Papers by Robert (Bort) Edwards
Invertebrate Systematics, 2010
Despite the widespread and common use of DNA-sequence data to estimate phylogenies, support or co... more Despite the widespread and common use of DNA-sequence data to estimate phylogenies, support or contest classifications, and identify species using barcodes, they are not commonly used as the primary or sole source of data for describing species. This is possibly due to actual or perceived pressure from peers to include morphology as the primary source of data for species descriptions. We find no compelling evidence to exclude DNA-only descriptions, or to insist that morphology always be included in a species description. It is not the data type per se that is important, but the science behind the taxonomic conclusions. Using alternative kinds of data for descriptions should not cause problems for taxonomy if links are kept with type specimens.
PlosONE, 2019
Resolving the phylogenetic relationships of closely related species using a small set of loci is ... more Resolving the phylogenetic relationships of closely related species using a small set of loci is challenging as sufficient information may not be captured from a limited sample of the genome. Relying on few loci can also be problematic when conflict between gene-trees arises from incomplete lineage sorting and/or ongoing hybridization, problems especially likely in recently diverged lineages. Here, we developed a method using limited genomic resources that allows identification of many low copy candidate loci from across the nuclear and chloroplast genomes, design probes for target capture and sequence the captured loci. To validate our method we present data from Eucalyptus and Melaleuca, two large and phy-logenetically problematic genera within the Myrtaceae family. With one annotated genome, one transcriptome and two whole-genome shotgun sequences of one Eucalyptus and four Melaleuca species, respectively, we identified 212 loci representing 263 kbp for targeted sequence capture and sequencing. Of these, 209 were successfully tested from 47 samples across five related genera of Myrtaceae. The average percentage of reads mapped back to the reference was 57.6% with coverage of more than 20 reads per position across 83.5% of the data. The methods developed here should be applicable across a large range of taxa across all kingdoms. The core methods are very flexible, providing a platform for various genomic resource availabilities and are useful from shallow to deep phylogenies.
Australian Systematic Botany, 2018
The Australian monsoon tropics are currently dominated by savanna and tropical woodland biomes th... more The Australian monsoon tropics are currently dominated by savanna and tropical woodland biomes that have arisen in response to a cooling and drying trend within the past ~3 million years. It is expected that organisms well adapted to these conditions have expanded into available habitats, leading to the differentiation of populations and species across this landscape, a process that could be magnified by the presence of several biogeographic barriers. The broad-leaved paperbark (Melaleuca leucadendra (L.) L.) complex is one such group of plants, with 14 poorly morphologically differentiated species occupying large overlapping distributions across the region, and across several recognised biogeographic barriers. Using phylogenetic and network analyses of nuclear and plastid sequences, we tested species limits among currently described species within the complex and for phylogeographic structure within species across seven of these barriers. Overall, our data suggested patterns of differentiation among species consistent with the early to middle stages of incomplete lineage sorting, and evidence for an idiosyncratic cryptic response of species to biogeographic barriers. Unexpectedly, we found a deep molecular split across all species, broadly coinciding with the northern part of the Great Dividing Range, a feature not typically considered to be a barrier to dispersal. Our study has offered one of the first insights into the dynamics within and among widespread species across the north of Australia, suggesting considerably more geographic structure than was previously recognised.
Taxon, 2018
The taxonomic history of the Melanthera alliance is long and convoluted with many generic name ch... more The taxonomic history of the Melanthera alliance is long and convoluted with many generic name changes and requires a robust phylogeny to clarify taxonomic concepts within the group and to begin asking questions of its evolutionary history. For a time, prevailing classifications placed all species in the genus Melanthera except for a handful of tetraploids from the Hawaiian Islands being recognized as a distinct genus: Lipochaeta. Recent morphological revision has reopened debate by proposing six genera: Apowollastonia, Echinocephalum, Lipotriche, and Melanthera, and two Pacific Island genera representing diploids (Wollastonia) and tetraploids (Lipochaeta), plus four closely related genera expected to fall outside the alliance (Acunniana, Indocypraea, Lipoblepharis, Quadribractea). Here, we present the most comprehensive molecular phylogeny to date of the taxa variously associated with Melanthera in order to test these competing generic limits and explore the biogeographic history of this pan-tropical lineage. The data are consistent with six segregate genera, including the sinking of Hawaiian Islands members of Wollastonia (Melanthera) back into a broader concept of Lipochaeta, although there is currently no recognized morphological synapomorphy to distinguish Lipochaeta s.l. from Wollastonia. Our results suggest that the Melanthera alliance originated some time during the Pliocene or Pleistocene and a strong contemporary presence of the alliance and closely related Ecliptinae outgroups in the Americas suggests that this region may have been the center of origin with subsequent dispersal. We illustrate the difficulty of reconstructing the dispersal history of the remaining genera and present the most parsimonious colonization hypotheses.
