, Hankinson M, McArthur SM, Van Leeuwen S (2016) High nuclear genetic differentiation, but low chloroplast diversity in a rare species, Aluta quadrata (Myrtaceae), with a disjunct distribution in the Pilbara, Western Australia. Australian Journal of Botany 64, 687–695.
High nuclear genetic differentiation, but low chloroplast diversity in a rare species, Aluta quadrata (Myrtaceae), with a disjunct distribution in the Pilbara, Western Australia.Crossref | GoogleScholarGoogle Scholar |

Byrne M, Millar MA, Coates DJ, Macdonald BM, McArthur SM, Zhou M, van Leeuwen S (2017) Refining expectations for environmental characteristics of refugia: two ranges of differing elevation and topographical complexity are mesic refugia in an arid landscape. Journal of Biogeography 44, 2539–2550.
Refining expectations for environmental characteristics of refugia: two ranges of differing elevation and topographical complexity are mesic refugia in an arid landscape.Crossref | GoogleScholarGoogle Scholar |

Catchen J, Hohenlohe PA, Bassham S, Amores A, Cresko WA (2013) Stacks: an analysis tool set for population genomics. Molecular Ecology 22, 3124–3140.
Stacks: an analysis tool set for population genomics.Crossref | GoogleScholarGoogle Scholar | 23701397PubMed |

Chinnock RJ (2007a) ‘Eremophila and allied genera: a monograph of the plant family Myoporaceae.’ (Rosenberg Pub Pty Ltd: Sydney, NSW, Australia)

Chinnock RJ (2007b) Eremophila tietkensii F.Muell. & Tate (Myoporaceae), a misinterpreted species. Journal of the Adelaide Botanic Gardens 21, 1–3.

Chinnock RJ, Doley AB (2011) Eremophila koobabbiensis (Scrophulariaceae), a new, rare species from the wheatbelt of Western Australia. Nuytsia 21, 158–161.

Clarke KR, Gorley RN (2006) ‘PRIMER v6: user manual/tutorial.’ (Plymouth Marine Laboratory: Plymouth, UK)

Coates DJ, Llorens TM, Byrne M, McArthur S, Macdonald B (2014) Disjunct, highly divergent genetic lineages within two rare Eremophila (Scrophulariaceae: Myoporeae) species in a biodiversity hotspot: implications for taxonomy and conservation. Botanical Journal of the Linnean Society 177, 96–111.
Disjunct, highly divergent genetic lineages within two rare Eremophila (Scrophulariaceae: Myoporeae) species in a biodiversity hotspot: implications for taxonomy and conservation.Crossref | GoogleScholarGoogle Scholar |

Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST (2011) The variant call format and VCFtools. Bioinformatics 27, 2156–2158.
The variant call format and VCFtools.Crossref | GoogleScholarGoogle Scholar | 21653522PubMed |

de Queiroz K (2007) Species concepts and species delimitation. Systematic Biology 56, 879–886.
Species concepts and species delimitation.Crossref | GoogleScholarGoogle Scholar | 18027281PubMed |

Department of Mines and Petroleum (2016) Clearing permit decision report. Government of Western Australia. Available at ftp://ftp.dwer.wa.gov.au/permit/4615/4615-6%20Decision%20Report.pdf [Verified 15 May 2020]

Doughty P, Rolfe JK, Burbidge AH, Pearson DJ, Kendrick PG (2011) Herpetological assemblages of the Pilbara biogeographic region, Western Australia: ecological associations, biogeographic patterns and conservation. Records of the Western Australian Museum 78, 315–341.
Herpetological assemblages of the Pilbara biogeographic region, Western Australia: ecological associations, biogeographic patterns and conservation.Crossref | GoogleScholarGoogle Scholar |

Durrant BJ, Harvey M, Framenau V, Ott R, Waldock JM (2010) Patterns in the composition of ground-dwelling spider communities in the Pilbara bioregion, Western Australia. Records of the Western Australian Museum 78, 185–204.
Patterns in the composition of ground-dwelling spider communities in the Pilbara bioregion, Western Australia.Crossref | GoogleScholarGoogle Scholar |

Edginton MA (2015) Eremophila woodiae Edginton (Scrophulariaceae), a new species from Queensland. Austrobaileya 9, 408–415.

Ewart AJ, Jarrett PH (1928) Contributions to the Flora of Australia, No. 34. Additions to the Flora of the Northern Territory and locality records. Proceedings of the Royal Society of Victoria 40, 81–87.

Forrest LL, Hart ML, Hughes M, Wilson HP, Chung KF, Tseng YH, Kidner CA (2019) The limits of Hyb-Seq for herbarium specimens: impact of preservation techniques. Frontiers in Ecology and Evolution 7, 439
The limits of Hyb-Seq for herbarium specimens: impact of preservation techniques.Crossref | GoogleScholarGoogle Scholar |

Fowler RM (2018) Phylogeny of Eremophila and tribe Myoporeae (Scrophulariaceae). PhD thesis, The University of Melbourne, Melbourne, Vic., Australia.

