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Article ; Online: Using RADseq to resolve species boundaries in a morphologically complex group of yellow-flowered shrubs (<i>Geleznowia</i>, Rutaceae)

Anderson, Benjamin M. / Binks, Rachel M. / Byrne, Margaret / Crawford, Andrew D. / Shepherd, Kelly A.

Australian Systematic Botany. 2023, v. 36, no. 4 p.277-311

2023

Abstract: The morphologically complex and charismatic genus Geleznowia (Rutaceae) is endemic to south-western Australia and faces existing and potential conservation issues associated with land clearing, climate change and commercial harvesting. Two species are ... ...

Abstract	The morphologically complex and charismatic genus Geleznowia (Rutaceae) is endemic to south-western Australia and faces existing and potential conservation issues associated with land clearing, climate change and commercial harvesting. Two species are currently recognised in the genus, but horticulturally recognised forms and phrase-named taxa reflect additional suspected species diversity. The genus exhibits complicated and subtle patterns of morphological variation that have historically inhibited delimitation of taxonomic entities and, as a result, precluded effective conservation assessments. Here we used ddRAD data from 25 populations across the range of Geleznowia to elucidate genomic diversity in the group in conjunction with morphological re-assessment so as to delimit species and revise the taxonomy. Our analyses consistently identified seven entities that maintain genomic distinctiveness even in sympatry with other entities, supporting the inference of reproductive barriers and lineage divergence. Morphological assessment of more than 300 specimens corroborated these seven taxa. Consequently, we recognise seven species of Geleznowia in Western Australia, retaining G . amabilis K.A.Sheph. & A.D.Crawford, recircumscribing G . verrucosa Turcz., reinstating G . calycina (J.Drumm. ex Harv.) Benth., and naming four new species as G . eximia K.A.Sheph. & A.D.Crawford, G . narcissoides K.A.Sheph. & A.D.Crawford, G . occulta K.A.Sheph. & A.D.Crawford, and G . uberiflora K.A.Sheph. & A.D.Crawford.
Keywords	Rutaceae ; botany ; climate change ; genetic variation ; genomics ; new species ; species diversity ; sympatry ; Western Australia ; angiosperm ; conservation genomics ; ddRAD ; reduced representation ; SNP ; species delimitation ; taxonomy
Language	English
Size	p. 277-311.
Publishing place	CSIRO Publishing
Document type	Article ; Online
ISSN	1030-1887
DOI	10.1071/SB23010
Database	NAL-Catalogue (AGRICOLA)

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Article: Genomic divergence in sympatry indicates strong reproductive barriers and cryptic species within

Binks, Rachel M / Steane, Dorothy A / Byrne, Margaret

Ecology and evolution

2021 Volume 11, Issue 10, Page(s) 5096–5110

Abstract: Genetic studies are increasingly detecting cryptic taxa that likely represent a significant component of global biodiversity. However, cryptic taxa are often criticized because they are typically detected serendipitously and may not receive the follow-up ...

Abstract	Genetic studies are increasingly detecting cryptic taxa that likely represent a significant component of global biodiversity. However, cryptic taxa are often criticized because they are typically detected serendipitously and may not receive the follow-up study required to verify their geographic or evolutionary limits. Here, we follow-up a study of
Language	English
Publishing date	2021-03-29
Publishing country	England
Document type	Journal Article
ZDB-ID	2635675-2
ISSN	2045-7758
ISSN	2045-7758
DOI	10.1002/ece3.7403
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Article: Genomic data inform conservation of rare tree species: clonality, diversity and hybridity in Eucalyptus series in a global biodiversity hotspot

Bradbury, Donna / Binks, Rachel M / Byrne, Margaret

Biodiversity and conservation. 2021 Mar., v. 30, no. 3

2021

Abstract: Rare species are key targets of biodiversity conservation worldwide, but assessments of genetic diversity and conservation priority can be impeded by limited sample size. Reduced-representation genome sequencing improves resolution of analysis in this ... ...

