ORCID Profile
0000-0002-4445-4026
Current Organisations
CSIRO
,
University of Western Australia
,
NSW Department of Primary Industries
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Publisher: Elsevier BV
Date: 03-2016
DOI: 10.1016/J.FSIGEN.2015.12.010
Abstract: Pollen can be a critical forensic marker in cases where determining geographic origin is important, including investigative leads, missing persons cases, and intelligence applications. However, its use has previously been limited by the need for a high level of specialization by expert palynologists, slow speeds of identification, and relatively poor taxonomic resolution (typically to the plant family or genus level). By contrast, identification of pollen through DNA barcoding has the potential to overcome all three of these limitations, and it may seem surprising that the method has not been widely implemented. Despite what might seem a straightforward application of DNA barcoding to pollen, there are technical issues that have delayed progress. However, recent developments of standard methods for DNA barcoding of pollen, along with improvements in high-throughput sequencing technology, have overcome most of these technical issues. Based on these recent methodological developments in pollen DNA barcoding, we believe that now is the time to start applying these techniques in forensic palynology. In this article, we discuss the potential for these methods, and outline directions for future research to further improve on the technology and increase its applicability to a broader range of situations.
Publisher: Wiley
Date: 03-2017
DOI: 10.3732/APPS.1600110
Publisher: Wiley
Date: 10-10-2007
Publisher: No publisher found
Date: 2013
DOI: 10.5061/DRYAD.JD183
Publisher: The Royal Society
Date: 04-2017
DOI: 10.1098/RSOS.170105
Abstract: 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 dispersal. Our study uses genetic analysis and information from historical sources to test the relative roles of chance and human-mediated dispersal in its distribution. The results confirm the Mesoamerican origins of the plant and show three patterns of human-mediated dispersal. S les from Spain showed greater genetic ersity than those from other Old World tropics, suggesting more instances of transatlantic introductions from the Americas to that country than to other parts of Africa and Asia. In iduals from the Philippines matched a population from South Central Mexico and were likely to have been direct, trans-Pacific introductions. Australian s les were genetically unique, indicating that the arrival of the species in the continent was independent of these European colonial activities. This suggests the possibility of pre-European human-mediated dispersal across the Pacific Ocean. These significant findings raise new questions for biogeographic studies that assume chance or transoceanic dispersal for disjunct plant distributions.
Publisher: Authorea, Inc.
Date: 02-06-2023
DOI: 10.22541/AU.168569305.58343243/V1
Abstract: Efforts to explore optimal molecular methods for identifying plant mixtures, particularly pollen, are increasing. Pollen identification (ID) and quantification is important in many fields, including pollination ecology and agricultural sciences, but quantifying mixture proportions remains challenging. Traditional pollen ID using microscopy is time-consuming, requires expertise, and has limited accuracy and throughput. Molecular barcoding approaches being explored offer improved accuracy and throughput. The common approach, licon sequencing, employs PCR lification to isolate DNA barcodes, but introduces significant bias, impairing downstream quantification. We apply a novel molecular hybridisation capture approach to artificial pollen mixtures, to improve upon current taxon ID and quantification methods. The method randomly fragments DNA, and uses RNA baits to capture DNA barcodes, which allows for PCR duplicate removal, reducing downstream quantification bias. Metabarcoding was tested using two reference libraries constructed from publicly available sequences the matK plastid barcode, and RefSeq complete chloroplast references. Single barcode-based taxon ID did not consistently resolve to species or genus level. The RefSeq chloroplast database performed better qualitatively but had limited taxon coverage (relative to species used here) and introduced ID issues. At family level, both databases yielded comparable qualitative results, but the RefSeq database performed better quantitatively. A restricted matK database containing only mixture species yielded sequence proportions highly correlated with input pollen proportions, demonstrating that hybridization capture usefulness for metabarcoding and quantifying pollen mixtures. The choice of reference database remains one of the most important factors affecting qualitative and quantitative accuracy.
