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Article ; Online: Chloroplast genome analysis of box-ironbark Eucalyptus.

Alwadani, Khawla G / Janes, Jasmine K / Andrew, Rose L

2019 Volume 136, Page(s) 76–86

Abstract: Eucalyptus L'Hérit. (Myrtaceae) is a taxonomically complex and highly speciose genus that dominates much of Australia's woody vegetation. However, very little information is available about the molecular biology and chloroplast diversity of certain ... ...

Abstract	Eucalyptus L'Hérit. (Myrtaceae) is a taxonomically complex and highly speciose genus that dominates much of Australia's woody vegetation. However, very little information is available about the molecular biology and chloroplast diversity of certain groups, such as Eucalyptus section Adnataria, which is found in many woodland habitats of eastern Australia. We report four new complete chloroplast genomes of Eucalyptus, including three genomes from species previously lacking any chloroplast reference sequences. Plastomes of E. albens, E. conica, E. crebra and E. melliodora assembled using a de novo approach were shown to be largely identical to each other, and similar in size and structure to previously published chloroplast genomes from Eucalyptus. A total of 132 genes (114 single-copy genes and 18 duplicated genes in the IR regions) were identified, and shown to be highly conserved in terms of gene order, content and organization. Slightly higher divergence in the intergenic spacers was identified through comparative genomic analyses. Chloroplast sequences of 35 additional individuals representing 12 species were assembled using a reference guided approach. Rates of nucleotide substitution varied among the protein coding genes, with 17 genes under possible positive selection, and 29 invariant genes. Phylogenetic analysis of either the whole reconstructed plastome sequences or the individual genes revealed extreme discordance with expected species boundaries or higher-level relationships. Plastome relationships were better predicted by geography than by nuclear DNA or taxonomic relationships, suggesting a substantial influence of gene flow over and above the effects of incomplete lineage sorting. These results provide resources for future research and valuable insights into the prevalence of interspecific gene flow among Eucalyptus species.
MeSH term(s)	Australia ; Chloroplasts/genetics ; Chromosome Mapping ; Eucalyptus/genetics ; Gene Order ; Genes, Plant ; Genome, Chloroplast ; Likelihood Functions ; Phylogeny ; Plant Bark/genetics
Language	English
Publishing date	2019-04-04
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	33610-5
ISSN	1095-9513 ; 1055-7903
ISSN (online)	1095-9513
ISSN	1055-7903
DOI	10.1016/j.ympev.2019.04.001
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Article: Nestling sex does not influence provisioning effort of parents or helpers in a cooperative bird with a male-biased helper contingent

Barati, Ahmad / Andrew, Rose L. / McDonald, Paul G.

Behavioral ecology and sociobiology. 2021 June, v. 75, no. 6

2021

Abstract: In cooperatively breeding species, the level of investment by both breeders and helpers may be influenced by the sex of offspring in broods that they attend, due to different fitness payoffs associated with investing in male versus female offspring. This ...

