Darren Crayn

Elaeocarpus carbinensis J.N.Gagul and Crayn (Elaeocarpaceae), a new species endemic to the Mt Carbine Tableland of northeast Queensland, Australia

Publisher: Biodiversity Heritage Library

Date: 2018

DOI: 10.5962/P.299906

Anti-inflammatory properties of novel galloyl glucosides isolated from the Australian tropical plant Uromyrtus metrosideros

Publisher: Elsevier BV

Date: 12-2022

DOI: 10.1016/J.CBI.2022.110124

Abstract: Two new galloyl glucosides, galloyl-lawsoniaside A (4) and uromyrtoside (6), were isolated from the polar fraction of Uromyrtus metrosideros leaf extract along with another four previously identified phytochemicals (1, 2, 3, and 5). The structures of these six compounds were characterised using low and high-resolution mass spectrometry (L/HRMS) and 1D and 2D Nuclear Magnetic Resonance (NMR) spectroscopy. These compounds were not toxic to human peripheral blood mononuclear cells (PBMCs) at 10 μg/mL over 24 h, yet showed significant in vitro suppression of proinflammatory cytokines involved in the pathogenesis of inflammatory bowel disease (IBD). Specifically, the release of interferon γ (IFN-γ), interleukin (IL)-17A, and IL-8 from phorbol myristate acetate/ionomycin (P/I) and anti-CD3/anti-CD28-activated cells were significantly suppressed by compounds 4 and 5. Interestingly, no effect on tumour necrosis factor (TNF) release was observed. These results show that the newly characterised compound 4 has promising cytokine suppressive properties, which could be further investigated as a candidate for IBD treatment.

Building a plant DNA barcode reference library for a diverse tropical flora: an example from Queensland, Australia

Publisher: MDPI AG

Date: 29-02-2016

DOI: 10.3390/D8010005

Generic concepts in Styphelieae (Ericaceae): the Cyathodes group

Publisher: CSIRO Publishing

Date: 2005

DOI: 10.1071/SB05005

Abstract: Non-molecular and atpB−rbcL spacer sequence datasets for 38 taxa representing Cyathodes Labill. sensu lato and its relatives, together with several outgroups from Styphelieae, Oligarrheneae, Epacreae and Archerieae, were subjected to cladistic analyses. The monophyly of Cyathodes sensu Weiller, Leptecophylla Weiller, Lissanthe R.Br. sensu Crayn et al. and Planocarpa Weiller is supported. Cyathopsis Brongn. & Gris is expanded to include two other New Caledonian species, Styphelia violaceospicata (Guillaumin) McPherson and S. albicans (Brongn. & Gris) Sleumer. Androstoma Hook.f. is redefined to include Leucopogon milliganii (F.Muell.) Rodway. Leucopogon durus Benth. is transferred to Acrotriche R.Br. Two new genera are described: Acrothamnus C.J.Quinn, comprising at least five species in eastern Australia, New Zealand, New Guinea and the Pacific Agiortia C.J.Quinn, comprising three species in north-eastern New South Wales and south-eastern Queensland. Keys to the species of Acrothamnus, Agiortia, Androstoma and Cyathopsis are provided.

Validation of two informally named species of Melichrus (Ericaceae: Epacridoideae) from north-eastern New South Wales.

Publisher: Royal Botanical Gardens and Domain Trust

Date: 15-12-2020

DOI: 10.7751/TELOPEA14704

Abstract: Two narrowly endemic, endangered species of Melichrus (Ericaceae subfam. Epacridoideae) from north-eastern New South Wales currently bearing phrase names are formally named and described. Melichrus hirsutus J.B.Williams ex H.T.Kenn. & I.Telford is validly published more than 50 years after the first herbarium specimens were collected. Melichrus gibberagee J.B.Williams ex H.T.Kenn. & J.J.Bruhl is also described as new. Notes are provided on the distribution, habitat and conservation status of both species. An updated key to Melichrus species in New South Wales is provided.

Evidence for convergent evolution among phylogenetically distant rare species of Tetratheca (Elaeocarpaceae, formerly Tremandraceae) from Western Australia

Publisher: CSIRO Publishing

Date: 2007

DOI: 10.1071/SB06017

Abstract: Morphological and molecular investigations of taxon relationships among rare species of Tetratheca Sm. occurring near Koolyanobbing, Western Australia, have confirmed the distinctness of T. aphylla F.Muell., T. harperi F.Muell. and T. paynterae Alford and identified three new rare taxa from collections affiliated with T. aphylla and T. paynterae. The recognition of these taxa at specific and sub-specific ranks is based on their different degrees of morphological and molecular ergence, combined with geographic disjunction. Cladistic analysis of nrDNA internal transcribed spacer and cpDNA trnL-trnF sequences from a range of Tetratheca species from Western Australia and the eastern states indicates that T. aphylla, T. harperi and T. paynterae belong to three separate evolutionary lineages and that the endemism displayed among these taxa to small, disjunct ranges within the same geographic area, is a result of in situ speciation due to historical fragmentation. These results exemplify the extremely high conservation value of the Yilgarn banded ironstone ranges. The superficial similarity among the study taxa in having a ‘leafless’ habit can be seen to be adaptive convergence in response to the marginal and semi-arid environments in which they occur, and this character is highly homoplastic within the genus.

Decline of a biome: evolution, contraction, fragmentation, extinction and invasion of the Australian mesic zone biota

Publisher: Wiley

Date: 26-05-2011

DOI: 10.1111/J.1365-2699.2011.02535.X

Are Tropical Mountaintop Trees Constrained in Their Distributions by Physiological Limitations? Thermal Adaptation and Acclimation to Climate Change

Publisher: The Royal Society of Queensland

Date: 2022

DOI: 10.53060/PRSQ.2022-08

Comparative Analysis of Plastid Genomes in the Non-photosynthetic Genus Thismia Reveals Ongoing Gene Set Reduction

Publisher: Frontiers Media SA

Date: 16-03-2021

DOI: 10.3389/FPLS.2021.602598

Abstract: Heterotrophic plants provide intriguing ex les of reductive evolution. This is especially evident in the reduction of their plastid genomes, which can potentially proceed toward complete genome loss. Several milestones at the beginning of this path of degradation have been described however, little is known about the latest stages of plastome reduction. Here we analyze a ersity of plastid genomes in a set of closely related non-photosynthetic plants. We demonstrate how a gradual loss of genes shapes the miniaturized plastomes of these plants. The subject of our study, the genus Thismia , represents the mycoheterotrophic monocot family Thismiaceae, a group that may have experienced a very ancient (60–80 mya) transition to heterotrophy. In all 18 species examined, the plastome is reduced to 14–18 kb and is highly AT-biased. The most complete observed gene set includes accD , seven ribosomal protein genes, three rRNA, and two tRNA genes. Different clades of Thismia have undergone further gene loss (complete absence or pseudogenization) compared to this set: in particular, we report two independent losses of rps2 and rps18 .

Hybphaser identifies hybrid evolution in Australian Thelypterid ferns

Publisher: Cold Spring Harbor Laboratory

Date: 12-2021

DOI: 10.1101/2021.11.29.470477

Abstract: Hybridisation can lead to reproductive isolation and consequently speciation. It has been proposed to play an important role in fern evolution, but has been difficult to investigate. This study explores the utility of target sequence capture and reference guided read phasing to investigate the role of evolutionary reticulation in ferns using Australian Thelypteridaceae as a model. The bioinformatics workflow HybPhaser was used to assess ergence between alleles, phase sequence reads to references to construct accessions resembling parental haplotpes, and include them in phylogenetic and network analyses to detect hybrids and parentage. This approach identified two novel hybrid lineages in Thelypteridaceae, one occurring between two different genera (Abacopteris and Christella), and provided evidence that reticulation is likely to have played an important role in the ersification of Australian thelypterids. In addition, hybrid phasing successfully reduced conflicting data and improved overall resolution in the Thelypteridaceae phylogeny, highlighting the power of this approach for reconstructing evolutionary history in reticulated lineages.

Phylodiversity to inform conservation policy: An Australian example

Publisher: Elsevier BV

Date: 11-2015

DOI: 10.1016/J.SCITOTENV.2015.04.113

Abstract: Phylo ersity measures summarise the phylogenetic ersity patterns of groups of organisms. By using branches of the tree of life, rather than its tips (e.g., species), phylo ersity measures provide important additional information about bio ersity that can improve conservation policy and outcomes. As a bio erse nation with a strong legislative and policy framework, Australia provides an opportunity to use phylogenetic information to inform conservation decision-making. We explored the application of phylo ersity measures across Australia with a focus on two highly bio erse regions, the south west of Western Australia (SWWA) and the South East Queensland bioregion (SEQ). We analysed seven erse groups of organisms spanning five separate phyla on the evolutionary tree of life, the plant genera Acacia and Daviesia, mammals, hylid frogs, myobatrachid frogs, passerine birds, and camaenid land snails. We measured species richness, weighted species endemism (WE) and two phylo ersity measures, phylogenetic ersity (PD) and phylogenetic endemism (PE), as well as their respective complementarity scores (a measure of gains and losses) at 20 km resolution. Higher PD was identified within SEQ for all fauna groups, whereas more PD was found in SWWA for both plant groups. PD and PD complementarity were strongly correlated with species richness and species complementarity for most groups but less so for plants. PD and PE were found to complement traditional species-based measures for all groups studied: PD and PE follow similar spatial patterns to richness and WE, but highlighted different areas that would not be identified by conventional species-based bio ersity analyses alone. The application of phylo ersity measures, particularly the novel weighted complementary measures considered here, in conservation can enhance protection of the evolutionary history that contributes to present day bio ersity values of areas. Phylogenetic measures in conservation can include important elements of bio ersity in conservation planning, such as evolutionary potential and feature ersity that will improve decision-making and lead to better bio ersity conservation outcomes.

Vegetation and floristics of a lowland tropical rainforest in northeast Australia

Publisher: Pensoft Publishers

Date: 24-02-2016

DOI: 10.3897/BDJ.4.E7599

Paleo‐Antarctic rainforest into the modern Old World tropics: The rich past and threatened future of the “southern wet forest survivors”

Publisher: Wiley

Date: 12-2014

DOI: 10.3732/AJB.1400340

Abstract: • Have Gondwanan rainforest floral associations survived? Where do they occur today? Have they survived continuously in particular locations? How significant is their living floristic signal? We revisit these classic questions in light of significant recent increases in relevant paleobotanical data.• We traced the extinction and persistence of lineages and associations through the past across four now separated regions-Australia, New Zealand, Patagonia, and Antarctica-using fossil occurrence data from 63 well-dated Gondwanan rainforest sites and 396 constituent taxa. Fossil sites were allocated to four age groups: Cretaceous, Paleocene-Eocene, Neogene plus Oligocene, and Pleistocene. We compared the modern and ancient distributions of lineages represented in the fossil record to see if dissimilarity increased with time. We quantified similarity-dissimilarity of composition and taxonomic structure among fossil assemblages, and between fossil and modern assemblages.• Strong similarities between ancient Patagonia and Australia confirmed shared Gondwanan rainforest history, but more of the lineages persisted in Australia. S les of ancient Australia grouped with the extant floras of Australia, New Guinea, New Caledonia, Fiji, and Mt. Kinabalu. Decreasing similarity through time among the regional floras of Antarctica, Patagonia, New Zealand, and southern Australia reflects multiple extinction events.• Gondwanan rainforest lineages contribute significantly to modern rainforest community assembly and often co-occur in widely separated assemblages far from their early fossil records. Understanding how and where lineages from ancient Gondwanan assemblages co-occur today has implications for the conservation of global rainforest vegetation, including in the Old World tropics.