Abstract	Rare species are key targets of biodiversity conservation worldwide, but assessments of genetic diversity and conservation priority can be impeded by limited sample size. Reduced-representation genome sequencing improves resolution of analysis in this context, enabling applications in conservation genomics. The tree genus Eucalyptus contains many rare taxa, but clarity on conservation actions can be confounded in this group due to taxonomic complexity, unrecognised clonality and hybridisation. Using SNPs, we address key questions surrounding taxonomy, clonality and genetic diversity in two rare species, Eucalyptus virginea and a putative hybrid E. × phylacis, to inform conservation. We confirm that a highly disjunct population belongs to E. virginea despite sharing a multi-stemmed short-statured (‘mallee’) growth form and geographic proximity with a closely-related species, indicating that growth form was unrelated to phylogenetic distance. Clonality was confirmed in the disjunct population but the number of discrete clumps vs unique genets was not equal, reflecting the importance of genetic assessments of population size. The small, clonal, disjunct population had the lowest allelic richness and highest differentiation, as expected. However, heterozygosity excess suggested that clonality may prevent the loss of heterozygosity in mallee eucalypts by facilitating long-term persistence, contrary to expectations that small, isolated populations face increased conservation genetic threat. Analyses also confirmed that the Critically Endangered E. × phylacis is an F1 hybrid of E. decipiens and E. virginea, therefore its conservation listing should be revised. Our data highlight the usefulness of genomic analysis in applied conservation of non-model taxa.
Keywords	Eucalyptus ; biodiversity ; biodiversity conservation ; genetic distance ; genetic variation ; genome ; genomics ; heterozygosity ; hybridization ; hybrids ; loss of heterozygosity ; population size ; rare species ; sample size ; taxonomy ; trees
Language	English
Dates of publication	2021-03
Size	p. 619-641.
Publishing place	Springer Netherlands
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	2000787-5
ISSN	1572-9710 ; 0960-3115
ISSN (online)	1572-9710
ISSN	0960-3115
DOI	10.1007/s10531-020-02106-2
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Article: Phylogenomic analysis confirms polyphyly of Leptospermum and delineates five major clades that warrant generic recognition

Binks, Rachel M. / Heslewood, Margaret / Wilson, Peter G. / Byrne, Margaret

Taxon. 2022 Apr., v. 71, no. 2

2022

Abstract: Leptospermum is an ecologically and economically important genus with a long unresolved taxonomic issue concerning polyphyly, as indicated from early molecular analysis on two chloroplast regions. To resolve this, we used genome skimming to obtain high‐ ... ...

Abstract	Leptospermum is an ecologically and economically important genus with a long unresolved taxonomic issue concerning polyphyly, as indicated from early molecular analysis on two chloroplast regions. To resolve this, we used genome skimming to obtain high‐copy chloroplast and nuclear ribosomal DNA for a comprehensive phylogenomic analysis of 110 accessions comprising of 38 Leptospermum taxa, 6 closely allied genera and 5 outgroup genera. Maximum likelihood and Bayesian analyses resolved congruent clades for the chloroplast (132,143 bp: 80 CDSs, 4 rRNA genes, 29 tRNA genes, 17 introns and 97 IGSs) and nuclear (1219 bp: ITS1, ITS2, ETS, 5.8S) alignments to provide a robust interpretation of evolutionary relationships. Together, these data confirmed extensive polyphyly of Leptospermum that separated the genus into five monophyletic clades spread amongst clades representing six closely allied genera: Agonis, Asteromyrtus, Homalospermum, Kunzea, Neofabricia and Pericalymma. These five Leptospermum clades share some similarities with morphological and genetic groupings identified previously but provide greater resolution to inform a clear pathway to taxonomic revision. The evidence presented here provides support for resolution of the current polyphyly of Leptospermum through the recognition of five genera, while retaining all other genera of Leptospermeae in their current circumscription.
Keywords	Bayesian theory ; Kunzea ; Leptospermum ; chloroplasts ; introns ; monophyly ; polyphyly ; ribosomal DNA ; statistical analysis ; taxonomic revisions
Language	English
Dates of publication	2022-04
Size	p. 348-359.
Publishing place	John Wiley & Sons, Inc.
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	204216-2
ISSN	0040-0262
ISSN	0040-0262
DOI	10.1002/tax.12650
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Dihydroxyacetone in the Floral Nectar of

Obeng-Darko, Sylvester A / Sloan, Jean / Binks, Rachel M / Brooks, Peter R / Veneklaas, Erik J / Finnegan, Patrick M

Journal of agricultural and food chemistry

2023 Volume 71, Issue 20, Page(s) 7703–7709

Abstract: Ma̅nuka honey is known for its strong bioactivity, which arises from the autocatalytic conversion of 1,3-dihydroxyacetone (dihydroxyacetone, DHA) in the floral nectar ... ...