Abstract	In cooperatively breeding species, the level of investment by both breeders and helpers may be influenced by the sex of offspring in broods that they attend, due to different fitness payoffs associated with investing in male versus female offspring. This might be expected if the sexes differ markedly in either the cost of their rearing, due to factors such as sexual size dimorphism, or the level of help that they may provide in later life that might benefit helpers in the future. Here we investigate how nestling sex influences the provisioning efforts provided by helpers and the subsequent growth and development of offspring in the cooperatively breeding noisy miner (Manorina melanocephala). In this species, helpers are predominantly philopatric males, as females disperse to other colonies to find breeding positions. We therefore predicted that helpers might invest more in helpful male-biased broods rather than those with dispersive female offspring, particularly if larger males required more resources than female offspring to successfully fledge. Male miners grew faster, fledging at the same age as their female siblings but with a heavier body mass. Male offspring therefore possibly require more resources than female offspring to raise. However, despite possible differences in the fitness returns of investing in different sexes, we were unable to detect any significant influence of brood sex ratio on the provisioning rate of pair or their helper contingent. Noisy miner helpers provision the brood irrespective of offspring sex. This could be due to an inability to recognise nestling sex, or potential future costs that might be imposed by philopatric males that subsequently compete for resources and/or mating opportunities with the helpers that reared them. From a male helper perspective, these potential costs may ultimately nullify benefits that male offspring provide in future. SIGNIFICANCE STATEMENT: Male and female offspring might have different fitness benefits for helpers in the cooperatively breeding species. Given this, helpers in this breeding system might have sex-dependant preferences and direct their help towards the apparently more beneficial sex (i.e. the sex that is expected to stay at the same population and provide help in return). In this study, we showed that in the cooperatively breeding noisy miner (Manorina melanocephala), although male offspring are expected to provide higher level of care with over 90% of helpers being male, this apparent difference in the fitness return did not result in higher provisioning rate in the male-biased broods compared to female-biased broods. We argue that (a) this could be due insufficient cues for recognition of nestling sex or (b) despite the higher level of help that male offspring are expected to provide into the future, the overall inclusive fitness benefits do not vary among the sexes.
Keywords	body weight ; ecology ; females ; fledglings ; growth and development ; males ; philopatry ; progeny ; sex ratio ; sexual dimorphism ; sociobiology
Language	English
Dates of publication	2021-06
Size	p. 94.
Publishing place	Springer Berlin Heidelberg
Document type	Article
ZDB-ID	194510-5
ISSN	1432-0762 ; 0340-5443
ISSN (online)	1432-0762
ISSN	0340-5443
DOI	10.1007/s00265-021-03038-9
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Article ; Online: Molecular and morphological analyses support recognition of <i>Prostanthera volucris</i> (Lamiaceae), a new species from the Central Tablelands of New South Wales

O’Donnell, Ryan P. / Bruhl, Jeremy J. / Telford, Ian R. H. / Wilson, Trevor C. / Zimmer, Heidi C. / Taseski, Guy M. / Andrew, Rose L.

Australian Systematic Botany. 2023, v. 36, no. 1 p.1-20

2023

Abstract: Research into the systematics of Prostanthera recently revealed close evolutionary relationship among P. phylicifolia sens. str. , the critically endangered P. gilesii , and a population of uncertain identity from the Central Tablelands of New South ... ...

Abstract	Research into the systematics of Prostanthera recently revealed close evolutionary relationship among P. phylicifolia sens. str. , the critically endangered P. gilesii , and a population of uncertain identity from the Central Tablelands of New South Wales (NSW), Australia. Previous analyses were unable to establish whether genetic boundaries separated these taxa. This study assessed species boundaries among these three taxa by using a combination of single-nucleotide polymorphisms (SNPs) sampled at the population-scale and multivariate analysis of morphological characters. Ordination, model-based clustering, F -statistics, neighbour-network analysis, phylogenetic analysis, and ancestry coefficient estimates all provided support for discrete genetic differences among the three taxa. Morphological phenetic analysis recovered congruent morphological clusters and identified a suite of corresponding diagnostic characters. This congruence of molecular and morphological evidence supports the presence of three independently evolving lineages, two of which correspond with the previously described P. gilesii and P. phylicifolia sens. str. The third taxon, represented by a single population from the Central Tablelands of NSW, is here described as P. volucris R.P.O’Donnell. A detailed description, diagnostic line drawings and photographs are provided. We evaluate P. volucris as satisfying criteria to be considered Critically Endangered .
Keywords	Prostanthera ; ancestry ; botany ; multivariate analysis ; new species ; phylogeny ; Australia ; critically endangered ; DArTseq ; genotyping-by-sequencing ; Lamiaceae ; population genomics ; species delimitation ; systematics ; taxonomy
Language	English
Size	p. 1-20.
Publishing place	CSIRO Publishing
Document type	Article ; Online
ISSN	1030-1887
DOI	10.1071/SB22017
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Article ; Online: Phylogenetic relationships of Xerochrysum, Coronidium and Helichrysum leucopsideum reveal a new genus, Leucozoma (Asteraceae: Gnaphalieae)

Collins, Timothy L. / Bruhl, Jeremy J. / Andrew, Rose L. / Telford, Ian R.H. / Schmidt‐Lebuhn, Alexander N.