Caribbean Naturalist, 2018
The Lesser Antilles is part of the Caribbean biodiversity hotspot and a priority for conservation... more The Lesser Antilles is part of the Caribbean biodiversity hotspot and a priority for conservation of its flora is its endemic taxa. Using data from herbarium specimen labels, we recently carried out a preliminary conservation assessment of the 263 seed plant taxa unique to these islands, reporting that 70% of them are potentially threatened. In an effort to make conservation recommendations for the threatened species, we have further analyzed the specimen data for patterns in their distribution. We found that just over ⅓ of the region's endemics are restricted to a single island, and the majority of these are only found at a single location, whereas the others are found at multiple sites on each island. Diversity of regional endemics appears to be associated with larger islands, and while there appears to be a loose correlation between areas of high diversity of regional endemics and local endemism, there are a number of isolated centers of local endemism scattered across the island chain that may be of particular conservation concern. We also detected a relationship between diversity and elevation, with a peak in the number of endemic species occurred at mid-elevations (400–800 m). This correlation translates to a relationship between endemism and habitat type, with elevated numbers of endemics found in rainforest and elfin woodland, both communities that typically occur at mid-to high elevations, respectively. The highest proportion of threatened taxa is found in restricted and fragmented communities (elfin woodland, summit-herb vegetation, river bank, and moist forest) and the lowest proportion is found in the largest, most contiguous community (rainforest). Focused conservation action should occur in these important areas where plant endemism is locally high and habitat types are restricted and fragmented.
Asexual lineages provide a challenge to species delimitation because species concepts either have... more Asexual lineages provide a challenge to species delimitation because species concepts either have little biological meaning for them or are arbitrary, since every individual is monophyletic and reproductively isolated from all other individuals. However, recognition and naming of asexual species is important to conservation and economic applications. Some scale insects are widespread and polyphagous pests of plants, and several species have been found to comprise cryptic species complexes. Parasaissetia nigra (Nietner, 1861) (Hemiptera: Coccidae) is a parthenogenetic, cosmopolitan and polyphagous pest that feeds on plant species from more than 80 families. Here, we implement multiple approaches to assess the species status of P. nigra, including coalescence-based analyses of mitochondrial and nuclear genes, and ecological niche modelling. Our results indicate that the sampled specimens of P. nigra should be considered to comprise at least two ecotypes (or "species") that are ecologically differentiated, particularly in relation to temperature and moisture. The presence of more than one ecotype under the current concept of P. nigra has implications for biosecurity because the geographic extent of each type is not fully known: some countries may currently have only one of the biotypes. Introduction of additional lineages could expand the geographic extent of damage by the pest in some countries.
Aim: To test whether novel and previously hypothesized biogeogaphic barriers in the Australian Tr... more Aim: To test whether novel and previously hypothesized biogeogaphic barriers in the Australian Tropics represent significant disjunction points or hard barriers, or both, to the distribution of plants.
Background Uncertainty in comparative analyses can come from at least two sources: a) phylogeneti... more Background Uncertainty in comparative analyses can come from at least two sources: a) phylogenetic uncertainty in the tree topology or branch lengths, and b) uncertainty due to intraspecific variation in trait values, either due to measurement error or natural individual variation. Most phylogenetic comparative methods do not account for such uncertainties.
New combinations and names in Melaleuca (Myrtaceae)
Taxon, Jun 30, 2014
The taxonomy of Melaleuceae has been re-assessed in the light of DNA sequence studies and it is c... more The taxonomy of Melaleuceae has been re-assessed in the light of DNA sequence studies and it is concluded that all genera should be placed within Melaleuca. Beaufortia, Calothamnus, Conothamnus, Eremaea, Lamarchea, Petraeomyrtus, Phymatocarpus and Regelia and their constituent species are formally transferred to Melaleuca. One hundred and six nomenclatural changes are provided of which 72 are new combinations and 34 are new names.
