
Daniel John MurphyRoyal Botanic Gardens Victoria · Science
Daniel John Murphy
PhD
About
111
Publications
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Introduction
Plant systematist interested in the evolution and biogeography of Australian and Malesian flowering plants; President, Australasian Systematic Botany Society
Additional affiliations
February 2002 - July 2003
July 2003 - present
Publications
Publications (111)
Grasses (Poaceae) comprise c . 11 800 species and are central to human livelihoods and terrestrial ecosystems. Knowing their relationships and evolutionary history is key to comparative research and crop breeding. Advances in genome‐scale sequencing allow for increased breadth and depth of phylogenomic analyses, making it possible to infer a new re...
The generation and analysis of genome-scale data—genomics—is driving a rapid increase in plant biodiversity knowledge. However, the speed and complexity of technological advance in genomics presents challenges for its widescale use in evolutionary and conservation biology. Here, we introduce and describe a national-scale collaboration conceived to...
Grasses (Poaceae) comprise around 11,800 species and are central for human livelihoods and terrestrial ecosystems. Knowing their relationships and evolutionary history is key to comparative research and crop breeding. Advances in genome-scale sequencing allow for increased breadth and depth of phylogenomic analyses, making it possible to infer a ne...
Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods1,2. A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome3,4. Many studies have drawn on this foundation...
Caesalpinioideae is the second largest subfamily of legumes (Leguminosae) with ca. 4680 species and 163 genera. It is an ecologically and economically important group formed of mostly woody perennials that range from large canopy emergent trees to functionally herbaceous geoxyles, lianas and shrubs, and which has a global distribution, occurring on...
Model species continue to underpin groundbreaking plant science research. At the same time, the phylogenetic resolution of the land plant Tree of Life continues to improve. The intersection of these two research paths creates a unique opportunity to further extend the usefulness of model species across larger taxonomic groups. Here we promote the u...
Model species continue to underpin groundbreaking plant science research. At the same time, the phylogenetic resolution of the land plant Tree of Life continues to improve. The intersection of these two research paths creates a unique opportunity to further extend the usefulness of model species across larger taxonomic groups. Here we promote the u...
Lomandra is the largest genus in Asparagaceae subfamily Lomandroideae and possesses economic, ecological, and ethnobotanical significance in Australia. Lomandra comprises four sections, L. section Capitatae, L. section Macrostachya, L. section Typhopsis and L. section Lomandra, the latter comprising series Lomandra and series Sparsiflorae, all reco...
Eucalypts are a large and ecologically important group of plants on the Australian continent, and understanding their evolution is important in understanding evolution of the unique Australian flora. Previous phylogenies using plastome DNA, nuclear-ribosomal DNA, or random genome-wide SNPs, have been confounded by limited genetic sampling or by idi...
Early natural historians-Comte de Buffon, von Humboldt, and De Candolle-established environment and geography as two principal axes determining the distribution of groups of organisms, laying the foundations for biogeography over the subsequent 200 years, yet the relative importance of these two axes remains unresolved. Leveraging phylogenomic and...
Acacia (Leguminosae, Caesalpinioideae, mimosoid clade) is the largest and most widespread genus of plants in the Australian flora, occupying and dominating a diverse range of environments, with an equally diverse range of forms. For a genus of its size and importance, Acacia currently has surprisingly few genomic resources. Acacia pycnantha, the go...
Philotheca sect. Erionema includes 14 species from eastern Australia and one from south-western Australia. We conducted a phylogenetic analysis of the section, including samples of all species, using sequences of the ITS and ETS regions of nuclear ribosomal DNA. Results were broadly congruent with a previous analysis based on morphological and flav...
Subfamily Caesalpinioideae with ca. 4,600 species in 152 genera is the second-largest subfamily of legumes (Leguminosae) and forms an ecologically and economically important group of trees, shrubs and lianas with a pantropical distribution. Despite major advances in the last few decades towards aligning genera with clades across Caesalpinioideae, g...
The morphologically variable genus Archidendron is the second largest mimosoid legume genus from the Indomalayan-Australasian region, yet it has not been well represented in phylogenetic studies. Phylogenies that have included multiple representatives of Archidendron suggest it may not be monophyletic, and the same applies to Archidendropsis , anot...
Early natural historians - Compte de Buffon, von Humboldt and De Candolle - established ecology and geography as two principal axes determining the distribution of groups of organisms, laying the foundations for biogeography over the subsequent 200 years, yet the relative importance of these two axes remains unresolved. Leveraging phylogenomic and...
Organelle genomes are typically represented as single, static, circular molecules. However, there is evidence that the chloroplast genome exists in two structural haplotypes and that the mitochondrial genome can display multiple circular, linear or branching forms. We sequenced and assembled chloroplast and mitochondrial genomes of the Golden Wattl...