TAXON. 2022 Oct., v. 71, no. 5 p.1044-1062

2022

Abstract: We gathered morphological data and genome‐wide single nucleotide polymorphisms to infer the evolutionary relationships of Xerochrysum, Coronidium, and Helichrysum leucopsideum, and to test the circumscription of the genera. SVDquartets species tree ... ...

Abstract	We gathered morphological data and genome‐wide single nucleotide polymorphisms to infer the evolutionary relationships of Xerochrysum, Coronidium, and Helichrysum leucopsideum, and to test the circumscription of the genera. SVDquartets species tree topology resolved relationships between the genera and within subsets of the Xerochrysum data. Results corroborated previous conclusions that Coronidium is non‐monophyletic as presently circumscribed and forms, in addition to the more distantly related Coronidium scorpioides group, three morphologically distinct clades. SVDquartets returned two clades in Xerochrysum, though species‐level relationships were unclear. Bayesian coalescent analysis using SNAPP produced tree topologies for the three clades of Coronidium with most species‐level relationships well resolved. The new genus Leucozoma is described for seven taxa previously included in Coronidium. A revised description of Coronidium and images of phyllary and fruit diagnostic morphological characters are provided.
Keywords	Bayesian theory ; Helichrysum ; Xerochrysum ; new genus ; phylogeny ; topology
Language	English
Dates of publication	2022-10
Size	p. 1044-1062.
Publishing place	John Wiley & Sons, Inc.
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	204216-2
ISSN	0040-0262
ISSN	0040-0262
DOI	10.1002/tax.12771
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Article: There’s gold in them thar hills! Morphology and molecules delimit species in <i>Xerochrysum</i> (Asteraceae; Gnaphalieae) and reveal many new taxa

Collins, Timothy L. / Schmidt-Lebuhn, Alexander N. / Andrew, Rose L. / Telford, Ian R. H. / Bruhl, Jeremy J.

Australian systematic botany. 2022, v. 35, no. 2

2022

Abstract: Golden everlasting paper daisies in the genus Xerochrysum Tzvelev are iconic Australian native plants grown worldwide. The X. bracteatum species complex has been regarded as taxonomically confusing and in need of revision for over 60years. We applied ... ...

Abstract	Golden everlasting paper daisies in the genus Xerochrysum Tzvelev are iconic Australian native plants grown worldwide. The X. bracteatum species complex has been regarded as taxonomically confusing and in need of revision for over 60years. We applied morphological and molecular analyses to delimit species, detect common ancestry among populations, and identify putative hybrids in the genus Xerochrysum (Asteraceae: Gnaphalieae). Multiple lines of evidence provided strong support for the recognition of new taxa. Here we describe the following 11 new species: X. andrewiae T.L.Collins & J.J.Bruhl, X. berarngutta T.L.Collins & I.Telford, X. copelandii J.J.Bruhl & I.Telford, X. frutescens J.J.Bruhl & I.Telford, X. gudang T.L.Collins & J.J.Bruhl, X. hispidum T.L.Collins & I.Telford, X. macsweeneyorum T.L.Collins, X. murapan T.L.Collins & I.Telford, X. neoanglicum J.J.Bruhl & I.Telford, X. strictum T.L.Collins, and X. wilsonii T.L.Collins, reinstate Helichrysum banksii A.Cunn. ex DC. (as X. banksii (A.Cunn. ex DC.) T.L.Collins & I.Telford), lectotypify X. banksii and X. papillosum (Labill.) R.J.Bayer, and recircumscribe X. bicolor (Lindl.) R.J.Bayer to include X. halmaturorum Paul G.Wilson and some populations of X. bracteatum sens. lat . from mainland South Australia and Victoria. We also provide revised descriptions of all taxa in the genus, their conservation status, a dichotomous key, tables distinguishing closely related taxa and distribution maps.
Keywords	Helichrysum ; ancestry ; conservation status ; gold ; lectotypes ; new species ; taxonomic keys ; South Australia
Language	English
Size	p. 120-185.
Publishing place	CSIRO Publishing
Document type	Article
ISSN	1030-1887
DOI	10.1071/SB21014
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Article: Species-specific basecallers improve actual accuracy of nanopore sequencing in plants.