Publisher: Wiley
Date: 07-09-2022
Abstract: The microbiomes associated with bee nests influence colony health through various mechanisms, although it is not yet clear how honeybee congeners differ in microbiome assembly processes, in particular the degrees to which floral visitations and the environment contribute to different aspects of ersity. We used DNA metabarcoding to sequence bacterial 16S rRNA from honey and stored pollen from nests of 4 honeybee species ( Apis cerana , A. dorsata , A. florea , and A. laboriosa ) s led throughout Yunnan, China, a global bio ersity hotspot. We developed a computational pipeline integrating multiple databases for quantifying key facets of ersity, including compositional, taxonomic, phylogenetic, and functional ones. Further, we assessed candidate drivers of observed microbiome dissimilarity, particularly differences in floral visitations, habitat disturbance, and other key environmental variables. Analyses revealed that microbiome alpha ersity was broadly equivalent across the study sites and between bee species, apart from functional ersity which was very low in nests of the reclusive A. laboriosa . Turnover in microbiome composition across Yunnan was driven predominantly by pollen composition. Human disturbance negatively impacted both compositional and phylogenetic alpha ersity of nest microbiomes, but did not correlate with microbial turnover. We herein make progress in understanding microbiome ersity associated with key pollinators in a bio ersity hotspot, and provide a model for the use of a comprehensive informatics framework in assessing pattern and drivers of ersity, which enables the inclusion of explanatory variables both subtly and fundamentally different and enables elucidation of emergent or unexpected drivers.
Publisher: Canadian Science Publishing
Date: 09-2016
Abstract: Identification of the species origin of pollen has many applications, including assessment of plant–pollinator networks, reconstruction of ancient plant communities, product authentication, allergen monitoring, and forensics. Such applications, however, have previously been limited by microscopy-based identification of pollen, which is slow, has low taxonomic resolution, and has few expert practitioners. One alternative is pollen DNA barcoding, which could overcome these issues. Recent studies demonstrate that both chloroplast and nuclear barcoding markers can be lified from pollen. These recent validations of pollen metabarcoding indicate that now is the time for researchers in various fields to consider applying these methods to their research programs. In this paper, we review the nascent field of pollen DNA barcoding and discuss potential new applications of this technology, highlighting existing limitations and future research developments that will improve its utility in a wide range of applications.
Publisher: Frontiers Media SA
Date: 13-09-2018
Publisher: Springer Science and Business Media LLC
Date: 12-2013
Publisher: Authorea, Inc.
Date: 29-01-2022
DOI: 10.22541/AU.164346764.44098850/V1
Abstract: Anthropogenic activities are leading to changes in the environment at global scales, and understanding these changes requires rapid, high-throughput methods of assessment. Pollen DNA metabarcoding and related methods provide advantages in throughput and efficiency over traditional methods, such as microscopic identification of pollen and visual observation of plant-pollinator interactions. Pollen DNA metabarcoding is currently being applied to assessments of plant-pollinator interactions and their responses to land-use change such as increased agricultural intensity and urbanisation, surveillance of ecosystem change, and monitoring of spatiotemporal distribution of allergenic pollen. In combination with historical specimens, pollen DNA metabarcoding can compare contemporary and past ecosystems. Current technical challenges with pollen DNA metabarcoding include the need to understand the relationship between sequence read and species abundance, develop methods for determining confidence limits for detection and taxonomic classification, increase method standardisation, and improve of gaps in reference databases. Future research expanding the method to intraspecific identification, analysis of DNA in ancient pollen s les, and increased use of museum and herbarium specimens could open further avenues for research. Ongoing developments in sequencing technologies can accelerate progress towards these goals. Global ecological change is happening rapidly, and we anticipate that high-throughput methods such as pollen DNA metabarcoding are critical for assessing these changes and providing timely management recommendations to preserve bio ersity and the evolutionary and ecological processes that support it.