The genetic origin of evolidine, the first cyclopeptide discovered in plants, and related orbitides

Publisher: Elsevier BV

Date: 10-2020

DOI: 10.1074/JBC.RA120.014781

Phylogenomic analyses of Sapindales support new family relationships, rapid Mid-Cretaceous Hothouse diversification, and heterogeneous histories of gene duplication

Publisher: Frontiers Media SA

Date: 07-03-2023

DOI: 10.3389/FPLS.2023.1063174

Abstract: Sapindales is an angiosperm order of high economic and ecological value comprising nine families, c. 479 genera, and c. 6570 species. However, family and subfamily relationships in Sapindales remain unclear, making reconstruction of the order’s spatio-temporal and morphological evolution difficult. In this study, we used Angiosperms353 target capture data to generate the most densely s led phylogenetic trees of Sapindales to date, with 448 s les and c. 85% of genera represented. The percentage of paralogous loci and allele ergence was characterized across the phylogeny, which was time-calibrated using 29 rigorously assessed fossil calibrations. All families were supported as monophyletic. Two core family clades sub ide the order, the first comprising Kirkiaceae, Burseraceae, and Anacardiaceae, the second comprising Simaroubaceae, Meliaceae, and Rutaceae. Kirkiaceae is sister to Burseraceae and Anacardiaceae, and, contrary to current understanding, Simaroubaceae is sister to Meliaceae and Rutaceae. Sapindaceae is placed with Nitrariaceae and Biebersteiniaceae as sister to the core Sapindales families, but the relationships between these families remain unclear, likely due to their rapid and ancient ersification. Sapindales families emerged in rapid succession, coincident with the climatic change of the Mid-Cretaceous Hothouse event. Subfamily and tribal relationships within the major families need revision, particularly in Sapindaceae, Rutaceae and Meliaceae. Much of the difficulty in reconstructing relationships at this level may be caused by the prevalence of paralogous loci, particularly in Meliaceae and Rutaceae, that are likely indicative of ancient gene duplication events such as hybridization and polyploidization playing a role in the evolutionary history of these families. This study provides key insights into factors that may affect phylogenetic reconstructions in Sapindales across multiple scales, and provides a state-of-the-art phylogenetic framework for further research.

A five-marker molecular phylogeny of the Styphelieae (Epacridoideae, Ericaceae) supports a broad concept of Styphelia

Publisher: CSIRO Publishing

Date: 2016

DOI: 10.1071/SB14041

Abstract: The Styphelieae is the largest of the seven tribes within the subfamily Epacridoideae Arn. (Ericaceae Juss.). Recent molecular phylogenetic work has resulted in the recircumscription of some genera and the erection of new ones, but several non-monophyletic genera remain. Most of them are concentrated in the well-supported Styphelia–Astroloma clade, which contains species currently assigned to Leucopogon R.Br., Styphelia Sm., Astroloma R.Br., Croninia J.M. Powell and Coleanthera Stschegl. Parsimony and Bayesian analyses of sequence data from four plastid markers (rbcL, matK, trnH–psbA, and atpB–rbcL), and the nuclear ribosomal internal transcribed spacer (ITS) for 207 taxa corroborate the polyphyly of the genera Astroloma, Leucopogon and Styphelia and resolve 12 well supported groups. Of these groups, two can be distinguished by unique morphological features and another six by different character combinations. The remaining groups are morphologically heterogeneous and inconsistent, and not readily distinguishable. A number of species remain ungrouped either because their phylogenetic relationships are not clear or because they do not show strong morphological affinities with the group to which they have a close phylogenetic relationship. Translating the results into a phylogenetic classification is a choice between accepting a single, large genus or at least 12 smaller genera. The first option would result in a heterogeneous assemblage conveying limited morphological information. The multi-generic option would be a better reflection of the morphological ersity of the clade, but would result in many genera lacking readily observable, diagnostic morphological characters. We prioritise the nomenclatural stability inherent in the former approach and advocate expanding Styphelia to include all taxa in the Styphelia–Astroloma clade.

Analysis of the chloroplast genome of a coffee relative from northern Australia

Publisher: International Society for Horticultural Science (ISHS)

Date: 09-2015

DOI: 10.17660/ACTAHORTIC.2015.1101.27

Phylogenetics and evolution of bell frogs (Litoria aurea species-group, Anura : Hylidae) based on mitochondrial ND4 sequences

Publisher: Elsevier BV

Date: 05-2006

DOI: 10.1016/J.YMPEV.2005.11.017

A revision of Lissanthe (Styphelioideae: Ericaceae)

Publisher: CSIRO Publishing

Date: 2003

DOI: 10.1071/SB03014

Abstract: A revision of the styphelioid genus Lissanthe recognises seven species and two subspecies: L. brevistyla A.R.Bean, L. sapida R.Br., L. strigosa (Sm.) R.Br. subsp. strigosa, L. strigosa subsp. subulata (R.Br.) J.M.Powell. New combinations are made for two species transferred from Leucopogon: Lissanthe rubicunda (F.Muell.) J.M.Powell, D.M.Crayn & E.A.Br. and Lissanthe pluriloculata (F.Muell.) J.M.Powell, D.M.Crayn & E.A.Br. Two new species from Western Australia, Lissanthe powelliae D.M.Crayn & E.A.Br. and L. scabra D.M.Crayn & E.A.Br. are described, and Lissanthe sapida is lectotypified. Keys, illustrations and distribution maps are provided for all taxa. Lissanthe as defined here is a strongly supported clade based on analyses of sequence data from two chloroplast loci, the atpB–rbcL intergenic spacer and the matK gene. Potential morphological synapomorphies for Lissanthe include flowers pedicellate above the bracteoles, styles hairy at least at the base, and leaves with an abaxial surface that is grooved longitudinally.

The Sahul–Sunda floristic exchange: dated molecular phylogenies document Cenozoic intercontinental dispersal dynamics

Publisher: Wiley

Date: 09-09-2015

DOI: 10.1111/JBI.12405

A phylogenetic recircumscription of Styphelia (Ericaceae, Epacridoideae, Styphelieae)

Publisher: CSIRO Publishing

Date: 2020

DOI: 10.1071/SB18050

Abstract: The taxonomic limits of Styphelia (Ericaceae, Epacridoideae, Styphelieae) have been contentious since the genus was first described. At one extreme, it has been circumscribed so broadly as to include most epacrids with drupaceous fruit, at the other, to include only those species that also have long-exserted anthers and styles. Recent molecular phylogenetic analyses have indicated that while all previous circumscriptions of Styphelia are non-monophyletic, a large clade (the Astroloma–Styphelia clade) is consistently well supported. This clade comprises Astroloma, in part (i.e. section Stomarrhena sensu Bentham), Coleanthera, Croninia, Leucopogon, in part (i.e. section Pleuranthus sensu Bentham) and Styphelia sensu Bentham. On the basis of those analyses, we here recircumscribe Styphelia phylogenetically to include all species belonging to the Styphelia–Astroloma clade. The 146 taxa occur mostly in Australia, with smaller numbers in New Zealand, New Caledonia (1 species extends to Fiji and Vanuatu) and Malesia. An additional 74 phrase-named taxa belong to this clade, including 70 from Western Australia and 4 from eastern Australia (all other Australian states and territories). The Styphelia floras of Western Australia, eastern Australia, New Caledonia and Malesia are each endemic or nearly so 1 species (S. nesophila (DC.) Sleumer) is shared between New Zealand and eastern Australia, and 2 species (S. cordifolia (Lindl.) F.Muell. and S. woodsii (F.Muell.) F.Muell.) are shared between Western Australia and eastern Australia. An amended diagnosis of Styphelia is provided, new combinations are made for 25 taxa, and new names published for another 9. Lectotypes are designated for two names (Leucopogon brevicuspis Benth. and L. strictus Benth.) found to have taxonomically heterogeneous syntypes.

Diverse fossil epacrids (Styphelioideae; Ericaceae) from early pleistocene sediments at Stony Creek Basin, Victoria, Australia

Publisher: University of Chicago Press

Date: 11-2007

DOI: 10.1086/521686

A molecular estimate of the phylogeny of Styphelieae (Ericaceae)

Publisher: CSIRO Publishing

Date: 2003

DOI: 10.1071/SB03012

Abstract: Parsimony analyses of sequence data derived from two regions of the chloroplast genome, matK and the atpB-rbcL intergenic spacer, separately and together, are reported for Styphelieae. Taxonomic s ling includes representatives of all currently accepted genera apart from the two non-Australian monotypics, Cyathopsis Brongn. & Gris and Decatoca F.Muell., and of all subgenera or informal infrageneric groups except for Trochocarpa subgenus Pseudocyathodes Sleumer. A well resolved estimate of the phylogeny of the tribe is obtained, with high levels of jackknife support for terminal groupings. The results provide support for the current concepts of Acrotriche R.Br., Androstoma Hook.f., Croninia J.M.Powell, Cyathodes Labill. sensu Weiller, Leptecophylla C.M.Weiller, Leucopogon R.Br. sensu Taaffe et al., Pentachondra R.Br., Planocarpa C.M.Weiller and Trochocarpa R.Br., but the following genera appear paraphyletic: Astroloma R.Br., Brachyloma Sond., Cyathodes sensu Labill., Leucopogon R.Br. sensu lato, Lissanthe R.Br., Monotoca R.Br. and Styphelia Sm. (sensu Bentham). Several robust clades are identified as potential new genera but formalisation of nomenclatural changes is left, pending morphological analyses of the various clades to identify synapomorphies with which to characterise generic groupings. The general approach to be adopted in this endeavour is discussed, with narrower generic concepts being favoured as more informative and less disruptive of the existing nomenclature.