Ferguson, Scott / McLay, Todd / Andrew, Rose L / Bruhl, Jeremy J / Schwessinger, Benjamin / Borevitz, Justin / Jones, Ashley

Plant methods

2022 Volume 18, Issue 1, Page(s) 137

Abstract: Background: Long-read sequencing platforms offered by Oxford Nanopore Technologies (ONT) allow native DNA containing epigenetic modifications to be directly sequenced, but can be limited by lower per-base accuracies. A key step post-sequencing is ... ...

Abstract	Background: Long-read sequencing platforms offered by Oxford Nanopore Technologies (ONT) allow native DNA containing epigenetic modifications to be directly sequenced, but can be limited by lower per-base accuracies. A key step post-sequencing is basecalling, the process of converting raw electrical signals produced by the sequencing device into nucleotide sequences. This is challenging as current basecallers are primarily based on mixtures of model species for training. Here we utilise both ONT PromethION and higher accuracy PacBio Sequel II HiFi sequencing on two plants, Phebalium stellatum and Xanthorrhoea johnsonii, to train species-specific basecaller models with the aim of improving per-base accuracy. We investigate sequencing accuracies achieved by ONT basecallers and assess accuracy gains by training single-species and species-specific basecaller models. We also evaluate accuracy gains from ONT's improved flowcells (R10.4, FLO-PRO112) and sequencing kits (SQK-LSK112). For the truth dataset for both model training and accuracy assessment, we developed highly accurate, contiguous diploid reference genomes with PacBio Sequel II HiFi reads. Results: Basecalling with ONT Guppy 5 and 6 super-accurate gave almost identical results, attaining read accuracies of 91.96% and 94.15%. Guppy's plant-specific model gave highly mixed results, attaining read accuracies of 91.47% and 96.18%. Species-specific basecalling models improved read accuracy, attaining 93.24% and 95.16% read accuracies. R10.4 sequencing kits also improve sequencing accuracy, attaining read accuracies of 95.46% (super-accurate) and 96.87% (species-specific). Conclusions: The use of a single mixed-species basecaller model, such as ONT Guppy super-accurate, may be reducing the accuracy of nanopore sequencing, due to conflicting genome biology within the training dataset and study species. Training of single-species and genome-specific basecaller models improves read accuracy. Studies that aim to do large-scale long-read genotyping would primarily benefit from training their own basecalling models. Such studies could use sequencing accuracy gains and improving bioinformatics tools to improve study outcomes.
Language	English
Publishing date	2022-12-14
Publishing country	England
Document type	Journal Article
ZDB-ID	2203723-8
ISSN	1746-4811
ISSN	1746-4811
DOI	10.1186/s13007-022-00971-2
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Article ; Online: Repeated experimental removals unveil sex and age-specific dispersal strategies in a social passerine bird

Etezadifar, Farzaneh / Vickers, Jacob A. T. / French, Kristine / McDonald, Paul G. / Barati, Ahmad / Andrew, Rose L. / Major, Richard E.

Wildlife Research. 2022, v. 50, no. 2 p.141-151

2022

Abstract: Context Sex and age are frequently proposed as drivers of a number of behavioural and demographic patterns that can have important consequences for population dynamics including access to mates, sexual selection, parental care and lifetime productivity. ... ...