Abstract	Ma̅nuka honey is known for its strong bioactivity, which arises from the autocatalytic conversion of 1,3-dihydroxyacetone (dihydroxyacetone, DHA) in the floral nectar of
MeSH term(s)	Plant Nectar/chemistry ; Honey/analysis ; Leptospermum/chemistry ; Dihydroxyacetone/chemistry ; Myrtaceae ; Secale
Chemical Substances	Plant Nectar ; Dihydroxyacetone (O10DDW6JOO)
Language	English
Publishing date	2023-05-16
Publishing country	United States
Document type	Journal Article
ZDB-ID	241619-0
ISSN	1520-5118 ; 0021-8561
ISSN (online)	1520-5118
ISSN	0021-8561
DOI	10.1021/acs.jafc.3c00673
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Article ; Online: The nuanced nature of mesic refugia in arid landscapes: a tale of two peas.

Bradbury, Donna / Binks, Rachel M / van Leeuwen, Stephen / Coates, David J / McArthur, Shelley L / Macdonald, Bronwyn M / Hankinson, Margaret / Byrne, Margaret

Annals of botany

2022 Volume 130, Issue 6, Page(s) 901–916

Abstract: Background and aims: Understanding how genetic diversity is distributed and maintained within species is a central tenet of evolutionary and conservation biology, yet is understudied in arid regions of the globe. In temperate, glaciated environments, ... ...

Abstract	Background and aims: Understanding how genetic diversity is distributed and maintained within species is a central tenet of evolutionary and conservation biology, yet is understudied in arid regions of the globe. In temperate, glaciated environments, high genetic diversity in plant species is frequently found in refugial areas, which are often associated with southern non-glaciated landscapes. In arid, unglaciated environments, landscape features providing mesic conditions are likely to be refugia, although our understanding needs more refinement in these biomes. We test whether refugia and nuclear diversity hotspots occur in high-elevation, topographically complex areas for co-distributed shrubs (Petalostylis labicheoides and Indigofera monophylla; Fabaceae) in the ancient, arid Pilbara bioregion of north-western Australia. Methods: We conducted extensive sampling of the Pilbara (>1400 individuals from 62 widespread populations) to detect patterns in nuclear diversity and structure based on 13-16 microsatellite loci. Evidence of historical refugia was investigated based on patterns of diversity in three non-coding chloroplast (cp) sequence regions for approx. 240 individuals per species. Haplotype relationships were defined with median-joining networks and maximum likelihood phylogenetic trees. Key results: We found cpDNA evidence for a high-elevation refugium in P. labicheoides but not for I. monophylla that instead exhibited extraordinary haplotype diversity and evidence for persistence across a widespread area. Nuclear diversity hotspots occurred in, but were not exclusive to, high-elevation locations and extended to adjacent, low-elevation riparian areas in both species. Conclusions: Phylogeographic refugia in arid environments may occur in high-elevation areas for some species but not all, and may be influenced by species-specific traits: a mesic montane refugium in P. labicheoides could be related to its preference for growth in water-gaining areas, while a lack of such evidence in I. monophylla could be related to maintenance of cpDNA diversity in a large soil seed bank and dynamic evolutionary history. Mesic environments created by the intersection of topographically complex landscapes with riparian zones can be contemporary reservoirs of genetic diversity in arid landscapes.
MeSH term(s)	Refugium ; Phylogeny ; Pisum sativum/genetics ; Phylogeography ; DNA, Chloroplast/genetics ; Haplotypes ; Genetic Variation
Chemical Substances	DNA, Chloroplast
Language	English
Publishing date	2022-10-09
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1461328-1
ISSN	1095-8290 ; 0305-7364
ISSN (online)	1095-8290
ISSN	0305-7364
DOI	10.1093/aob/mcac126
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Article: Genomic data and morphological re‐assessment reveals synonymy and hybridisation among Seringia taxa (Lasiopetaleae, Malvaceae) in remote north‐western Australia

Binks, Rachel M. / Wilkins, Carolyn F. / Markey, Adrienne S. / Lyons, Michael N. / Byrne, Margaret

Taxon. 2020 Apr., v. 69, no. 2

2020

Abstract: Conservation of rare or threatened species requires a range of information, including a sound taxonomic foundation, to ensure appropriate management. However, rare species are often known from a limited number of specimens, and that can hinder taxonomic ... ...