In Acacia, 90% of species have drought-tolerant phyllodes as their adult foliage, the remaining species have bipinnate leaves. We conducted tests for relationships between foliage type and 35 bioclimatic variables at the continental scale and found significant correlations of both ‘moisture seasonality’ and ‘radiation in the coldest quarter’ with f...
Eremophila is the largest genus in the plant tribe Myoporeae (Scrophulariaceae) and exhibits incredible morphological diversity across the Australian continent. The Australian Aboriginal Peoples recognize many Eremophila species as important sources of traditional medicine, the most frequently used plant parts being the leaves. Recent phylogenetic...
Eremophila is a significant component of the Australian arid zone flora, but its generic limits and relationships to the other six genera of tribe Myoporeae remain largely untested. In this study, we assembled a dataset of the nuclear ribosomal cistron (ca. 6000 bases including ITS1+2, ETS regions, non‐transcribed spacer and associated genes) for a...
Question
To better understand the influence of deep‐time diversification on extant plant communities, we assessed how community dissimilarity increases with spatial and climatic distances at multiple taxonomic ranks (species, genus, family, and order) in angiosperm trees. We tested the prediction that the dissimilarity‐to‐distance relationship shou...
Although organelle genomes are typically represented as single, static, circular molecules, there is evidence that the chloroplast genome exists in two structural haplotypes and that the mitochondrial genome can display multiple circular, linear or branching forms. We sequenced and assembled chloroplast and mitochondrial genomes of the Golden Wattl...
Eremophila is the largest genus in the plant tribe Myoporeae (Scrophulariaceae) and exhibits incredible morphological diversity across the Australian continent. The Australian Aboriginal Peoples recognize many Eremophila species as important sources of traditional medicine, the most frequently used plant parts being the leaves. Recent phylogenetic...
A geospatial analysis of 1,906,302 records of 1938 species of Australian vertebrates has shown that the original regions proposed in the 19th century, namely the Eyrean, Torresian and Bassian still hold. The analysis has shown that the Eyrean region has an east-west divide, forming two, possibly independent arid regions (Eastern Desert and Western...
This study presents an analysis of plastomes to assess relationships among the seven genera of tribe Myoporeae (Scrophulariaceae). Sampling included individuals from type species for all seven genera included in Myoporeae (Bontia, Calamphoreus, Diocirea, Eremophila, Glycocystis, Myoporum, Pentacoelium), one additional species of the large genus Ere...
Asparagaceae: Lomandroideae are a species-rich and economically important subfamily in the monocot order Asparagales, with a center of diversity in Australia. Lomandroideae are ecologically diverse, occupying mesic and arid biomes in Australia possessing an array of key traits, including sexual dimorphism, storage organs and polyploidy potentially...
A morphometric multivariate analysis of Acacia rigens A.Cunn. ex G.Don and an entity previously recognised as Acacia sp. Gerang Gerung (M.G.Corrick 6451) was conducted, with the latter described here as a new species, Acacia cineramis H.K.Orel. This new species is considered endangered in accordance with IUCN classification, and known populations o...
The Eremaean region, Australia’s arid biome and biogeographic region, has been discussed by botanists (and as the Eyrean, its counterpart for zoogeographers) for over 150 years, yet little progress was made in defining it as an area of endemism until the 2000s. As Australia’s largest biome and biogeographic region, the Eremaean has been defined in...
The xeromorphic vegetation is a significant component of the Australian flora and phylogenetic and phylogeographic analysis of xeromorphic plants provides a basis for understanding the origins and evolutionary history of the Australian vegetation. Here we expand on previous reviews of the origins and maintenance of the Australian flora with an emph...
Australia is an excellent setting to explore relationships between climate change and diversification dynamics . Aridification since the Eocene has resulted in spectacular radiations within one or more Australian biomes. Acacia is the largest plant genus on the Australian continent, with around 1000 species, and is present in all biomes. We investi...
The Advances in Legume Systematics (ALS) series has provided the venues for publishing outputs from the series of seven International Legume Conferences (ILC) held over the last four decades. The first two editions arising from the first ILC in 1978 at the Royal Botanic Gardens, Kew, were published in 1981. The first ten parts of ALS were published...
The need for scientists to exchange, share and organise data has resulted in a proliferation of biodiversity research-data portals over recent decades. These cyber-infrastructures have had a major impact on taxonomy and helped the discipline by allowing faster access to bibliographic information, biological and nomenclatural data, and specimen info...