Abstract	Context Sex and age are frequently proposed as drivers of a number of behavioural and demographic patterns that can have important consequences for population dynamics including access to mates, sexual selection, parental care and lifetime productivity. Sex and age might also be important in shaping the movement patterns and colonisation processes of social species moving into vacant habitat. Such information is critical for the management of strongly interacting species such as the noisy miner (Manorina melanocephala), which structure ecological communities through aggressive exclusion of other taxa from areas that they occupy. Aims In Manorina colonies, young females are usually dispersive, while males remain in the natal colony as the philopatric sex. Following removal of individuals from an area, we aimed to determine whether female-biased dispersal, particularly of young females, would result in a more equal sex ratio and a younger age structure in the recolonising population. Methods These predictions were tested by anatomically ageing and sexing 1856 noisy miners that had been experimentally culled in two regions of New South Wales, Australia, to reduce the aggressive impact of this species on other native species. Key results Prior to removal, noisy miner populations were significantly male-biased in both regions (57% and 60%); however sex ratios after each of two removal episodes no longer differed from parity. Immature birds were a dominant feature (65%) of recolonising populations in both regions, however, the age structure of recolonising populations was different in each region, mostly likely due to the respective timing of culls during the year. Furthermore, the culling response in terms of age-specific sex ratio varied between regions. After the final cull, the sex ratio of mature birds had fallen to parity in one region but had become even more male biased (68%) in the other region. There was no sex-ratio bias among immature birds before or after culling. Conclusion These results confirm the expectation that immature birds are more likely to be colonisers, but the expectation of greater female dispersal was equivocal. Implications The differences in response between regions may reflect variation in population density, landscape connectivity or seasonality, highlighting challenges when implementing culling programs for conservation management.
Keywords	Passeriformes ; age structure ; birds ; females ; habitat connectivity ; indigenous species ; males ; philopatry ; population density ; population dynamics ; research ; sex ratio ; sexual selection ; wildlife ; Australia ; dispersal ; lethal management ; Manorina melanocephala ; noisy miner ; recolonisation ; superabundant species</kwd>
Language	English
Size	p. 141-151.
Publishing place	CSIRO Publishing
Document type	Article ; Online
ZDB-ID	1070380-9
ISSN	1035-3712
ISSN	1035-3712
DOI	10.1071/WR21170
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Multiple chromosomal inversions contribute to adaptive divergence of a dune sunflower ecotype.

Huang, Kaichi / Andrew, Rose L / Owens, Gregory L / Ostevik, Kate L / Rieseberg, Loren H

Molecular ecology

2020 Volume 29, Issue 14, Page(s) 2535–2549

Abstract: Both models and case studies suggest that chromosomal inversions can facilitate adaptation and speciation in the presence of gene flow by suppressing recombination between locally adapted alleles. Until recently, however, it has been laborious and time- ... ...

Abstract	Both models and case studies suggest that chromosomal inversions can facilitate adaptation and speciation in the presence of gene flow by suppressing recombination between locally adapted alleles. Until recently, however, it has been laborious and time-consuming to identify and genotype inversions in natural populations. Here we apply RAD sequencing data and newly developed population genomic approaches to identify putative inversions that differentiate a sand dune ecotype of the prairie sunflower (Helianthus petiolaris) from populations found on the adjacent sand sheet. We detected seven large genomic regions that exhibit a different population structure than the rest of the genome and that vary in frequency between dune and nondune populations. These regions also show high linkage disequilibrium and high heterozygosity between, but not within, arrangements, consistent with the behaviour of large inversions, an inference subsequently validated in part by comparative genetic mapping. Genome-environment association analyses show that key environmental variables, including vegetation cover and soil nitrogen, are significantly associated with inversions. The inversions colocate with previously described "islands of differentiation," and appear to play an important role in adaptive divergence and incipient speciation within H. petiolaris.
MeSH term(s)	Adaptation, Biological/genetics ; Chromosome Inversion/genetics ; Ecotype ; Gene Flow ; Gene-Environment Interaction ; Genetics, Population ; Genome, Plant ; Helianthus/genetics ; Linkage Disequilibrium
Language	English
Publishing date	2020-04-24
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1126687-9
ISSN	1365-294X ; 0962-1083
ISSN (online)	1365-294X
ISSN	0962-1083
DOI	10.1111/mec.15428
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Article: Chloroplast genome analysis of box-ironbark Eucalyptus

Alwadani, Khawla G / Janes, Jasmine K / Andrew, Rose L

Molecular phylogenetics and evolution. 2019 July, v. 136

2019

Abstract: Eucalyptus L’Hérit. (Myrtaceae) is a taxonomically complex and highly speciose genus that dominates much of Australia’s woody vegetation. However, very little information is available about the molecular biology and chloroplast diversity of certain ... ...