Aboriginal medicinal plants of Queensland: ethnopharmacological uses, species diversity, and biodiscovery pathways

Publisher: Springer Science and Business Media LLC

Date: 10-08-2022

DOI: 10.1186/S13002-022-00552-6

Abstract: Aboriginal peoples have occupied the island continent of Australia for millennia. Over 500 different clan groups or nations with distinctive cultures, beliefs, and languages have learnt to live sustainably and harmoniously with nature. They have developed an intimate and profound relationship with the environment, and their use of native plants in food and medicine is largely determined by the environment they lived in. Over 1511 plant species have been recorded as having been used medicinally in Australia. Most of these medicinal plants were recorded from the Aboriginal communities in Northern Territory, New South Wales, South Australia, and Western Australia. Not much has yet been reported on Aboriginal medicinal plants of Queensland. Therefore, the main aim of this review is to collect the literature on the medicinal plants used by Aboriginal peoples of Queensland and critically assess their ethnopharmacological uses. The information used in this review was collected from archival material and uploaded into the Tropical Indigenous Ethnobotany Centre (TIEC) database. Archival material included botanist’s journals/books and old hard copy books. Scientific names of the medicinal plant species were matched against the ‘World Flora Online Plant List’, and ‘Australian Plant Census’ for currently accepted species names to avoid repetition. An oral traditional medical knowledge obtained through interviewing traditional knowledge holders (entered in the TIEC database) has not been captured in this review to protect their knowledge. This review identified 135 species of Queensland Aboriginal medicinal plants, which belong to 103 genera from 53 families, with Myrtaceae being the highest represented plant family. While trees represented the biggest habit, leaves were the most commonly used plant parts. Of 62 different diseases treated by the medicinal plants, highest number of plants are used for treating skin sores and infections. Few plants identified through this review can be found in other tropical countries but many of these medicinal plants are native to Australia. Many of these medicinal plants are also used as bush food by Aboriginal peoples. Through extensive literature review, we found that 135 medicinal plants native to Queensland are used for treating 62 different diseases, especially skin infections. Since these medicinal plants are also used as bush food and are rarely studied using the Western scientific protocols, there is a huge potential for bioprospecting and bush food industry.

Low phylogeographic structure in a wide spread endangered australian frog Litoria aurea (Anura : Hylidae)

Publisher: Springer Science and Business Media LLC

Date: 23-06-2007

DOI: 10.1007/S10592-006-9143-8

Aglaia fellii W.E.Cooper & Joyce (Meliaceae), a new species for Cape York Peninsula

Publisher: Atlas of Living Australia

Date: 19-03-2023

DOI: 10.54102/AJT.P8TO6

Abstract: Aglaia fellii W.E.Cooper & Joyce (Meliaceae) is described from restricted areas of rainforest on Cape York Peninsula, Queensland, Australia. Given the unusual morphological features of the species, including solitary flowers and fruits, a molecular phylogenetic analysis was conducted to confirm its placement within Aglaia prior to formal description. All Australian Aglaia species and eight Australian representatives of closely allied Meliaceae genera were s led, and 353 nuclear loci were sequenced. Maximum likelihood analysis of these loci retrieved A. fellii as nested within Aglaia, most closely related to A. cooperae and A. monticola. This validates its assignment to Aglaia, making it the only Aglaia species with mostly solitary flowers (rarely 3- or 4-flowered) and solitary fruits. A full taxonomic description of Aglaia fellii and notes on its habitat are provided.

Plant DNA Barcodes Can Accurately Estimate Species Richness in Poorly Known Floras

Publisher: Public Library of Science (PLoS)

Date: 11-11-2011

DOI: 10.1371/JOURNAL.PONE.0026841

Will tropical mountaintop plant species survive climate change? Identifying key knowledge gaps using species distribution modelling in Australia

Publisher: Elsevier BV

Date: 11-2015

DOI: 10.1016/J.BIOCON.2015.07.022

Speciation in Howea Palms Occurred in Sympatry, Was Preceded by Ancestral Admixture, and Was Associated with Edaphic and Phenological Adaptation

Publisher: Oxford University Press (OUP)

Date: 18-07-2019

DOI: 10.1093/MOLBEV/MSZ166

Abstract: Howea palms are viewed as one of the most clear-cut cases of speciation in sympatry. The sister species Howea belmoreana and H. forsteriana are endemic to the oceanic Lord Howe Island, Australia, where they have overlapping distributions and are reproductively isolated mainly by flowering time differences. However, the potential role of introgression from Australian mainland relatives had not previously been investigated, a process that has recently put other ex les of sympatric speciation into question. Furthermore, the drivers of flowering time-based reproductive isolation remain unclear. We sequenced an RNA-seq data set that comprehensively s led Howea and their closest mainland relatives (Linospadix, Laccospadix), and collected detailed soil chemistry data on Lord Howe Island to evaluate whether secondary gene flow had taken place and to examine the role of soil preference in speciation. D-statistics analyses strongly support a scenario whereby ancestral Howea hybridized frequently with its mainland relatives, but this only occurred prior to speciation. Expression analysis, population genetic and phylogenetic tests of selection, identified several flowering time genes with evidence of adaptive ergence between the Howea species. We found expression plasticity in flowering time genes in response to soil chemistry as well as adaptive expression and sequence ergence in genes pleiotropically linked to soil adaptation and flowering time. Ancestral hybridization may have provided the genetic ersity that promoted their subsequent adaptive ergence and speciation, a process that may be common for rapid ecological speciation.

The genetic origin of evolidine, the first cyclopeptide discovered in plants, and related orbitides

Publisher: Cold Spring Harbor Laboratory

Date: 12-06-2020

DOI: 10.1101/2020.06.10.145326

Abstract: Cyclic peptides are reported to have antibacterial, antifungal and other bioactivities. Several genera of the Rutaceae family are known to produce orbitides, which are small head-to-tail cyclic peptides composed of proteinogenic amino acids and lacking disulfide bonds. Melicope xanthoxyloides is an Australian rain forest tree of the Rutaceae family in which evolidine - the first plant cyclic peptide - was discovered. Evolidine (cyclo-SFLPVNL) has subsequently been all but forgotten in the academic literature, but here we use tandem mass spectrometry to rediscover evolidine and using de novo transcriptomics we show its biosynthetic origin to be from a short precursor just 48 residues in length. In all, seven M. xanthoxyloides orbitides were found and they had atypically erse C-termini consisting of residues not recognized by either of the known proteases plants use to macrocyclize peptides. Two of the novel orbitides were studied by nuclear magnetic resonance spectroscopy and although one had definable structure, the other did not. By mining RNA-seq and whole genome sequencing data from other species, it was apparent that a large and erse family of peptides is encoded by sequences like these across the Rutaceae.

Plant Secondary Metabolites Produced in Response to Abiotic Stresses Has Potential Application in Pharmaceutical Product Development

Publisher: MDPI AG

Date: 05-01-2022

DOI: 10.3390/MOLECULES27010313

Abstract: Plant secondary metabolites (PSMs) are vital for human health and constitute the skeletal framework of many pharmaceutical drugs. Indeed, more than 25% of the existing drugs belong to PSMs. One of the continuing challenges for drug discovery and pharmaceutical industries is gaining access to natural products, including medicinal plants. This bottleneck is heightened for endangered species prohibited for large s le collection, even if they show biological hits. While cultivating the pharmaceutically interesting plant species may be a solution, it is not always possible to grow the organism outside its natural habitat. Plants affected by abiotic stress present a potential alternative source for drug discovery. In order to overcome abiotic environmental stressors, plants may mount a defense response by producing a ersity of PSMs to avoid cells and tissue damage. Plants either synthesize new chemicals or increase the concentration (in most instances) of existing chemicals, including the prominent bioactive lead compounds morphine, c tothecin, catharanthine, epicatechin-3-gallate (EGCG), quercetin, resveratrol, and kaempferol. Most PSMs produced under various abiotic stress conditions are plant defense chemicals and are functionally anti-inflammatory and antioxidative. The major PSM groups are terpenoids, followed by alkaloids and phenolic compounds. We have searched the literature on plants affected by abiotic stress (primarily studied in the simulated growth conditions) and their PSMs (including pharmacological activities) from PubMed, Scopus, MEDLINE Ovid, Google Scholar, Databases, and journal websites. We used search keywords: “stress-affected plants,” “plant secondary metabolites, “abiotic stress,” “climatic influence,” “pharmacological activities,” “bioactive compounds,” “drug discovery,” and “medicinal plants” and retrieved published literature between 1973 to 2021. This review provides an overview of variation in bioactive phytochemical production in plants under various abiotic stress and their potential in the biodiscovery of therapeutic drugs. We excluded studies on the effects of biotic stress on PSMs.

Phylogeny, adaptive radiation, and historical biogeography in Bromeliaceae: Insights from an eight-locus plastid phylogeny

Publisher: Wiley

Date: 05-2011

DOI: 10.3732/AJB.1000059

Abstract: Bromeliaceae form a large, ecologically erse family of angiosperms native to the New World. We use a bromeliad phylogeny based on eight plastid regions to analyze relationships within the family, test a new, eight-subfamily classification, infer the chronology of bromeliad evolution and invasion of different regions, and provide the basis for future analyses of trait evolution and rates of ersification. We employed maximum-parsimony, maximum-likelihood, and Bayesian approaches to analyze 9341 aligned bases for four outgroups and 90 bromeliad species representing 46 of 58 described genera. We calibrate the resulting phylogeny against time using penalized likelihood applied to a monocot-wide tree based on plastid ndhF sequences and use it to analyze patterns of geographic spread using parsimony, Bayesian inference, and the program S-DIVA. Bromeliad subfamilies are related to each other as follows: (Brocchinioideae, (Lindmanioideae, (Tillandsioideae, (Hechtioideae, (Navioideae, (Pitcairnioideae, (Puyoideae, Bromelioideae))))))). Bromeliads arose in the Guayana Shield ca. 100 million years ago (Ma), spread centrifugally in the New World beginning ca. 16-13 Ma, and dispersed to West Africa ca. 9.3 Ma. Modern lineages began to erge from each other roughly 19 Ma. Nearly two-thirds of extant bromeliads belong to two large radiations: the core tillandsioids, originating in the Andes ca. 14.2 Ma, and the Brazilian Shield bromelioids, originating in the Serro do Mar and adjacent regions ca. 9.1 Ma.

An updated estimate of intergeneric phylogenetic relationships in the Australian Vitaceae

Publisher: Canadian Science Publishing

Date: 08-2007

DOI: 10.1139/B07-022

Abstract: Previous molecular studies have suggested that the genus Cissus (Vitaceae) is not monophyletic. The majority of species are grouped, but four Australian taxa ( Cissus antarctica Vent., Cissus hypoglauca A. Gray, Cissus oblonga (Benth.) Planch., and Cissus sterculiifolia (F. Muell. ex Benth.) Planch.) form a distinct clade and Cissus opaca has now been recognized as belonging to the genus Clematicissus ( Clematicissus opaca (F. Muell.) Jackes & Rossetto). Here, we investigate relationships among the Australian Vitaceae by parsimony and Bayesian analysis of plastid trnL-trnF and nuclear internal transcribed spacer sequences and include a range of taxa that had not been previously investigated. We find no support for a close relationship between Nothocissus and the four distinct Australian Cissus, as suggested in previous morphology-based treatments. We find a robust sister relationship between Clematicissus and at least two southern American Cissus ( Cissus tweediana (Baker) Planch. and Cissus striata Ruiz & Pav.), suggesting a possible origin from an ancient southern progenitor. Finally, this study confirms the paraphyletic nature of Cayratia , with species occurring in two clades, both with Australian and non-Australian species. The necessity in future studies for data from additional and more tractable nuclear loci is also noted.