Publisher: CSIRO Publishing
Date: 2014
DOI: 10.1071/BT13209
Abstract: The Kimberley region of Western Australia is recognised for its high bio ersity 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 ersity and population structure of the tree species across its range in the Kimberley and adjacent areas to the east. Genetic variation at six microsatellite loci in 220 in iduals from the entire species range was examined. Five weakly ergent populations, separated by west–east and coast–inland ides, were distinguished using spatial principal components analysis. However, the predominant pattern was low geographic structure and high gene flow. Coalescent analysis detected a population bottleneck and significant gene flow across these inferred biogeographic ides. Climate cycles and coastline changes following the last glacial maximum are implicated in decreases in ancient A. gregorii population size. Of all the potential gene flow vectors, various macropod species and humans are the most likely.
Publisher: Wiley
Date: 10-2013
DOI: 10.3732/APPS.1300035
Publisher: Academy of Science of South Africa
Date: 03-2008
Publisher: Elsevier BV
Date: 05-2004
Publisher: Authorea, Inc.
Date: 24-06-2023
DOI: 10.22541/AU.168757928.84749825/V1
Abstract: Globally, the ersity of arthropods and the plants upon which they rely are under increasing pressure due to a combination of biotic and abiotic anthropogenic stressors. Unfortunately, conventional survey methods used to monitor ecosystems are often challenging to conduct at large scales. Pan traps are a commonly used pollinator survey method and environmental DNA (eDNA) metabarcoding of pan-trap water may offer a high-throughput alternative to aid in the detection of both arthropods and the plant resources they rely on. Here, we examined if eDNA metabarcoding can be used to identify arthropod and plant species from pan-trap water, and invesitigated the effect of different DNA extraction methods. We then compared plant species identified by metabarcoding with observation-based floral surveys and also assessed the contribution of airborne plant DNA (plant DNA not carried by arthropods) using marble traps to reduce putative false positives in the pan trap dataset. Arthropod eDNA was only detected in 17% of pan trap s les and there was minimal overlap between the eDNA results and morphological identifications. In contrast, for plants, we detected 64 taxa, of which 53 were unique to the eDNA dataset, and no differences were identified between the two extraction kits. We were able to significantly reduce the contribution of airborne plant DNA to the final dataset using marble traps. This study demonstrates that eDNA metabarcoding of pan-trap water can detect plant resources used by arthropods and highlights the potential for eDNA metabarcoding to be applied to investigations of plant-animal interactions.
Publisher: Springer Science and Business Media LLC
Date: 24-02-2023
DOI: 10.1007/S10530-023-03017-3
Abstract: Understanding the historical context of biological invasions can improve weed management outcomes. In this study, we aim to identify the introduction pathway of bitou bush ( Chrysanthemoides monilifera subsp. rotundata ) into Australia and its biogeographical origin in southern Africa by combining multiple lines of evidence from genomic tools and historical documentation. Geographic structure of genomic ersity based on SNPs supported the previous analysis of the invasion pathway of bitou bush between the two countries and within Australia, namely that all Australian material originated from the southern part of the South African distribution. Our synthesis of historical records points to the introduction of this plant into eastern Australia in Newcastle, New South Wales, from its native range in South Africa, via dry shipping ballast in about 1900. Variation in the chloroplast genome was also informative as to the biogeographical origin of Australian material and the context of the introduction. Ten unique haplotypes were discovered in South Africa with only one occurring throughout Australia, indicating an introduction from a single source population to eastern Australia. The matching haplotype was from East London, a port in South Africa with documented shipping connections to Newcastle in eastern Australia, where the weed was first recorded. Historical records suggest that the most plausible explanation for the origins of the isolated bitou bush population in Western Australia is via the shipping of steel billets or landscape plantings associated with shipping companies. The most likely introduction pathway linked the eastern Australian steel processing ports of Newcastle or Port Kembla to the Western Australian port of Kwinana in 1995. Discovering the origin and pathway of bitou bush invasions in Australia opens new opportunities for sourcing biological control agents with a higher chance of impact as well as identifying additional quarantine measures to improve outcomes and reduce long-term costs to management.