Abstract	Eucalyptus L’Hérit. (Myrtaceae) is a taxonomically complex and highly speciose genus that dominates much of Australia’s woody vegetation. However, very little information is available about the molecular biology and chloroplast diversity of certain groups, such as Eucalyptus section Adnataria, which is found in many woodland habitats of eastern Australia. We report four new complete chloroplast genomes of Eucalyptus, including three genomes from species previously lacking any chloroplast reference sequences. Plastomes of E. albens, E. conica, E. crebra and E. melliodora assembled using a de novo approach were shown to be largely identical to each other, and similar in size and structure to previously published chloroplast genomes from Eucalyptus. A total of 132 genes (114 single-copy genes and 18 duplicated genes in the IR regions) were identified, and shown to be highly conserved in terms of gene order, content and organization. Slightly higher divergence in the intergenic spacers was identified through comparative genomic analyses. Chloroplast sequences of 35 additional individuals representing 12 species were assembled using a reference guided approach. Rates of nucleotide substitution varied among the protein coding genes, with 17 genes under possible positive selection, and 29 invariant genes. Phylogenetic analysis of either the whole reconstructed plastome sequences or the individual genes revealed extreme discordance with expected species boundaries or higher-level relationships. Plastome relationships were better predicted by geography than by nuclear DNA or taxonomic relationships, suggesting a substantial influence of gene flow over and above the effects of incomplete lineage sorting. These results provide resources for future research and valuable insights into the prevalence of interspecific gene flow among Eucalyptus species.
Keywords	Eucalyptus crebra ; Eucalyptus melliodora ; chloroplast genome ; chloroplasts ; gene duplication ; gene flow ; gene order ; genes ; geography ; habitats ; intergenic DNA ; molecular biology ; nuclear genome ; phylogeny ; sequence analysis ; woodlands ; Australia
Language	English
Dates of publication	2019-07
Size	p. 76-86.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	33610-5
ISSN	1095-9513 ; 1055-7903
ISSN (online)	1095-9513
ISSN	1055-7903
DOI	10.1016/j.ympev.2019.04.001
Database	NAL-Catalogue (AGRICOLA)

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Article: Morphological, phytochemical and molecular analyses define species limits in Eucalyptus magnificata (Myrtaceae) and lead to the discovery of a new rare species

Collins, Timothy L / Andrew, Rose L / Bruhl, Jeremy J

Australian systematic botany. 2019, v. 32, no. 1

2019

Abstract: Eucalyptus magnificata L.A.S.Johnson & K.D.Hill is an endangered species endemic to the New England Tablelands Bioregion of eastern Australia, with taxonomic conflict regarding its recognition. Analyses of morphology, phytochemistry and genomic DNA were ... ...

Abstract	Eucalyptus magnificata L.A.S.Johnson & K.D.Hill is an endangered species endemic to the New England Tablelands Bioregion of eastern Australia, with taxonomic conflict regarding its recognition. Analyses of morphology, phytochemistry and genomic DNA were used to test species limits of E. magnificata. Morphometric and phytochemical phenetic analyses found distinct differences among E. magnificata, E. baueriana and a putative entity recognised during field collection, i.e. E. sp. Dalveen. Another putative entity, E. sp. Oxley, was morphologically and phytochemically intermediate between E. magnificata and E. conica. Phenetic analysis of single-nucleotide polymorphism (SNP) data supported the results from morphological and phytochemical analyses. The original circumscription of E. magnificata, as distinct from E. baueriana, was strongly corroborated. Eucalyptus magnificata was found to be restricted in distribution to the Macleay Gorges area south-east of Armidale. Multiple lines of evidence provided strong support for the recognition of E. sp. Dalveen as a separately evolving entity at a species level, here described as Eucalyptus dalveenica T.L.Collins, R.L.Andrew & J.J.Bruhl. A full description of the new species, a table distinguishing E. dalveenica from closely related taxa, and an identification key are provided. Distribution, habitat and conservation status are discussed.
Keywords	DNA ; Eucalyptus ; chemical constituents of plants ; conservation status ; endangered species ; habitats ; morphometry ; new species ; plant taxonomy ; rare species ; single nucleotide polymorphism ; taxonomic keys ; Australia
Language	English
Size	p. 12-28.
Publishing place	CSIRO Publishing
Document type	Article
ISSN	1030-1887
DOI	10.1071/SB18037
Database	NAL-Catalogue (AGRICOLA)

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