Abstract	Conservation of rare or threatened species requires a range of information, including a sound taxonomic foundation, to ensure appropriate management. However, rare species are often known from a limited number of specimens, and that can hinder taxonomic understanding. Seringia exastia and S. katatona are two conservation‐listed taxa that were poorly known in the remote Kimberley region of northern Western Australia. Recent surveys discovered additional populations of both species but also revealed extensive morphological variation that obscured the boundary between the two species and a third, more widespread species, S. nephrosperma. We applied genomic data (>5000 SNP loci) to investigate species boundaries and hybridisation within this group. We found unequivocal evidence that S. katatona is a hybrid between S. exastia and S. nephrosperma, which is consistent with its intermediate morphology in diagnostic characters between the two highly divergent parents. Unexpectedly, we also uncovered a lack of genome‐wide differentiation and polyphyly between S. exastia and an intended outgroup taxon, S. elliptica. These results have significant taxonomic implications, for which reason we present a revised taxonomic treatment that shows S. katatona to be a nothospecies, S. ×katatona, and synonymises S. elliptica under S. exastia, the oldest effectively published name. These taxonomic revisions present new information that will enable reconsideration of the current conservation status of these taxa and inform their management in northern Western Australia.
Keywords	Malvaceae ; conservation status ; genomics ; hybridization ; hybrids ; polyphyly ; rare species ; taxonomic revisions ; threatened species ; Western Australia
Language	English
Dates of publication	2020-04
Size	p. 307-320.
Publishing place	John Wiley & Sons, Inc.
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	204216-2
ISSN	0040-0262
ISSN	0040-0262
DOI	10.1002/tax.12233
Database	NAL-Catalogue (AGRICOLA)

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Article: Historical persistence and isolation by distance of <i>Mirbelia viminalis</i> (Fabaceae) across the Hamersley Range of the Pilbara bioregion

Millar, Melissa A. / Binks, Rachel M. / Tapper, Sarah-Louise / Macdonald, Bronwyn M. / McArthur, Shelley L. / Hankinson, Margaret / Coates, David J. / van Leeuwen, Stephen / Byrne, Margaret

Australian journal of botany. 2022, v. 70, no. 5

2022

Abstract: Context Empirical studies of intraspecific genetic diversity and population structure can inform the evolutionary and demographic history of individual species and of landscapes at the bioregional level. Aims We aimed to assess intraspecific genetic ... ...

Abstract	Context Empirical studies of intraspecific genetic diversity and population structure can inform the evolutionary and demographic history of individual species and of landscapes at the bioregional level. Aims We aimed to assess intraspecific genetic variation at macroevolutionary and microevolutionary temporal scales for Mirbelia viminalis , a key species present on the Hamersley Range in the ancient and highly diverse landscape of the Pilbara bioregion of northwest Western Australia. Methods We sampled extant populations and assessed diversity and structure using sequences (chloroplast DNA, 1759 base pairs) and microsatellite markers (nuclear DNA, 15 loci) data. Key results Significant phylogeographic structure and a lack of historical demographic signals of population contraction or expansion suggest historical population persistence. Moderate chloroplast haplotype diversity (h =15) and moderate divergence among extant haplotypes indicates a degree of historical connectivity via seed dispersal across central populations on the Hamersley Range. Levels of nuclear genetic diversity were low to moderate (allelic richness=3.554, expected heterozygosity=0.489, observed heterozygosity=0.462) and depauperate compared to another member of the Mirbelia genus present further south in the Midwest region. Nuclear diversity revealed a strong signal of isolation by distance with localised admixture among populations and some contemporary genetic clustering along a north-west to south-east transect of the Hamersley Range. Conclusions Low nuclear genetic diversity may be related to recent reductions in population size for M. viminalis . Historical population persistence with few barriers to dispersal other than geographic distance may be common for members of the Fabaceae across the Hamersley Range.
Keywords	Mirbelia ; chloroplast DNA ; chloroplasts ; genetic variation ; haplotypes ; landscapes ; microsatellite repeats ; nuclear genome ; phylogeography ; population size ; population structure ; seed dispersal ; Western Australia
Language	English
Size	p. 358-371.
Publishing place	CSIRO Publishing
Document type	Article
ISSN	0067-1924
DOI	10.1071/BT22014
Database	NAL-Catalogue (AGRICOLA)