HybPhaser: A workflow for the detection and phasing of hybrids in target capture data sets

Publisher: Wiley

Date: 07-2021

DOI: 10.1002/APS3.11441

Abstract: Hybrids contain ergent alleles that can confound phylogenetic analyses but can provide insights into reticulated evolution when identified and phased. We developed a workflow to detect hybrids in target capture data sets and phase reads into parental lineages using a similarity and phylogenetic framework. We used Angiosperms353 target capture data for Nepenthes , including known hybrids to test the novel workflow. Reference mapping was used to assess heterozygous sites across the data set and to detect hybrid accessions and paralogous genes. Hybrid s les were phased by mapping reads to multiple references and sorting reads according to similarity. Phased accessions were included in the phylogenetic framework. All known Nepenthes hybrids and nine additional s les had high levels of heterozygous sites, had reads associated with multiple ergent clades, and were phased into accessions resembling ergent haplotypes. Phylogenetic analysis including phased accessions increased clade support and confirmed parental lineages of hybrids. HybPhaser provides a novel approach to detect and phase hybrids in target capture data sets, which can provide insights into reticulations by revealing origins of hybrids and reduce conflicting signal, leading to more robust phylogenetic analyses.

Phylogeny of Acronychia (Rutaceae) and First Insights into Its Historical Biogeography and the Evolution of Fruit Characters

Publisher: Public Library of Science (PLoS)

Date: 24-08-2015

DOI: 10.1371/JOURNAL.PONE.0136296

Sunlight and red to far-red ratio impact germination of tropical montane cloud forest species

Publisher: CSIRO Publishing

Date: 2023

DOI: 10.1071/BT22126

Genome skimming provides well resolved plastid and nuclear phylogenies, showing patterns of deep reticulate evolution in the tropical carnivorous plant genus Nepenthes (Caryophyllales)

Publisher: CSIRO Publishing

Date: 2019

DOI: 10.1071/SB18057

Abstract: Nepenthes is a genus of carnivorous plants consisting of ~160 species that are distributed in the paleotropics. Molecular systematics has so far not been able to resolve evolutionary relationships of most species because of the limited genetic ergence in previous studies. In the present study, we used a genome-skimming approach to infer phylogenetic relationships on the basis of 81 plastid genes and the highly repetitive rRNA (external transcribed spacer (ETS)–26S) for 39 accessions representing 34 species from eight sections. Maximum-likelihood analysis and Bayesian inference were performed separately for the nuclear and the plastid datasets. Divergence-time estimations were conducted on the basis of a relaxed molecular-clock model, using secondary calibration points. The phylogenetic analyses of the nuclear and plastid datasets yielded well resolved and supported phylogenies. Incongruences between the two datasets were detected, suggesting multiple hybridisation events or incomplete lineage sorting in the deeper and more recent evolutionary history of the genus. The inclusion of several known and suspected hybrids in the phylogenetic analysis provided insights into their parentage. Divergence-time estimations placed the crown ersification of Nepenthes in the early Miocene, c. 20 million years ago. This study showed that genome skimming provides well resolved nuclear and plastid phylogenies that provide valuable insights into the complex evolutionary relationships of Nepenthes.

Australia lacks stem succulents but is it depauperate in plants with crassulacean acid metabolism (CAM)?

Publisher: Elsevier BV

Date: 06-2016

DOI: 10.1016/J.PBI.2016.03.018

Abstract: In the flora of Australia, the driest vegetated continent, crassulacean acid metabolism (CAM), the most water-use efficient form of photosynthesis, is documented in only 0.6% of native species. Most are epiphytes and only seven terrestrial. However, much of Australia is unsurveyed, and carbon isotope signature, commonly used to assess photosynthetic pathway ersity, does not distinguish between plants with low-levels of CAM and C3 plants. We provide the first census of CAM for the Australian flora and suggest that the real frequency of CAM in the flora is double that currently known, with the number of terrestrial CAM species probably 10-fold greater. Still unresolved is the question why the large stem-succulent life - form is absent from the native Australian flora even though exotic large cacti have successfully invaded and established in Australia.

HybPhaser identifies hybrid evolution in Australian Thelypteridaceae

Publisher: Elsevier BV

Date: 08-2022

DOI: 10.1016/J.YMPEV.2022.107526

Abstract: Hybridisation has been proposed to play an important role in fern evolution, but has been difficult to investigate. This study explores the utility of target sequence capture and read-to-reference phasing of putative hybrids to investigate the role of evolutionary reticulation in ferns using Australian Thelypteridaceae as a model. The bioinformatics workflow HybPhaser was used to assess ergence between alleles, phase sequence reads to references and construct accessions resembling parental haplotypes. These accessions were included in phylogenetic and network analyses to detect hybrids and infer their parentage. This approach identified two novel hybrid lineages in Thelypteridaceae, one occurring between two different genera (Abacopteris and Christella), and another as part of a complex of Christella. In addition, hybrid phasing successfully reduced conflicting data and improved overall resolution in the Thelypteridaceae phylogeny, highlighting the power of this approach for reconstructing evolutionary history in reticulated lineages.

Genomic insights into rapid speciation within the world’s largest tree genus

Publisher: Research Square Platform LLC

Date: 22-10-2021

DOI: 10.21203/RS.3.RS-969304/V1

Abstract: Species radiations have long fascinated biologists, but the contribution of adaptation to observed ersity and speciation is still an open question. Here, we explore this question using the clove genus, Syzygium, the world’s largest genus of tree species comprising approximately 1200 species. We dissect Syzygium ersity through shotgun sequencing of 182 distinct species and 58 additional as-yet unidentified taxa, and assess their genetic ersity against a chromosome-level reference genome of the sea apple, Syzygium grande. We show that Syzygium grande shares a whole genome duplication (WGD) event with other Myrtales. Genomic analyses confirm that Syzygium originated in Sahul (Australia-New Guinea), and later ersified eastward to the Hawaiian Islands and westward in multiple independent migration events. The migrations were associated with bursts of speciation events, visible by poorly resolved branches on phylogenies and networks, some of which were likely confounded by incomplete lineage sorting. Clinal genomic variation in some sublineages follows phylogenetic progression, which coupled with sympatric occurrences of distantly related species suggests that both geographic and ecological speciation have been important in the ersification of Syzygium. Together, these results point to a mixture of both neutral and adaptive drivers having contributed to the radiation of the genus.

Identifying evolutionary lineages in the Elaeocarpus obovatus complex: population genetics and morphometric analyses support a new subspecies, Elaeocarpus obovatus subsp. umbratilis, from northern Queensland, Australia

Publisher: CSIRO Publishing

Date: 2020

DOI: 10.1071/SB18054

Abstract: With the aim to solve long-standing problems of taxonomic delimitation within the E. obovatus species complex (E. obovatus G.Don, E. arnhemicus F.Muell., E. sp. Mt Bellenden Ker (L.J.Brass 18336) Qld Herbarium and E. coorangooloo J.F.Bailey & C.T.White), ersity and relatedness were assessed using a combined population genetics and morphometric approach among 181 and 102 in iduals respectively. Simple sequence-repeat (SSR) markers were analysed with clustering methods, analysis of molecular variance (AMOVA) and STRUCTURE. The morphometric data were analysed using cluster and classification and regression tree (CART) methods. The morphometric and genetic analyses together resolve discrete groups corresponding to E. arnhemicus, E. coorangooloo, E. obovatus and E. sp. Mt Bellenden Ker. Elaeocarpus arnhemicus is clearly distinct from all other entities on most of the morphometric and genetic analyses. By contrast, E. sp. Mt Bellenden Ker and E. obovatus were not clearly separated from each other in many morphometric analyses, but can be distinguished clearly by the strongly curved pedicels in early bud and hairy ovary, and, to a lesser extent, by the frequent occurrence of two racemes per axil and cuneate leaf bases, and on the results of the genetic analyses. Elaeocarpus coorangooloo exhibits considerable genetic admixture with the other entities, but it is morphologically distinct. SSR profiles suggested that E. arnhemicus and E. obovatus may be tetraploid, whereas the other entities are diploid. This study has clarified the taxonomic limits of the currently recognised species E. arnhemicus, E. obovatus and E. coorangooloo and supports recognition of E. sp. Mt Bellenden Ker at subspecies rank, described herein as E. obovatus subsp. umbratilis Y.Baba & Crayn. A key to all taxa and revised accounts of E. arnhemicus, E. obovatus subsp. obovatus and E. coorangooloo are provided.

Fruit developmental biology and endosperm rumination in Elaeocarpus ruminatus (Elaeocarpaceae), and its taxonomic significance

Publisher: CSIRO Publishing

Date: 2018

DOI: 10.1071/SB18010

Abstract: The genus Elaeocarpus is the largest genus in the family Elaeocarpaceae, comprising more than 350 species of trees and shrubs with a mainly Indo-Pacific distribution. Approximately 28 species in the genus, including nine species from Australia, are known to possess ruminate endosperm. To provide a basis for understanding fruit development and endosperm rumination in the genus and, therefore, its taxonomic and evolutionary significance, we studied the fruit anatomy of Elaeocarpus ruminatus F.Muell. at different developmental phases (petal-fall to maturity). We found lignin in pericarp and ovary wall tissues in the earliest stages of development. In contrast, endosperm rumination occurs only after fruits have fully expanded, and becomes more pronounced as fruits ripen. Its phylogenetic distribution suggests that ruminate endosperm is a derived, albeit homoplasious character in Elaeocarpus. Comparative studies on related species will be instructive in determining the utility of ruminate endosperm for informing infra-generic taxonomy of the genus, and gaining insight into its adaptive significance.

Antioxidant and Anti-Inflammatory Activities of Endemic Plants of the Australian Wet Tropics

Publisher: MDPI AG

Date: 26-09-2022

DOI: 10.3390/PLANTS11192519

Abstract: Plants have been a vital source of natural antioxidants since ancient times. Plants growing under various abiotic stress conditions often produce more defensive secondary metabolites such as phenolics, flavonoids, and terpenoids during adaptation to the environment. Many of these secondary metabolites are known to possess antioxidant and anti-inflammatory properties. This study tested seven plants sourced from the mountaintop areas (above 1000 m elevation) of Mount Lewis National Park (falls under the Wet Tropics of Queensland), Australia, for their antioxidant and anti-inflammatory activities. Of the seven studied plants, hydroethanolic extracts of six plants (Leptospermum wooroonooran, Ceratopetalum hylandii, Linospadix apetiolatus, Garcinia brassii, Litsea granitica, and Polyscias willmottii) showed high 2,2-diphenyl-1-picrylhydrazyl (DPPH)-free radical scavenging activity in a dose-dependent (25–1000 μg/mL) manner. At the highest concentration of 1 mg/mL, the DPPH free radical scavenged percentage varied between 75.4% and 92.3%. Only the species Alyxia orophila was inactive in the DPPH free radical scavenging assay. Pseudo-IC50 values of the extracts’ ferric reducing antioxidant power (FRAP) based on dose-response curves showed a significant positive correlation with total phenolic content. Five out of the seven plants, namely G. brassii, C. hylandii, L. apetiolatus, L. wooroonooran, and A. orophila, showed inhibitory effects on the secretion of proinflammatory cytokines, tumour necrosis factor (TNF), and interleukins (IL)-23 in a lipopolysaccharide (LPS)-stimulated human peripheral blood mononuclear cells (PBMCs) assay. The results of this study demonstrate the value of tropical mountaintop plants in the biodiscovery of antioxidant and anti-inflammatory lead compounds.