Publisher: Wiley
Date: 08-2022
DOI: 10.1002/ECE3.9179
Abstract: Many plants exchanged in the global redistribution of species in the last 200 years, particularly between South Africa and Australia, have become threatening invasive species in their introduced range. Refining our understanding of the genetic ersity and population structure of native and alien populations, introduction pathways, propagule pressure, naturalization, and initial spread, can transform the effectiveness of management and prevention of further introductions. We used 20,221 single nucleotide polymorphisms to reconstruct the invasion of a coastal shrub, Chrysanthemoides monilifera ssp. rotundata (bitou bush) from South Africa, into eastern Australia (EAU), and Western Australia (WAU). We determined genetic ersity and population structure across the native and introduced ranges and compared hypothesized invasion scenarios using Bayesian modeling. We detected considerable genetic structure in the native range, as well as differentiation between populations in the native and introduced range. Phylogenetic analysis showed the introduced s les to be most closely related to the southern‐most native populations, although Bayesian analysis inferred introduction from a ghost population. We detected strong genetic bottlenecks during the founding of both the EAU and WAU populations. It is likely that the WAU population was introduced from EAU, possibly involving an uns led ghost population. The number of private alleles and polymorphic SNPs successively decreased from South Africa to EAU to WAU, although heterozygosity remained high. That bitou bush remains an invasion threat in EAU, despite reduced genetic ersity, provides a cautionary biosecurity message regarding the risk of introduction of potentially invasive species via shipping routes.
Publisher: Liverpool University Press
Date: 02-2015
DOI: 10.3197/096734015X14183179969827
Abstract: The history of botanical exchanges between Africa and the Indian subcontinent reaches back in time over 5,000 years. Recent advances in archaeobotany have revealed these connections through evidence of food crops of African origin found at various archaeological sites in the subcontinent. However, little is known about the people that brought the crops to these places and other parts of the Indian Ocean world. This is also the case with other plants from Africa such as the charismatic baobab tree ( Adansonia digitata L. ) that appears to have had a longstanding presence in South Asia. Most scholarly accounts assume that 'Arab traders' were responsible for introducing baobabs to this region but do not offer any reasons for their doing so. Few scholars, if any, have sought to relate the dispersal of baobabs with the history of African migrations to the region. This paper reveals the elusive traces of their entwined environmental histories by linking baobab genetics with historical accounts and cultural evidence of the presence of African diasporic communities in South Asia.
Publisher: CSIRO Publishing
Date: 28-10-2021
DOI: 10.1071/ZO20085
Abstract: Determining the diet of flying-foxes can increase understanding of how they function as pollinators and seed dispersers, as well as managing any negative impacts of large roosts. Traditional methods for diet analysis are time consuming, and not feasible to conduct for hundreds of animals. In this study, we optimised a method for diet analysis, based on DNA metabarcoding of environmental DNA (eDNA) from pollen and other plant parts in the faeces. We found that existing eDNA metabarcoding protocols are suitable, with the most useful results being obtained using a commercial food DNA extraction kit, and sequencing 350–450 base pairs of a DNA barcode from the internally transcribed spacer region (ITS2), with ~550 base pairs of the chloroplast rubisco large subunit (rbcL) as a secondary DNA barcode. A list of forage plants was generated for the little red flying-fox (Pteropus scapulatus), the black flying-fox (Pteropus alecto) and the spectacled flying-fox (Pteropus conspicillatus) from our collection sites across Queensland. The diets were determined to comprise predominantly Myrtaceae species, particularly those in the genera Eucalyptus, Melaleuca and Corymbia. With more plant genomes becoming publicly available in the future, there are likely to be further applications of eDNA methods in understanding the role of flying-foxes as pollinators and seed dispersers.