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Article: Limited phylogeographic and genetic connectivity in

Millar, Melissa A / Binks, Rachel M / Tapper, Sarah-Louise / Macdonald, Bronwyn M / McArthur, Shelley L / Hankinson, Margaret / Coates, David J / van Leeuwen, Stephen / Byrne, Margaret

Ecology and evolution

2022 Volume 12, Issue 7, Page(s) e9052

Abstract: Widespread plant species are expected to maintain genetic diversity and gene flow via pollen and seed dispersal. Stature is a key life history trait that affects seed and potentially pollen dispersal, with limited stature associated with limited ... ...

Abstract	Widespread plant species are expected to maintain genetic diversity and gene flow via pollen and seed dispersal. Stature is a key life history trait that affects seed and potentially pollen dispersal, with limited stature associated with limited dispersal and greater genetic differentiation. We sampled Hill's tabletop wattle (
Language	English
Publishing date	2022-07-06
Publishing country	England
Document type	Journal Article
ZDB-ID	2635675-2
ISSN	2045-7758
ISSN	2045-7758
DOI	10.1002/ece3.9052
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Not all rare species are the same: contrasting patterns of genetic diversity and population structure in two narrow‐range endemic sedges

Binks, Rachel M / Millar, Melissa A / Byrne, Margaret

Biological journal of the Linnean Society. 2015 Apr., v. 114, no. 4

2015

Abstract: The many spatial and temporal configurations in which species can be classified as rare may result in various genetic signatures, despite a persistent generalization that populations of rare species are genetically depauperate and highly differentiated. ... ...

Abstract	The many spatial and temporal configurations in which species can be classified as rare may result in various genetic signatures, despite a persistent generalization that populations of rare species are genetically depauperate and highly differentiated. We assessed genetic diversity and differentiation in two narrow endemics with contrasting geographical distributions using 12 nuclear and six chloroplast microsatellite loci. Consistent with both marker types, the smaller, more isolated Lepidosperma sp. Parker Range populations were characterized by lower diversity and stronger divergence, relative to higher diversity and extensive connectivity among the geographically clustered L. sp. Mt Caudan populations. However, neither species exhibited low diversity, despite high inbreeding. Together, our results suggest that these species are naturally rare and have long persisted in this landscape while maintaining genetic diversity and tolerating considerable inbreeding. Their resilience is probably due to large population sizes and the flexibility afforded by employing sexual and asexual reproduction. Their contrasting genetic dynamics demonstrate that not all rare species share generalized patterns, even within the same rarity category. Moreover, these patterns were better predicted by fine‐scale descriptors of rarity, population size and distribution, rather than the more typically used geographical range. This study highlights the complex dynamics of rare species and cautions against using broad assumptions to classify and manage rare species. © 2015 State of Western Australia, Biological Journal of the Linnean Society, 2015, 114, 873–886.
Keywords	Cyperaceae ; asexual reproduction ; chloroplasts ; genetic variation ; inbreeding ; landscapes ; microsatellite repeats ; population size ; population structure ; rare species ; Western Australia
Language	English
Dates of publication	2015-04
Size	p. 873-886.
Publishing place	Published for the Linnean Society of London by Blackwell [etc.]
Document type	Article
ZDB-ID	1461865-5
ISSN	1095-8312 ; 0024-4066
ISSN (online)	1095-8312
ISSN	0024-4066
DOI	10.1111/bij.12465
Database	NAL-Catalogue (AGRICOLA)

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