Elaeocarpus hylobroma (Elaeocarpaceae): a new species endemic to mountain tops in northeast Queensland, Australia

Publisher: Springer Science and Business Media LLC

Date: 22-09-2012

DOI: 10.1007/S12225-012-9398-9

ROSID AFFINITIES OF SURIANACEAE - MOLECULAR EVIDENCE

Publisher: Elsevier BV

Date: 12-1993

DOI: 10.1006/MPEV.1993.1034

Abstract: Nucleotide sequences of the chloroplast gene, rbcL, were obtained for Suriana maritima, Cadellia pentastylis, Guilfoylia monostylis, Stylobasium australe, Quassia amara, Brucea mollis, Cupaniopsis anacardioides, Mangifera indica, Connarus conchocarpus, and Comesperma ericinum. Phylogenetic analyses of these, along with published sequences of representatives of rosid families, support the monophyly of the Surianaceae sensu Cronquist and provide evidence of an affinity with the Polygalaceae and Fabaceae. These conclusions are discussed in the light of available morphological data.

Checklist of the vascular flora of the Sunda-Sahul Convergence Zone

Publisher: Pensoft Publishers

Date: 18-05-2020

DOI: 10.3897/BDJ.8.E51094

Abstract: Background The Sunda-Sahul Convergence Zone, defined here as the area comprising Australia, New Guinea, and Southeast Asia (Indonesia to Myanmar), straddles the Sunda and Sahul continental shelves and is one of the most biogeographically famous and important regions in the world. Floristically, it is thought to harbour a large amount of the world’s ersity. Despite the importance of the area, a checklist of the flora has never before been published. Here we present the first working checklist of vascular plants for the Sunda-Sahul Convergence Zone. The list was compiled from 24 flora volumes, online databases and unpublished plot data. Taxonomic nomenclature was updated, and each species was coded into nested biogeographic regions. The list includes 60,415 species in 5,135 genera and 363 families of vascular plants. New information This is the first species-level checklist of the region and presents an updated census of the region’s floristic bio ersity. The checklist confirms that species richness of the SSCZ is comparable to that of the Neotropics, and highlights areas in need of further documentation and taxonomic work. This checklist provides a novel dataset for studying floristic ecology and evolution in this biogeographically important region of very high global bio ersity.

A reappraisal of the generic concepts of Epacris, Rupicola and Budawangia (Ericaceae, Epacridoideae, Epacrideae) based on phylogenetic analysis of morphological and molecular data

Publisher: CSIRO Publishing

Date: 2015

DOI: 10.1071/SB13009

Abstract: The genus Epacris Cav. (Ericaceae, Epacridoideae, Epacrideae) contains 46 species in south-eastern Australia and two species in New Zealand. Two small genera, Rupicola Maiden & Betche (four spp.) and Budawangia I.Telford (monotypic), both having restricted distributions in the mountains of central eastern New South Wales, have been generally regarded as closely related to but distinct from Epacris. We tested the monophyly and relationships of these three genera using parsimony and Bayesian analysis of morphological and plastid atpB–rbcL DNA sequence datasets. Separate and combined analyses all place Budawangia and Rupicola within Epacris with moderate to strong support. We conclude that there are insufficient grounds for maintaining Rupicola and Budawangia as distinct from Epacris. The required nomenclatural changes are made herein.

Contrasting levels of connectivity and localised persistence characterise the latitudinal distribution of a wind-dispersed rainforest canopy tree

Publisher: Springer Science and Business Media LLC

Date: 06-2014

DOI: 10.1007/S10709-014-9771-8

Abstract: Contrasting signals of genetic ergence due to historic and contemporary gene flow were inferred for Coachwood, Ceratopetalum apetalum (Cunoniaceae), a wind-dispersed canopy tree endemic to eastern Australian warm temperate rainforest. Analysis of nine nuclear microsatellites across 22 localities revealed two clusters between northern and southern regions and with vicariance centred on the wide Hunter River Valley. Within populations ersity was high indicating a relatively high level of pollen dispersal among populations. Genetic variation was correlated to differences in regional biogeography and ecology corresponding to IBRA regions, primary factors being soil type and rainfall. Eleven haplotypes were identified by chloroplast microsatellite analysis from the same 22 localities. A lack of chloroplast ersity within sites demonstrates limited gene flow via seed dispersal. Network representation indicated regional sharing of haplotypes indicative of multiple Pleistocene refugia as well as deep ergences between regional elements of present populations. Chloroplast differentiation between sites in the upper and lower sections of the northern population is reflective of historic vicariance at the Clarence River Corridor. There was no simple vicariance explanation for the distribution of the ergent southern chlorotype, but its distribution may be explained by the effects of drift from a larger initial gene pool. Both the Hunter and Clarence River Valleys represent significant dry breaks within the species range, consistent with this species being rainfall dependent rather than cold-adapted.

Plants will cross the lines: climate and available land mass are the major determinants of phytogeographical patterns in the Sunda–Sahul Convergence Zone

Publisher: Oxford University Press (OUP)

Date: 17-12-2020

DOI: 10.1093/BIOLINNEAN/BLAA194

Abstract: The Miocene convergence of the Sunda shelf, Sahul shelf and Wallacea facilitated the exchange of previously isolated floras across the Sunda–Sahul Convergence Zone (SSCZ). The SSCZ is a hotspot of biogeographical research however, phytogeographical patterns across the region remain poorly understood. We conducted multivariate analysis on a comprehensive species checklist of SSCZ vascular plants to quantify the extent of exchange, characterize phytogeographical patterns and investigate their abiotic drivers. We found that Lydekker’s and Wallace’s Lines are not reflected in floristic composition at any taxonomic level, with 46% of genera distributed across these biogeographical lines. In contrast, environment is significantly correlated with floristic composition, with annual rainfall and seasonality being the strongest correlates. Mainland Asia, Borneo, the Philippines, New Guinea and Australia were major routes of exchange throughout the Cenozoic, possibly because these areas have been persistent landmasses throughout the entire period of convergence. We conclude that Sunda–Sahul floristic exchange has substantially influenced the assembly of the regional flora and that modern phytogeographical patterns have been influenced more by environmental variables and available landmass (i.e. establishment conditions) than by putative barriers to movement such as Wallace’s and Lydekker’s Lines (i.e. vagility).

Multiple origins of crassulacean acid metabolism and the epiphytic habit in the Neotropical family Bromeliaceae

Publisher: Proceedings of the National Academy of Sciences

Date: 24-02-2004

DOI: 10.1073/PNAS.0400366101

Abstract: The large Neotropical family Bromeliaceae presents an outstanding ex le of adaptive radiation in plants, containing a wide range of terrestrial and epiphytic life-forms occupying many distinct habitats. Diversification in bromeliads has been linked to several key innovations, including water- and nutrient-impounding phytotelmata, absorptive epidermal trichomes, and the water-conserving mode of photosynthesis known as crassulacean acid metabolism (CAM). To clarify the origins of CAM and the epiphytic habit, we conducted a phylogenetic analysis of nucleotide sequences for 51 bromeliad taxa by using the plastid loci matK and the rps16 intron, combined with a survey of photosynthetic pathway determined by carbon-isotope ratios for 1,873 species representing 65% of the family. Optimization of character-states onto the strict consensus tree indicated that the last common ancestor of Bromeliaceae was a terrestrial C 3 mesophyte, probably adapted to moist, exposed, nutrient-poor habitats. Both CAM photosynthesis and the epiphytic habit evolved a minimum of three times in the family, most likely in response to geological and climatic changes in the late Tertiary. The great majority of epiphytic forms are now found in two lineages: in subfamily Tillandsioideae, in which C 3 photosynthesis was the ancestral state and CAM developed later in the most extreme epiphytes, and in subfamily Bromelioideae, in which CAM photosynthesis predated the appearance of epiphytism. Subsequent radiation of the bromelioid line into less xeric habitats has led to reversion to C 3 photosynthesis in some taxa, showing that both gain and loss of CAM have occurred in the complex evolutionary history of this family.

Plastid phylogenomics clarifies broad-level relationships inBulbophyllum(Orchidaceae) and provides insights into range evolution of Australasian sectionAdelopetalum

Publisher: Cold Spring Harbor Laboratory

Date: 25-07-2022

DOI: 10.1101/2022.07.24.500920

Abstract: The hyper erse orchid genus Bulbophyllum is the second largest genus of flowering plants and exhibits a pantropical distribution with a center of ersity in tropical Asia. The only Bulbophyllum section with a center of ersity in Australasia is sect. Adelopetalum . However, phylogenetic placement, interspecific relationships, and spatio-temporal evolution of the section have remained largely unclear. To infer broad-level relationships within Bulbophyllum and interspecific relationships within sect. Adelopetalum , a genome skimming dataset was generated for 89 s les, yielding 70 plastid coding regions and the nuclear ribosomal DNA cistron. For 18 additional s les, Sanger data from two plastid loci ( mat K, ycf 1) and nuclear ITS were added using a supermatrix approach. The study provided new insights into broad-level relationships in Bulbophyllum , including phylogenetic evidence for the non-monophyly of sections Beccariana, Brachyantha, Brachypus, Cirrhopetaloides, Cirrhopetalum, Desmosanthes, Minutissima, Oxysepala, Polymeres and Sestochilos . Section Adelopetalum and sect. Minutissima s . s . formed a highly supported clade that was resolved in sister group position to the remainder of the genus. Divergence time estimations based on a relaxed molecular clock model placed the origin of Bulbophyllum in the early Oligocene (ca. 33.2 Ma) and of sect. Adelopetalum in the late Oligocene (ca. 23.6 Ma). Ancestral range estimations based on a BAYAREALIKE model identified the Australian continent as ancestral area of sect. Adelopetalum . The section underwent crown ersification during the mid-Miocene to the late Pleistocene, predominantly in continental Australia. At least two independent long-distance dispersal events were inferred eastwards from the Australian continent to New Zealand, and New Caledonia from the early Pliocene onwards, likely mediated by the predominantly westerly winds of the southern hemisphere. Retraction and fragmentation of eastern Australian rainforests from the early Miocene onwards are discussed as likely drivers of lineage ergence within sect. Adelopetalum , facilitating allopatric speciation.

Molecular phylogeography reveals two geographically and temporally separated floristic exchange tracks between Southeast Asia and northern Australia

Publisher: Wiley

Date: 28-02-2021

DOI: 10.1111/JBI.14072

Seed banking is more applicable to the preservation of tropical montane flora than previously assumed: A review and cloud forest case study

Publisher: Elsevier BV

Date: 11-2023

DOI: 10.1016/J.GECCO.2023.E02627

Leucopogon extremus (Styphelieae, Styphelioideae, Ericaceae), a remarkable new species that expands the morphological circumscription of Leucopogon sens. str

Publisher: CSIRO Publishing

Date: 2012

DOI: 10.1071/SB11033

Abstract: Leucopogon extremus Hislop & Puente-Lelievre, a new species of Leucopogon s. str. with a remarkably anomalous morphology, is described, illustrated and its distribution mapped. Its placement within the genus is confirmed through phylogenetic analyses of the plastid rbcL, matK, atpB–rbcL and trnH–psbA sequences.