Guthrie NA, Weir T, Will K (2010) Localised and regional patterns in ground-dwelling beetle assemblages in a semi-tropical arid zone environment. Records of the Western Australian Museum 78, 169–184.
Localised and regional patterns in ground-dwelling beetle assemblages in a semi-tropical arid zone environment.Crossref | GoogleScholarGoogle Scholar |

Joyce EM, Pannell CM, Rossetto M, Yap JYS, Thiele KR, Wilson PD, Crayn DM (2021) Molecular phylogeography reveals two geographically and temporally separated floristic exchange tracks between Southeast Asia and northern Australia. Journal of Biogeography 48, 1213–1227.
Molecular phylogeography reveals two geographically and temporally separated floristic exchange tracks between Southeast Asia and northern Australia.Crossref | GoogleScholarGoogle Scholar |

Katz LS, Griswold T, Morrison S, Caravas J, Zhang S, den Bakker HC, Deng X, Carleton HA (2019) Mashtree: a rapid comparison of whole genome sequence files. Journal of Open Source Software 4, 1762
Mashtree: a rapid comparison of whole genome sequence files.Crossref | GoogleScholarGoogle Scholar |

Ladiges PY, Ariati SR, Murphy DJ (2006) Biogeography of the Acacia victoriae, pyrifolia and murrayana species groups in arid Australia. Journal of Arid Environments 66, 462–476.
Biogeography of the Acacia victoriae, pyrifolia and murrayana species groups in arid Australia.Crossref | GoogleScholarGoogle Scholar |

Maruki T, Lynch M (2017) Genotype calling from population-genomic sequencing data. G3: Genes, Genomes, Genetics 7, 1393–1404.
Genotype calling from population-genomic sequencing data.Crossref | GoogleScholarGoogle Scholar |

Office of the Environmental Protection Authority (2014) Kintyre Uranium project, Government of Western Australia. Available at https://www.epa.wa.gov.au/sites/default/files/EPA_Report/Rep%201522%20Kintyre%20PER%20280714.pdf [Verified 15 August 2021]

Oliveira U, Soares-Filho BS, Paglia AP, Brescovit AD, De Carvalho CJB, Silva DP, Rezende DT, Leite FSF, Batista JAN, Barbosa JPPP, Stehmann JR, Ascher JS, De Vasconcelos MF, De Marco P, Löwenberg-Neto P, Ferro VG, Santos AJ (2017) Biodiversity conservation gaps in the Brazilian protected areas. Scientific Reports 7, 9141
Biodiversity conservation gaps in the Brazilian protected areas.Crossref | GoogleScholarGoogle Scholar | 28831073PubMed |

Paris JR, Stevens JR, Catchen JM (2017) Lost in parameter space: a road map for STACKS. Methods in Ecology and Evolution 8, 1360–1373.
Lost in parameter space: a road map for STACKS.Crossref | GoogleScholarGoogle Scholar |

Pepper M, Doughty P, Fujita MK, Moritz C, Keogh JS (2013a) Speciation on the rocks: integrated systematics of the Heteronotia spelea species complex (Gekkota; Reptilia) from western and central Australia. PLoS One 8, e78110
Speciation on the rocks: integrated systematics of the Heteronotia spelea species complex (Gekkota; Reptilia) from western and central Australia.Crossref | GoogleScholarGoogle Scholar | 24244289PubMed |

Pepper M, Doughty P, Keogh JS (2013b) Geodiversity and endemism in the iconic Australian Pilbara region: a review of landscape evolution and biotic response in an ancient refugium. Journal of Biogeography 40, 1225–1239.
Geodiversity and endemism in the iconic Australian Pilbara region: a review of landscape evolution and biotic response in an ancient refugium.Crossref | GoogleScholarGoogle Scholar |

Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE (2012) Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS One 7, e37135
Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species.Crossref | GoogleScholarGoogle Scholar | 22675423PubMed |

Severn-Ellis AA, Scheben A, Neik TX, Saad NSM, Pradhan A, Batley J (2020) Genotyping for species identification and diversity assessment using double-digest restriction site-associated DNA Sequencing (ddRAD-Seq). In ‘Legume genomics’. (Eds M Jain, R Garg) pp. 159–187. (Springer New York: New York, NY, USA)

Thackway R, Cresswell ID (1995) An interim biogeographic regionalisation for Australia: a framework for setting priorities in the National Reserves System Cooperative Program. (Australian Nature Conservation Agency, Reserve Systems Unit: Canberra, ACT, Australia). Available at https://www.awe.gov.au/sites/default/files/documents/ibra-framework-setting-priorities-nrs-cooperative-program.pdf

von Mueller FJH, Tate R (1890) List of Plants collected during Mr Tietkens’ expedition into Central Australia, 1889. Transactions, Proceedings and Reports of the Royal Society of South Australia 13, 94–109.

Wege J, Thiele K, Shepherd K, Butcher R, Macfarlane T, Coates D (2015) Strategic taxonomy in a biodiverse landscape: a novel approach to maximizing conservation outcomes for rare and poorly known flora. Biodiversity and Conservation 24, 17–32.
Strategic taxonomy in a biodiverse landscape: a novel approach to maximizing conservation outcomes for rare and poorly known flora.Crossref | GoogleScholarGoogle Scholar |