Niche differentiation and spatial partitioning in the evolution of two Australian monsoon tropical tree species
Abstract
Aim
Geographical and climatic barriers to organismal dispersal and distribution pl... more Abstract
Aim
Geographical and climatic barriers to organismal dispersal and distribution play a major role in speciation. We use a sister-pair of widespread savanna trees (Melaleuca argentea and M. fluviatilis) to test the influence of putative barriers on divergence within and between species across an otherwise continuous landscape.
Location
The Australian monsoon tropics (AMT).
Methods
Chloroplast and nuclear DNA sequences were used to estimate variation between and within species. Hypotheses invoking vicariance and ecological speciation as the mechanisms of divergence between species were explicitly tested using ecological niche modelling.
Results
We found little evidence for divergence across the Carpentaria Basin, although some chloroplast DNA haplotypes were restricted to regions to the east or west. Pilbara populations were distinct from those to the east across the Great Sandy Desert, including those from the Kimberley. There was a complex pattern of genetic divergence and niche differentiation among M. argentea and M. fluviatilis within a region of secondary range overlap coincident with currently recognized species boundaries across the Great Dividing Range.
Main conclusions
The two morphospecies are ecologically and genetically distinct, and maintain those differences in sympatry. Speciation might have occurred in allopatry in separate drainage basins that later came into contact. The Pilbara population appears to be distinct but requires further investigation.
Need morphology always be required for new species descriptions?
Despite the widespread and common use of DNA-sequence data to estimate phylogenies, support or co... more Despite the widespread and common use of DNA-sequence data to estimate phylogenies, support or contest classifications, and identify species using barcodes, they are not commonly used as the primary or sole source of data for describing species. This is possibly due to actual or perceived pressure from peers to include morphology as the primary source of data for species descriptions. We find no compelling evidence to exclude DNA-only descriptions, or to insist that morphology always be included in a species description. It is not the data type per se that is important, but the science behind the taxonomic conclusions. Using alternative kinds of data for descriptions should not cause problems for taxonomy if links are kept with type specimens.
Melaleuca revisited: cpDNA and morphological data confirm that Melaleuca L. (Myrtaceae) is not monophyletic
With about 335 species, the tribe Melaleuceae comprises a major lineage within the Australian Myr... more With about 335 species, the tribe Melaleuceae comprises a major lineage within the Australian Myrtaceae. Here we investigate relationships within Melaleuceae using cpDNA sequences (ndhF) and 27 morphological characters. We find strong evidence for the non-monophyly of Melaleuca, with all other currently recognized genera of Melaleuceae (Beaufortia, Calothamnus, Conothamnus, Eremaea, Lamarchea, Petraeomyrtus, Phymatocarpus, Regelia) falling within that genus. Our findings are broadly consistent with previous studies using nuclear ITS DNA sequence data; however, the cpDNA phylogeny estimate is more resolved and has higher support for major nodes. Melaleuceae is found to comprise three major clades, each containing species of Melaleuca and each with good support. The M. leucadendra (broad-leaf paper-barks), M. uncinata, M. pungens and M. acacioides groups, New Caledonian callistemons, and all other currently recognized genera of Melaleuceae form one clade. Australian Callistemon species, which have been synonymised recently with Melaleuca, cluster within a second clade of Melaleuca that includes the M. fulgens, M. laxiflora and M. ordinifolia groups, and some members of the M. lanceolata and M. cuticularis groups. A third clade includes other members of the M. lanceolata and M. cuticularis groups, M. foliolosa and the M. huegelii group. No morphological support or diagnostic synapomorphies are identified for any of these clades. Together with previous studies, our findings indicate that the circumscription of Melaleuca, and the generic status of other genera within Melaleuceae, is poorly supported, and we propose that all genera within the Melaleuceae are synonymised with Melaleuca.