Photosynthetic pathways in Bromeliaceae: phylogenetic and ecological significance of CAM and C₃based on carbon isotope ratios for 1893 species

Publisher: Oxford University Press (OUP)

Date: 03-05-2015

DOI: 10.1111/BOJ.12275

Understanding seed dormancy and germination aids conservation of rainforest species from tropical montane cloud forest: a case study confirming morphophysiological dormancy in the genus

Publisher: CSIRO Publishing

Date: 09-2022

DOI: 10.1071/BT22011

Abstract: Context Seed dormancy is one issue hindering implementation of conservation actions for rainforest species. Aims We studied dormancy and germination in Tasmannia sp. Mt Bellenden Ker and Tasmannia membranea, two tropical montane rainforest species threatened by climate change, to develop a better understanding of dormancy in the species and the genus. Methods Dormancy was classified for T. sp. Mt Bellenden Ker on the basis of an imbibition test, analysis of embryo to seed length (E:S) ratios and germination in response to the following four dormancy-breaking treatments: (1) scarification of the seedcoat near the micropylar end (2) removal of the seedcoat (3) application of 100 mg L−1 or (4) 500 mg L−1 gibberellic acid. The most effective treatment was then tested on T. membranea. The requirement for light for germination was also assessed. Key results Both scarified and intact seeds imbibed water. Initial E:S ratios were .22 for both species and increased up to 0.74 after 40 days, just before radicle emergence, for T. sp. Mt Bellenden Ker. Germination proportions were significantly higher in Treatments 1 and 2 than the remaining treatments for T. sp. Mt Bellenden Ker T. membranea responded similarly well to Treatment 1. Germination under alternating light/dark conditions was slightly, but not significantly, greater than germination in the dark alone. Conclusions Both species have morphophysiological dormancy and treatments that remove seedcoat resistance to embryo growth facilitate germination. These treatments may improve germination in other species from the genus Tasmannia. Implications This knowledge will aid the germination of seeds to implement conservation strategies for Tasmannia spp.

Hibiscus diversifolius subsp. rivularis  (Bremek. & Oberm.) Exell (Malvaceae) in Australia

Publisher: Biodiversity Heritage Library

Date: 2017

DOI: 10.5962/P.299893

Evolution of Geosiris (Iridaceae): historical biogeography and plastid-genome evolution in a genus of non-photosynthetic tropical rainforest herbs disjunct across the Indian Ocean

Publisher: CSIRO Publishing

Date: 2018

DOI: 10.1071/SB18028

Abstract: Mycoheterotrophs, i.e. plants that acquire carbon from root-associated soil fungi, often have highly degraded plastomes, reflecting relaxed selective constraints on plastid genes following the loss of photosynthesis. Geosiris Baill. is the only mycoheterotrophic genus in Iridaceae and comprises two species in Madagascar and nearby islands, and a third recently discovered species in north-eastern Australia. Here, we characterise the plastomes of the Australian and one Madagascan species to compare patterns of plastome degradation in relation to autotrophic and other mycoheterotrophic taxa and investigate the evolutionary and biogeographical history of the genus in Iridaceae. Both examined species have lost approximately half their plastid-encoded genes and a small but significant reduction in purifying selection in retained non-photosynthetic genes was observed. Geosiris is confirmed as monophyletic, with initial ergence of the genus occurring c. 53 million years ago, and subsequent ersification occurring c. 30 million years ago. Africa (including Madagascar) is reconstructed as the most likely ancestral area of the genus, implying a major range-expansion event of one lineage to Australia after its ergence in the Oligocene. Our study has highlighted the dynamic evolutionary history of Geosiris, contributed to the characterisation of mycoheterotrophic plastomes, and furthered our understanding of plastome structure and function.

Temperature, nutrient availability, and species traits interact to shape elevation responses of Australian tropical trees

Publisher: Frontiers Media SA

Date: 19-01-2023

DOI: 10.3389/FFGC.2023.1089167

Abstract: Elevation gradients provide natural laboratories for investigating tropical tree ecophysiology in the context of climate warming. Previously observed trends with increasing elevation include decreasing stem diameter growth rates (GR), increasing leaf mass per area (LMA), higher root-to-shoot ratios (R:S), increasing leaf δ 13 C, and decreasing leaf δ 15 N. These patterns could be driven by decreases in temperature, lower soil nutrient availability, changes in species composition, or a combination thereof. We investigated whether these patterns hold within the genus Flindersia (Rutaceae) along an elevation gradient (0–1,600 m) in the Australian Wet Tropics. Flindersia species are relatively abundant and are important contributors to biomass in these forests. Next, we conducted a glasshouse experiment to better understand the effects of temperature, soil nutrient availability, and species on growth, biomass allocation, and leaf isotopic composition. In the field, GR and δ 15 N decreased, whereas LMA and δ 13 C increased with elevation, consistent with observations on other continents. Soil C:N ratio also increased and soil δ 15 N decreased with increasing elevation, consistent with decreasing nutrient availability. In the glasshouse, relative growth rates (RGR) of the two lowland Flindersia species responded more strongly to temperature than did those of the two upland species. Interestingly, leaf δ 13 C displayed an opposite relationship with temperature in the glasshouse compared with that observed in the field, indicating the importance of covarying drivers in the field. Leaf δ 15 N increased in nutrient-rich compared to nutrient-poor soil in the glasshouse, like the trend in the field. There was a significant interaction for δ 15 N between temperature and species upland species showed a steeper increase in leaf δ 15 N with temperature than lowland species. This could indicate more flexibility in nitrogen acquisition in lowland compared to upland species with warming. The distinguishing feature of a mountaintop restricted Flindersia species in the glasshouse was a very high R:S ratio in nutrient-poor soil at low temperatures, conditions approximating the mountaintop environment. Our results suggest that species traits interact with temperature and nutrient availability to drive observed elevation patterns. Capturing this complexity in models will be challenging but is important for making realistic predictions of tropical tree responses to global warming.

Plant systematics and biogeography in the Australasian tropics

Publisher: CSIRO Publishing

Date: 2018

DOI: 10.1071/SBV31N6_ED

Supermatrices, supertrees and serendipitous scaffolding: Inferring a well-resolved, genus-level phylogeny of Styphelioideae (Ericaceae) despite missing data

Publisher: Elsevier BV

Date: 2012

DOI: 10.1016/J.YMPEV.2011.09.011

Abstract: For the predominantly southern hemisphere plant group Styphelioideae (Ericaceae) published sequence datasets of five markers are now available for all except one of the 38 recognised genera. However, several markers are highly incomplete therefore missing data is problematic for producing a genus level phylogeny. We explore the relative utility of supertree and supermatrix approaches for addressing this challenge, and examine the effects of missing data on tree topology and resolution. Although the supertree approach returned a more conservative hypothesis, overall, both supermatrix and supertree analyses concurred in the topologies they returned. Using multiple genes and a dataset of variably complete taxa we found improved support for the monophyly and position of the tribes and genus level relationships. However, there was mixed support for the Richeeae tribe appearing one node basal to the Cosmelieae tribe or vice versa. It is probable that this will only be resolved through further sequencing. Our study supports previous findings that the amount of data is more critical than the completeness of the dataset in estimating well-resolved trees. Our results suggest that a "serendipitous" scaffolding approach that includes a mixture of well and poorly sequenced taxa can lead to robust phylogenetic hypotheses.

Taxonomic recircumscriptions in the Aglaia elaeagnoidea complex (Meliaceae)

Publisher: Naturalis Biodiversity Center

Date: 18-08-2023

DOI: 10.3767/BLUMEA.2023.68.01.02

Abstract: Aglaia is the most widespread and species-rich genus in Meliaceae , comprising 124 species. Aglaia elaeagnoidea has presented along standing dilemma for taxonomists it is highly morphologically and ecologically variable, and has a range extending across India, South east Asia, Australia and islands of the western Pacific Ocean. Previous work has examined molecular variation in the eastern part of the species 'range however, molecular variation in the western half of its distribution remained uncharacterised, precluding taxonomic resolution of the complex. In this study, we used DArT-seq analysis to investigate genetic structure in A. elaeagnoidea from India, Sri Lanka, Bangladesh, Thailand, Java and Bali. Wefind a strong genetic disjunction between Sri Lanka and Bangladesh, suggesting that western A. elaeagnoidea comprises two taxa. On the basis of these results, in combination with morphology and previous molecular work on eastern A. elaeagnoidea , we resolve A. elaeagnoidea into three species, retaining A. elaeagnoidea for the eastern (type)species, and reinstating A. wallichii for a species in Bangladesh, Thailand, Java and Bali, and A. roxburghiana for a species occurring in India and Sri Lanka. We provide descriptions for each taxon and a key to the species, thereby resolving a previously difficult species group in a notoriously complex genus.

Australian Oryza: Utility and Conservation

Publisher: Springer Science and Business Media LLC

Date: 30-12-2009

DOI: 10.1007/S12284-009-9034-Y

Abstract: Australian Oryza are an understudied and underexploited genetic resource for rice improvement. Four species are indigenous: Oryza rufipogon , Oryza meridionalis , Oryza australiensis are widespread across northern Australia, whereas Oryza officinalis is known from two localities only. Molecular analysis of these wild populations is required to better define the distinctness of the taxa and the extent of any gene flow between them and rice. Limited collections of these wild populations are held in seed and DNA banks. These species have potential for domestication in some cases but also have many traits of potential value in the improvement of domesticated rice. Stress tolerance (biotic and abiotic) and grain quality characteristics in these populations may be useful.

Unusual new species of Styphelia (Ericaceae, Epacridoideae, Styphelieae) from north-eastern Australia

Publisher: CSIRO Publishing

Date: 2019

DOI: 10.1071/SB18026

Abstract: Styphelia geniculata Crayn and S. piliflora Crayn are described, phylogenetically placed and compared with related species. Their relationships within Ericaceae tribe Styphelieae, resolved by phylogenetic analysis of plastid and nuclear DNA sequences, support their description in the expanded genus Styphelia. Illustrations, pollen scanning electron micrographs, distribution maps and a key to the species and related northern Queensland taxa are provided, along with notes on the ecology and conservation status.

ORIGIN, DIVERSIFICATION, AND CLASSIFICATION OF THE AUSTRALASIAN GENUS DRACOPHYLLUM (RICHEEAE, ERICACEAE)

Publisher: Missouri Botanical Garden Press

Date: 06-2010

DOI: 10.3417/2008130

The influence of environment and life-history traits on the distribution of genes and individuals: a comparative study of 11 rainforest trees

Publisher: Wiley

Date: 19-03-2009

DOI: 10.1111/J.1365-294X.2009.04111.X

Beyond the model: expert knowledge improves predictions of species’ fates under climate change

Publisher: Wiley

Date: 30-11-2018

DOI: 10.1002/EAP.1824

Abstract: The need to proactively manage landscapes and species to aid their adaptation to climate change is widely acknowledged. Current approaches to prioritizing investment in species conservation generally rely on correlative models, which predict the likely fate of species under different climate change scenarios. Yet, while model statistics can be improved by refining modeling techniques, gaps remain in understanding the relationship between model performance and ecological reality. To investigate this, we compared standard correlative species distribution models to highly accurate, fine-scale, distribution models. We critically assessed the ecological realism of each species' model, using expert knowledge of the geography and habitat in the study area and the biology of the study species. Using interactive software and an iterative vetting with experts, we identified seven general principles that explain why the distribution modeling under- or overestimated habitat suitability, under both current and predicted future climates. Importantly, we found that, while temperature estimates can be dramatically improved through better climate downscaling, many models still inaccurately reflected moisture availability. Furthermore, the correlative models did not account for biotic factors, such as disease or competitor species, and were unable to account for the likely presence of micro refugia. Under-performing current models resulted in widely ergent future projections of species' distributions. Expert vetting identified regions that were likely to contain micro refugia, even where the fine-scale future projections of species distributions predicted population losses. Based on the results, we identify four priority conservation actions required for more effective climate change adaptation responses. This approach to improving the ecological realism of correlative models to understand climate change impacts on species can be applied broadly to improve the evidence base underpinning management responses.