The need for scientists to exchange, share, and organise data has resulted in a proliferation of research data portals in the past decades. These cyberinfrastructures have had a major impact on taxonomy and helped to revitalise the discipline, by allowing quick access to bibliographic information, biological and nomenclatural data, and specimen inf...
We present the largest comparative biogeographical analysis that has complete coverage of Australia's geography (20 phytogeographical subregions), using the most complete published molecular phylogenies to date of large Australian plant clades (Acacia, Banksia and the eucalypts). Two distinct sets of areas within the Australian flora were recovered...
A morphometric analysis of specimens determined as Acacia boormanii Maiden and A. infecunda Molyneux & Forrester supported a distinctive population centred on Mt Typo in northeastern Victoria, which is described here as A. boormanii subsp. gibba K.J.Tucker subsp. nov. The characters that best separate the new subspecies are the phyllode width, the...
Proteaceae subfamily Persoonioideae, as presently circumscribed, consists of the monogeneric tribe Placospermeae (Placospermum) and the tribe Persoonieae. The latter comprises the diverse genus Persoonia and monospecific genera found in New Zealand (Toronia), New Caledonia (Garnieria) and south-western Western Australia (Acidonia). Persoonia has 10...
In Australia, Poaceae tribe Poeae are represented by 19 genera and 99 species, including economically and environmentally important native and introduced pasture grasses [e.g. Poa (Tussock-grasses) and Lolium (Ryegrasses)]. We used this tribe, which are well characterised in regards to morphological diversity and evolutionary relationships, to test...
Success rates (percentages) for specimen identification using distance-based methods (nearest neighbour, best close match, and threshold ID [24], as outlined in the text) based on individual (ITS) and concatenated (rbcL+matK, rbcL+matK+ITS) DNA barcode markers.
BCM, Best close match; ITS, Internal transcribed spacer; NN, Nearest neighbour; TID, Thr...
Voucher specimen data for individuals, presence or absence of sequence data in individual and concatenated DNA barcode markers, Barcode Of Life Data System (BOLD) reference numbers, and presence or absence of voucher specimen images.
AD, State Herbarium of South Australia; BRI, Queensland Herbarium; CANB, Australian National Herbarium; HO, Tasmania...
Summary statistics and sequence quality of individual and concatenated DNA barcode markers for specimen identification and species discovery based on distance- (dataset A) and tree- (dataset B) based methods.
(PDF)
Success rates for specimen identification using tree-based (maximum likelihood or Bayesian inference phylogenies with specimens identified according to the “liberal” tree-based method of Meier et al. [24], as outlined in the text) methods for individual (ITS) and concatenated (rbcL+matK+ITS) DNA barcode markers.
BA, Bayesian inference; ITS, Interna...
The Bayesian inference of phylogenetic relationships among Australian tribe Poeae based on the concatenated (rbcL+matK+ITS) DNA barcode markers.
Support values are provided above the branches including bootstrap (maximum likelihood) and posterior probabilities (Bayesian inference) before and after the forward slash, respectively.
(EPS)
Acacia s.l. farnesiana, which originates from Mesoamerica, is the most widely distributed Acacia s.l. species across the tropics. It is assumed that the plant was transferred across the Atlantic to southern Europe by Spanish explorers, and then spread across the Old World tropics through a combination of chance long-distance and human-mediated disp...
The classification of the legume family proposed here addresses the long-known non-monophyly of the traditionally recognised subfamily Caesalpinioideae, by recognising six robustly supported monophyletic subfamilies. This new classification uses as its framework the most comprehensive phylogenetic analyses of legumes to date, based on plastid matK...
The classification of the legume family proposed here addresses the long-known non-monophyly of the traditionally recognised subfamily Caesalpinioideae, by recognising six robustly supported monophyletic subfamilies. This new classification uses as its framework the most comprehensive phylogenetic analyses of legumes to date, based on plastid matK...
Soil salinity is a major environmental stress factor caused by diverse natural causes and also has anthropogenic contributions. The effects of salinity stress are diverse, the end results ranging from reductions in growth and yield of crops, to devastating effects on biodiversity and ecosystems. However, certain plants are found to be well adapted...
Social media, government, industry and science use data in the same way, through the pursuit of correlations in large data sets. As this critique shows, however, there is greater dialogue about the potential pitfalls of Big Data and the Big Data Cycle in non-historical science fields, such as medicine and advertising. Pitfalls, such as the Big Data...
To investigate the pathways of introduction of the African baobab, Adansonia digitata, to the Indian subcontinent, we examined 10 microsatellite loci in individuals from Africa, India, the Mascarenes and Malaysia, and matched this with historical evidence of human interactions between source and destination regions. Genetic analysis showed broad co...