Invasion of two exotic terrestrial flatworms to subantarctic Macquarie Island
Invasive species are a serious threat to biodiversity worldwide. The relatively simple ecological... more Invasive species are a serious threat to biodiversity worldwide. The relatively simple ecological systems of the subantarctic have the potential to be significantly damaged by predatory species that invade. Two species of exotic, predatory, terrestrial flatworms were first collected in 1997 from two localities only 2 km apart, in the southeast of subantarctic Macquarie Island. The species were later identified as Kontikia andersoni and Arthurdendyus vegrandis. We report here the results of fieldwork in 2004 that established that both species now occupy about a seventh of the southeast of the island which has a total area of only 170 km2 and that there seem to be no barriers to further expansion. The island was first discovered in 1810 and so it is likely the species were introduced by means of human intervention within the last 200 years. We provide evidence to show that both species originated in New Zealand and have probably been on the island for ∼100 years giving an average rate of spread of about 10 m per year. Other species of Arthurdendyus have been introduced from New Zealand to the United Kingdom where they prey on earthworms. The quarantine significance of A. vegrandis for Australia is discussed and recommendations made to reduce the probability of it entering Tasmania where it has the potential to become an agricultural pest.
Reticulate evolution in the natural range of the invasive wetland tree species Melaleuca quinquenervia
The Melaleuca leucadendra complex (broad-leaf paperbarks; Myrtaceae) is a dominant component of t... more The Melaleuca leucadendra complex (broad-leaf paperbarks; Myrtaceae) is a dominant component of the tropical and sub-tropical biota of Australia, particularly in wetlands of high conservation significance. In Florida and other parts of the Americas, however, one member of the group (Melaleuca quinquenervia) is a serious ecological and economic weed. Understanding the relationships and evolution of the group is integral to both conservation and biocontrol efforts. Although the complex is currently considered to include up to 14 species, there has been some concern over taxonomic boundaries within the complex because most species are circumscribed only by combinations of characters, each of which also occurs in other species. Here, DNA sequence data derived from the chloroplast and two nuclear regions are used to explore the relationships of M. quinquenervia. We find little evidence for clear species boundaries within the M. leucadendra complex in general, with regional sharing of chloroplast haplotypes across morphologically defined taxa, indicating asymmetrical introgression or retention of ancestral haplotypes (lineage sorting). Phylogenies were further confounded by the recovery of multiple copies of both nuclear regions sequenced (ITS and rpb2) from many individuals. There was no clear evidence of polyploidy or pseudogenes, but multiple duplications of rpb2 could not be ruled out. Parsimony networks of the nuclear ITS region show some clustering of haplotypes by morphospecies but there is also evidence of both hybridisation and recombination. Signals of introgression were also evident in rpb2, supporting an hypothesis of recent or ongoing gene flow between M. quinquenervia and other members of the M. leucadendra complex. Both relaxed and fixed molecular-clock dating estimate the introgression to have occurred sometime within the past seven million years (95% CI: 0.7–18). The New Caledonian population of M. quinquenervia appears to have been established by dispersal from Australia during this period. M. quinquenervia is found to have alleles closely related to multiple different morphotaxa within the M. leucadendra complex, suggesting considerable past introgression into this taxon from some other members of the M. leucadendra complex, and this has implications for biocontrol efforts. The M. leucadendra complex appears to reflect early to intermediate stages of speciation, possibly driven by different ecologies.
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Papers by Robert (Bort) Edwards
Aim
Geographical and climatic barriers to organismal dispersal and distribution play a major role in speciation. We use a sister-pair of widespread savanna trees (Melaleuca argentea and M. fluviatilis) to test the influence of putative barriers on divergence within and between species across an otherwise continuous landscape.
Location
The Australian monsoon tropics (AMT).
Methods
Chloroplast and nuclear DNA sequences were used to estimate variation between and within species. Hypotheses invoking vicariance and ecological speciation as the mechanisms of divergence between species were explicitly tested using ecological niche modelling.
Results
We found little evidence for divergence across the Carpentaria Basin, although some chloroplast DNA haplotypes were restricted to regions to the east or west. Pilbara populations were distinct from those to the east across the Great Sandy Desert, including those from the Kimberley. There was a complex pattern of genetic divergence and niche differentiation among M. argentea and M. fluviatilis within a region of secondary range overlap coincident with currently recognized species boundaries across the Great Dividing Range.
Main conclusions
The two morphospecies are ecologically and genetically distinct, and maintain those differences in sympatry. Speciation might have occurred in allopatry in separate drainage basins that later came into contact. The Pilbara population appears to be distinct but requires further investigation.