The comparative study of range-wide genetic structure across related, co-distributed rainforest trees reveals contrasting evolutionary histories

Publisher: CSIRO Publishing

Date: 2007

DOI: 10.1071/BT06195

Abstract: Australia’s rainforests exhibit high taxonomic ersity and endemism, yet relatively little is known about patterns of genetic ersity across the flora. Habitat contractions caused by the aridification of the continent and the recent glacial cycles have left discrete genetic signatures on modern-day populations, with the nature of between-population differentiation likely to be influenced by a range of ecological and environmental factors. We used microsatellites to examine range-wide population genetic structure in two congeneric rainforest trees, Elaeocarpus angustifolius and E. largiflorens (Elaeocarpaceae), with similar habitat preference and dispersal potential. The aim was to investigate the relationships between genetic structure, geographic disjunction and morphological differentiation and attempt to clarify the likely evolutionary processes responsible for the observed patterns. We found substantial differences in the amount and type of genetic differentiation within the two co-distributed species. While Elaeocarpus largiflorens revealed an abrupt genetic disjunction front between two subspecies separated by a recognised biogeographic barrier (the Black Mountain Corridor), E. angustifolius showed lower genetic differentiation across a much wider geographic area. Our findings suggest that biogeographic features have different impacts on related species, and that generalisations on evolutionary patterns can be untenable without considering a range of factors. Also, on the basis of the available molecular data, a likely hypothesis is of pre-Pleistocene differentiation followed by reinforcement of differentiation patterns during recent glacial cycles (further studies are needed to conclusively date ergence).

Origins and assembly of Malesian rainforests

Publisher: Annual Reviews

Date: 02-11-2019

DOI: 10.1146/ANNUREV-ECOLSYS-110218-024737

Abstract: Unraveling the origins of Malesia's once vast, hyper erse rainforests is a perennial challenge. Major contributions to rainforest assembly came from floristic elements carried on the Indian Plate and montane elementsfrom the Australian Plate (Sahul). The Sahul component is now understood to include substantial two-way exchanges with Sunda inclusive of lowland taxa. Evidence for the relative contributions of the great Asiatic floristic interchanges (GAFIs) with India and Sahul, respectively, to the flora of Malesia comes from contemporary lineage distributions, the fossil record, time-calibrated phylogenies, functional traits, and the spatial structure of genetic ersity. Functional-trait and biome conservatism are noted features of montane austral lineages from Sahul (e.g., erse Podocarpaceae), whereas the abundance and ersity of lowland lineages, including Syzygium (Myrtaceae) and the Asian dipterocarps (Dipterocarpoideae), reflect a less well understood combination of dispersal, ecology, and adaptive radiations. Thus, Malesian rainforest assembly has been shaped by sharply contrasting evolutionary origins and biogeographic histories.

Additions to Lissanthe (Styphelioideae: Ericaceae) in Western Australia: L. synandra sp. nov. and L. pleurandroides comb. nov.

Publisher: CSIRO Publishing

Date: 2005

DOI: 10.1071/SB05017

Abstract: The genus Lissanthe R.Br. (Styphelioideae: Ericaceae) has been recently revised but further field and herbarium studies have brought to light two further species from southern Western Australia. Parsimony analysis of plastid atpB–rbcL spacer sequence data confirms the placement of these two species in Lissanthe. Thus, L. synandra Crayn & Hislop is described as new and L. pleurandroides (F.Muell.) Crayn & Hislop is transferred from Leucopogon. Lissanthe synandra is unique in the genus in having angled branchlets, corolla lobes that remain almost completely closed, and anthers that are fused and cohere around the style and stigma, forming a synandrium. Illustrations and distribution maps are provided for both species. A key to species of Lissanthe is included.

Historical biogeography of Melicope (Rutaceae) and its close relatives with a special emphasis on Pacific dispersals

Publisher: Wiley

Date: 08-02-2018

DOI: 10.1111/JSE.12299

Adaptive radiation, correlated and contingent evolution, and net species diversification in Bromeliaceae

Publisher: Elsevier BV

Date: 02-2014

DOI: 10.1016/J.YMPEV.2013.10.010

Abstract: We present an integrative model predicting associations among epiphytism, the tank habit, entangling seeds, C₃ vs. CAM photosynthesis, avian pollinators, life in fertile, moist montane habitats, and net rates of species ersification in the monocot family Bromeliaceae. We test these predictions by relating evolutionary shifts in form, physiology, and ecology to time and ancestral distributions, quantifying patterns of correlated and contingent evolution among pairs of traits and analyzing the apparent impact of in idual traits on rates of net species ersification and geographic expansion beyond the ancestral Guayana Shield. All predicted patterns of correlated evolution were significant, and the temporal and spatial associations of phenotypic shifts with orogenies generally accorded with predictions. Net rates of species ersification were most closely coupled to life in fertile, moist, geographically extensive cordilleras, with additional significant ties to epiphytism, avian pollination, and the tank habit. The highest rates of net ersification were seen in the bromelioid tank-epiphytic clade (D(crown) = 1.05 My⁻¹), associated primarily with the Serra do Mar and nearby ranges of coastal Brazil, and in the core tillandsioids (D(crown) = 0.67 My⁻¹), associated primarily with the Andes and Central America. Six large-scale adaptive radiations and accompanying pulses of speciation account for 86% of total species richness in the family. This study is among the first to test a priori hypotheses about the relationships among phylogeny, phenotypic evolution, geographic spread, and net species ersification, and to argue for causality to flow from functional ersity to spatial expansion to species ersity.

Elaeocarpus sedentarius sp. nov. (Elaeocarpaceae) - Morphometric analysis of a new, rare species from eastern Australia

Publisher: CSIRO Publishing

Date: 2008

DOI: 10.1071/SB07031

Abstract: To assess the status of a putative new species of Elaeocarpus L. (Elaeocarpaceae) from north-eastern New South Wales (NSW), with respect to the morphologically similar E. blepharoceras Schltr. from New Guinea, we undertook morphometric analysis of 11 vegetative attributes measured on 11 specimens of the putative new species and eight of E. blepharoceras. Cluster analysis (flexible UPGMA) and ordination (PCC) separates highland specimens of E. blepharoceras from the NSW material plus lowland E. blepharoceras. Furthermore, the ordination shows some separation of the NSW material into Koonyum Range and Nightcap Range groups. Although it is not clearly differentiated from lowland E. blepharoceras on morphometric analysis, description of the NSW material as E. sedentarius D.J.Maynard & Crayn is justified by (1) additional features such as the anther awns (short and sparsely hairy in E. sedentarius and much longer and densely bristly in E. blepharoceras), variation in the number of locules (3(–4) in E. sedentarius and (2–)3 in E. blepharoceras), leaf margin features (short setae terminating veins on leaf margins of E. blepharoceras, lacking in E. sedentarius) and (2) geographic isolation ( km) is likely to prevent gene flow. The distribution, relationships and conservation status of E. sedentarius are discussed.

Evolution in Australia’s mesic biome under past and future climates: Insights from a phylogenetic study of the Australian Rock Orchids (Dendrobium speciosum complex, Orchidaceae)

Publisher: Elsevier BV

Date: 2018

DOI: 10.1016/J.YMPEV.2017.09.004

Abstract: The Australian mesic biome spans c. 33° of latitude along Australia's east coast and ranges and is dissected by historical and contemporary biogeographical barriers. To investigate the impact of these barriers on evolutionary ersification and to predict the impact of future climate change on the distribution of species and genetic ersity within this biome, we inferred phylogenetic relationships within the Dendrobium speciosum complex (Orchidaceae) across its distribution and undertook environmental niche modelling (ENM) under past, contemporary and projected future climates. Neighbor Joining tree inference, NeighborNet and Structure analyses of Amplified Fragment Length Polymorphism (AFLP) profiles for D. speciosum s led from across its distribution showed that the complex consists of two highly supported main groups that are geographically separated by the St. Lawrence gap, an area of dry sclerophyll forest and woodland. The presence of several highly admixed in iduals identified by the Structure analysis provided evidence of genetic exchange between the two groups across this gap. Whereas previous treatments have recognised between one to eleven species, the molecular results support the taxonomic treatment of the complex as a single species with two subspecies. The ENM analysis supported the hypothesis that lineage ergence within the complex was driven by past climatic changes. The St. Lawrence gap represented a stronger biogeographic barrier for the D. speciosum complex during the cool and dry glacial climatic conditions of the Pleistocene than under today's interglacial conditions. Shallow genetic ergence was found within the two lineages, which mainly corresponded to three other biogeographic barriers: the Black Mountain Corridor, Glass House Mountains and the Hunter Valley. Our ENM analyses provide further support for the hypothesis that biogeographic barriers along Australia's east coast were somewhat permeable to genetic exchange due to past episodic range expansions and contractions caused by climatic change resulting in recurrent contact between previously isolated populations. An overall southward shift in the distribution of the complex under future climate scenarios was predicted, with the strongest effects on the northern lineage. This study contributes to our understanding of the factors shaping bio ersity patterns in Australia's mesic biome.

Using phylogenetic diversity to identify ancient rain forest refugia and diversification zones in a biodiversity hotspot

Publisher: Wiley

Date: 12-10-2015

DOI: 10.1111/DDI.12266

Molecular relationships between Australian annual wild rice, Oryza meridionalis, and two related perennial forms

Publisher: Springer Science and Business Media LLC

Date: 28-10-2013

DOI: 10.1186/1939-8433-6-26

Abstract: The perennial, Oryza rufipogon distributed from Asia to Australia and the annual O. meridionalis indigenous to Australia are AA genome species in the Oryza . However, recent research has demonstrated that the Australian AA genome perennial populations have maternal genomes more closely related to those of O. meridionalis than to those found in Asian populations of O. rufipogon suggesting that the Australian perennials may represent a new distinct gene pool for rice. Analysis of an Oryza core collection covering AA genome species from Asia to Oceania revealed that some Oceania perennials had organellar genomes closely related to that of O meridionalis (meridionalis-type). O. rufipogon accessions from New Guinea carried either the meridionalis-type or rufirpogon-type (like O. rufipogon ) organellar genomes. Australian perennials carried only the meridionalis-type organellar genomes when accompanied by the rufipogon-type nuclear genome. New accessions were collected to better characterize the Australian perennials, and their life histories (annual or perennial) were confirmed by field observations. All of the material collected carried only meridionalis-type organellar genomes. However, there were two distinct perennial groups. One of them carried an rufipogon-type nuclear genome similar to the Australian O. rufipogon in the core collection and the other carried an meridionalis-type nuclear genome not represented in the existing collection. Morphologically the rufipogon-type shared similarity with Asian O. rufipogon . The meridionalis-type showed some similarities to O. meridionalis such as the short anthers usually characteristic of annual populations. However, the meridionalis-type perennial was readily distinguished from O. meridionalis by the presence of a larger lemma and higher number of spikelets. Analysis of current accessions clearly indicated that there are two distinct types of Australian perennials. Both of them differed genetically from Asian O. rufipogon . One lineage is closely related to O. meridionalis and another to Asian O. rufipogon . The first was presumed to have evolved by ergence from O. meridionalis becoming differentiated as a perennial species in Australia indicating that it represents a new gene pool. The second, apparently derived from Asian O. rufipogon , possibly arrived in Australia later.