Appendix S1 Collection localities of Adansonia digitata individuals used in this study and genetic cluster assignments based on STRUCTURE analysis. Appendix S2 Details of Adansonia digitata populations used in this study and predominant genetic cluster assignments of individuals within poopulations based on STRUCTURE analysis. Appendix S3 Values of...
Taxonomic uncertainty exists regarding the circumscription of the following seven phenotypically similar Australian species: Poa crassicaudex Vickery, P. hookeri Vickery, P. labillardierei Steud., P. phillipsiana Vickery, P. poiformis (Labill.) Druce, P. porphyroclados Nees (including P. serpentum Nees) and P. sieberiana Spreng. Multivariate ordina...
This study investigates the role of human agency in the gene flow and geographical distribution of the Australian baobab, Adansonia gregorii. The genus Adansonia is a charismatic tree endemic to Africa, Madagascar, and northwest Australia that has long been valued by humans for its multiple uses. The distribution of genetic variation in baobabs in...
The phytogeographical regions and sub-regions of Australia are revised in light of new data from a recent analysis by González-Orozco, Ebach et al. (2014). The new revision includes two new regions, Northern regio nova and Northern Desert regio nova, and five new sub-regions, Nullarbor sub-regio nova, Central Desert sub-regio nova, Great Sandy Dese...
The deleterious effects of soil salinity on biodiversity and agricultural productivity make it essential to devise strategies that would reduce its impact and expansion. For sustainable agriculture on dryland salinity affected areas, the use of native salt-tolerant plant species of economic value could provide a solution. In this work, the salinity...
Plant associations with protective ants are widespread among angiosperms, but carry the risk that ants will deter pollinators as well as herbivores. Such conflict, and adaptations to ameliorate or prevent the conflict, have been documented in African and neotropical acacias. Ant–acacia associations occur in Australia, but little is known of their e...
The Australasian region contains a significant proportion of worldwide Poa diversity, but the evolutionary relationships of taxa from this region are incompletely understood. Most Australasian species have been placed in a monophyletic Poa subgenus, Poa supersection Homalopoa section Brizoides clade, but with limited resolution of relationships. In...
The Kimberley region of Western Australia is recognised for its high biodiversity and many endemic species, including the charismatic boab tree, Adansonia gregorii F.Muell. (Malvaceae: Bombacoideae). In order to assess the effects of biogeographic barriers on A. gregorii, we examined the genetic diversity and population structure of the tree specie...
In this paper, a novel approach for preliminary identification of salt tolerance in Acacia species is presented, based on molecular phylogenetic analysis using nuclear ribosomal DNA markers (ITS and ETS). Four species of Acacia, i.e., A. pendula, A. salicina, A. victoriae and A. stenophylla, had been initially identified as salt tolerant and were b...
• Premise of the study: We isolated 15 polymorphic microsatellite markers from Vachellia farnesiana for use in population genetic studies to determine the native range of the species.
• Methods and Results: Initially, 454 shotgun sequencing was used to identify and design primers for 68 microsatellite loci. Of these, we trialed 47 loci in the targe...
Soil salinity and drought severely affect all aspects of plant physiology, leading to significant losses of crop pro-ductivity and native biodiversity. A key to sustainable land use in such areas is to cultivate well-adapted native plants that are also commercially important and have the appropriate gene pool. Glycine betaine (GB) is an osmoprotect...
Use of saline lands for agroforestry relies primarily on plant species that have the trait of salinity tolerance, and also other economic and agronomic benefits. The selection of species, however, also needs to consider other key factors such as compatibility with existing flora, and potential for environmental benefits such as improved soil fertil...
After the publication of “Towards an Australian Bioregionalisation Atlas: A provisional area taxonomy of Australia’s biogeographical regions” (Ebach et al . 2013), we were informed of an incorrect, and missing type locality for the Cape York Peninsula respectively. The correct type locality for the Cape York Peninsula Cracraft 1991 phyto- and zooge...
The Leguminosae, the third-largest angiosperm family, has a global distribution and high ecological and economic importance. We examine how the legume systematic research community might join forces to produce a comprehensive phylogenetic estimate for the ca. 751 genera and ca. 19,500
species of legumes and then translate it into a phylogeny-based...
The large number, definition, varied application and validity of named Australian biogeographical regions reflect their ad hoc development via disparate methods or case study idiosyncracies. They do not represent a coherent system. In order to resolve these uncertainties an Australian Bioregionalisation Atlas is proposed as a provisional hierarchic...
Stipoid grasses (Poaceae, tribe Stipeae) include many species that are highly invasive. In Australia, several species are problematic environmental and economic weeds, degrading pastures, injuring livestock, and invading native grasslands. An accurate means of identification is the first line of defense against importation and establishment of pote...