Origins and evolution of cinnamon and camphor: A phylogenetic and historical biogeographical analysis of the Cinnamomum group (Lauraceae)

Publisher: Elsevier BV

Date: 03-2016

DOI: 10.1016/J.YMPEV.2015.12.007

Abstract: Tropical and subtropical hi-Pacific disjunction is among the most fascinating distribution patterns, but received little attention. Here we use the fossil-rich Cinnamomum group, a primarily tropical and subtropical Asian lineage with some species distributed in Neotropics, Australasia and Africa to shed light upon this disjunction pattern. Phylogenetic and biogeographic analyses were carried out using sequences of three nuclear loci from 94 Cinnamomum group and 13 outgroup s les. Results show that although there are three clades within a monophyletic Cinnamomum group, Cinnamomum and previously recognized sub isions within this genus were all rejected as natural groups. The Cinnamomum group appears to have originated in the widespread boreotropical paleoflora of Laurasia during the early Eocene (ca. 55Ma). The formation and breakup of the boreotropics seems to have then played a key role in the formation of intercontinental disjunctions within the Cinnamomum group. The first cooling interval (50-48Ma) in the late early Eocene resulted in a floristic discontinuity between Eurasia and North America causing the tropical and subtropical hi-Pacific disjunction. The second cooling interval in the mid-Eocene (42-38Ma) resulted in the fragmentation of the boreotropics within Eurasia, leading to an African-Asian disjunction. Multiple dispersal events from North into South America occurred from the early Eocene to late Miocene and a single migration event from Asia into Australia appears to have occurred in the early Miocene.

Cenozoic extinction and recolonization in the New Zealand flora: the case of the fleshy-fruited epacrids (Styphelieae, Styphelioideae, Ericaceae)

Publisher: Elsevier BV

Date: 2013

DOI: 10.1016/J.YMPEV.2012.09.027

Abstract: The origins and evolutionary history of the New Zealand flora has been the subject of much debate. The recent description of Cyathodophyllum novaezelandieae from early Miocene sediments in New Zealand provides possible evidence for the antiquity of the fleshy fruited epacrids (tribe Styphelieae, Ericaceae) in New Zealand. Yet the extant species in this tribe are thought to be very closely related to or conspecific with Australian taxa, suggesting recent trans-Tasman origins. In order to investigate the origins and evolution of the extant New Zealand Styphelieae we produced molecular phylogenetic trees based on sequences of three plastid regions that include representatives of all the genera of the tribe and eight of the ten New Zealand species. We estimated the range of minimum ages of the New Zealand lineages with Bayesian relaxed-clock analyses using different calibration methods and relative dating. We found strong support for each of the eight extant species of New Zealand Styphelieae being a distinct lineage that is nested within an Australian clade. In all except one case the sister is from Tasmania and/or the east coast of mainland Australia for Acrothamnus colensoi the sister is in New Guinea. Estimated dates indicate that all of the New Zealand lineages erged from their non-New Zealand sisters within the last 7 Ma. Time discontinuity between the fossil C.novae-zelandiae (20-23 Ma) and the origins of the extant New Zealand lineages (none older than 5 Ma) indicates that the fossil and extant Styphelieae in New Zealand are not related. The relative dating analysis showed that to accept this relationship, it would be necessary to accept that the Styphelieae arose in the early-mid Mesozoic (210-120 Ma), which is starkly at odds with multiple lines of evidence on the age of Ericales and indeed the angiosperms. Therefore, our results do not support the hypothesis that Styphelieae have been continuously present in New Zealand since the early Miocene. Instead they suggest a historical biogeographical scenario in which the lineage to which C. novae-zelandiae belongs went extinct in New Zealand, and the extant New Zealand Styphelieae are derived from Australian lineages that recolonised (presumably by long distance dispersal) no earlier than the late Miocene to Pliocene.

Genomic insights into rapid speciation within the world’s largest tree genus Syzygium

Publisher: Springer Science and Business Media LLC

Date: 12-09-2022

DOI: 10.1038/S41467-022-32637-X

Abstract: Species radiations, despite immense phenotypic variation, can be difficult to resolve phylogenetically when genetic change poorly matches the rapidity of ersification. Genomic potential furnished by palaeopolyploidy, and relative roles for adaptation, random drift and hybridisation in the apportionment of genetic variation, remain poorly understood factors. Here, we study these aspects in a model radiation, Syzygium , the most species-rich tree genus worldwide. Genomes of 182 distinct species and 58 unidentified taxa are compared against a chromosome-level reference genome of the sea apple, Syzygium grande . We show that while Syzygium shares an ancient genome doubling event with other Myrtales, little evidence exists for recent polyploidy events. Phylogenomics confirms that Syzygium originated in Australia-New Guinea and ersified in multiple migrations, eastward to the Pacific and westward to India and Africa, in bursts of speciation visible as poorly resolved branches on phylogenies. Furthermore, some sublineages demonstrate genomic clines that recapitulate cladogenetic events, suggesting that stepwise geographic speciation, a neutral process, has been important in Syzygium ersification.

A review of Austrocallerya and Pongamia (Leguminosae subfamily Papilionoideae) in Australia, and the description of a new monotypic genus, Ibatiria

Publisher: CSIRO Publishing

Date: 2019

DOI: 10.1071/SB18039

Abstract: A review of Austrocallerya J.Compton & Schrire and Pongamia Adans. (Leguminosae subfamily Papilionoideae) in Australia, and the description of a new monotypic genus, Ibatiria W.E.Cooper, is presented with the support of fresh, dried, spirit-preserved specimens, molecular phylogenetic analysis of plastid and nuclear data, and illustrations. Three Austrocallerya species are confirmed, described and distinguished for Australia. Two varieties of Pongamia pinnata (L.) Pierre are recognised P. pinnata var. minor (Benth.) Domin is reinstated and is distinguished from var. pinnata by habitat, leaflet number and width, floral bract length and bracteole length. The new genus, Ibatiria, includes a single species, Ibatiria furfuracea W.E.Cooper, from Queensland’s Wet Tropics Bioregion. A second-step lectotype is designated for Pterocarpus australis Endl., and lectotypes are designated for Wisteria megasperma F.Muell. and Pongamia glabra var. minor Benth.

A predominantly southern distribution conceals a northern reservoir of diversity in a wet sclerophyll tree

Publisher: CSIRO Publishing

Date: 2019

DOI: 10.1071/BT19065

Abstract: The wet forests of south-east Australia can be coarsely ided into cool-temperate communities characterised by relictual Gondwanan lineages with a history of persistence in scattered refugia, and subtropical communities showing stronger Malesian floristic influences, with post-glacial expansion dynamics. Insights into the assembly and dynamics of these two biomes can be gained by studying taxa that inhabit both, such as the tree species Elaeocarpus reticulatus Sm. (blueberry ash). Here we use data generated from eight microsatellite loci to investigate population structure and eco-evolutionary dynamics across the core of this species’ range. Our nested s ling design allowed us to test for population differentiation along both axes of latitude and altitude, with the aim of detecting post-glacial colonisation dynamics. Our results show that the strongest genetic differentiation was associated with latitude zones, and population differentiation obeyed a typical pattern of isolation by distance. We did not find strong support for differentiation being driven by altitude. A trend towards higher ersity in the north of the range reveals that E. reticulatus conforms more to the post-glacial colonisation dynamics typifying subtropical, rather than cool-temperate lineages.

Speciation with gene flow on Lord Howe Island

Publisher: Proceedings of the National Academy of Sciences

Date: 05-07-2011

DOI: 10.1073/PNAS.1106085108

Abstract: Understanding the processes underlying the origin of species is a fundamental goal of biology. It is widely accepted that speciation requires an interruption of gene flow between populations: ongoing gene exchange is considered a major hindrance to population ergence and, ultimately, to the evolution of new species. Where a geographic barrier to reproductive isolation is lacking, a biological mechanism for speciation is required to counterbalance the homogenizing effect of gene flow. Speciation with initially strong gene flow is thought to be extremely rare, and few convincing empirical ex les have been published. However, using phylogenetic, karyological, and ecological data for the flora of a minute oceanic island (Lord Howe Island, LHI), we demonstrate that speciation with gene flow may, in fact, be frequent in some instances and could account for one in five of the endemic plant species of LHI. We present 11 potential instances of species ergence with gene flow, including an in situ radiation of five species of Coprosma (Rubiaceae, the coffee family). These results, together with the speciation of Howea palms on LHI, challenge current views on the origin of species ersity.

Global analysis of Poales diversification – parallel evolution in space and time into open and closed habitats

Publisher: Cold Spring Harbor Laboratory

Date: 16-09-2023

DOI: 10.1101/2023.09.14.557735

Isolation and characterization of polymorphic microsatellite loci from Tetratheca ericifolia (Elaeocarpaceae)

Publisher: Wiley

Date: 28-06-2008

DOI: 10.1111/J.1755-0998.2008.02093.X

Abstract: We identified 11 informative microsatellite loci in Tetratheca ericifolia from an (AG)(n) -enriched library. Using these loci on 32 in iduals from two populations (16 in iduals from each), we detected an average of 11.3 alleles per locus (range of five to 21, average expected heterozygosity of 0.728), of which 56% were unique to one population or the other. All loci were lifiable in seven to 12 of a further 12 species of Tetratheca under the same reaction conditions. The markers will be useful tools for evolutionary studies of this Australian endemic group.

James Cook University Cairns Campus

Location: Australia

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University Of New South Wales

Location: Australia

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Linkage Projects - Grant ID: LP100100143

Start Date: 03-2011

End Date: 12-2014

Amount: $233,000.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP0665859

Start Date: 08-2006

End Date: 08-2009

Amount: $282,000.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP160100098

Start Date: 04-2016

End Date: 12-2019

Amount: $364,400.00

Funder: Australian Research Council

Linkage Projects - Grant ID: LP190100484

Start Date: 03-2021

End Date: 02-2024

Amount: $410,237.00

Funder: Australian Research Council

ARC Centres Of Excellence - Grant ID: CE230100009

Start Date: 07-2024

End Date: 06-2031

Amount: $35,000,000.00

Funder: Australian Research Council

Industrial Transformation Training Centres - Grant ID: IC230100027

Start Date: 2023

End Date: 12-2027

Amount: $5,000,000.00

Funder: Australian Research Council