Publisher: The Royal Society
Date: 09-2015
DOI: 10.1098/RSOS.150370
Abstract: To investigate the pathways of introduction of the African baobab, Adansonia digitata , to the Indian subcontinent, we examined 10 microsatellite loci in in iduals 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 congruence of African clusters with biogeographic regions except along the Zambezi (Mozambique) and Kilwa (Tanzania), where populations included a mixture of in iduals assigned to at least two different clusters. In iduals from West Africa, the Mascarenes, southeast India and Malaysia shared a cluster. Baobabs from western and central India clustered separately from Africa. Genetic ersity was lower in populations from the Indian subcontinent than in African populations, but the former contained private alleles. Phylogenetic analysis showed Indian populations were closest to those from the Mombasa-Dar es Salaam coast. The genetic results provide evidence of multiple introductions of African baobabs to the Indian subcontinent over a longer time period than previously assumed. In iduals belonging to different genetic clusters in Zambezi and Kilwa may reflect the history of trafficking captives from inland areas to supply the slave trade between the fifteenth and nineteenth centuries. Baobabs in the Mascarenes, southeast India and Malaysia indicate introduction from West Africa through eighteenth and nineteenth century European colonial networks.
Publisher: Public Library of Science (PLoS)
Date: 27-04-2015
Publisher: Wiley
Date: 26-09-2022
DOI: 10.1111/MEC.16689
Abstract: Anthropogenic activities are triggering global changes in the environment, causing entire communities of plants, pollinators and their interactions to restructure, and ultimately leading to species declines. To understand the mechanisms behind community shifts and declines, as well as monitoring and managing impacts, a global effort must be made to characterize plant-pollinator communities in detail, across different habitat types, latitudes, elevations, and levels and types of disturbances. Generating data of this scale will only be feasible with rapid, high-throughput methods. Pollen DNA metabarcoding provides advantages in throughput, efficiency and taxonomic resolution over traditional methods, such as microscopic pollen identification and visual observation of plant-pollinator interactions. This makes it ideal for understanding complex ecological networks and their responses to change. Pollen DNA metabarcoding is currently being applied to assess plant-pollinator interactions, survey ecosystem change and model the spatiotemporal distribution of allergenic pollen. Where s les are available from past collections, pollen DNA metabarcoding has been used to compare contemporary and past ecosystems. New avenues of research are possible with the expansion of pollen DNA metabarcoding to intraspecific identification, analysis of DNA in ancient pollen s les, and increased use of museum and herbarium specimens. Ongoing developments in sequencing technologies can accelerate progress towards these goals. Global ecological change is happening rapidly, and we anticipate that high-throughput methods such as pollen DNA metabarcoding are critical for understanding the evolutionary and ecological processes that support bio ersity, and predicting and responding to the impacts of change.
Publisher: Wiley
Date: 07-09-2018
DOI: 10.1111/MEC.14840
Abstract: Pollen DNA metabarcoding-marker-based genetic identification of potentially mixed-species pollen s les-has applications across a variety of fields. While basic species-level pollen identification using standard DNA barcode markers is established, the extent to which metabarcoding (a) correctly assigns species identities to mixes (qualitative matching) and (b) generates sequence reads proportionally to their relative abundance in a s le (quantitative matching) is unclear, as these have not been assessed relative to known standards. We tested the quantitative and qualitative robustness of metabarcoding in constructed pollen mixtures varying in species richness (1-9 species), taxonomic relatedness (within genera to across class) and rarity (5%-100% of grains), using Illumina MiSeq with the markers rbcL and ITS2. Qualitatively, species composition determinations were largely correct, but false positives and negatives occurred. False negatives were typically driven by lack of a barcode gap or rarity in a s le. Species richness and taxonomic relatedness, however, did not strongly impact correct determinations. False positives were likely driven by contamination, chimeric sequences and/or misidentification by the bioinformatics pipeline. Quantitatively, the proportion of reads for each species was only weakly correlated with its relative abundance, in contrast to suggestions from some other studies. Quantitative mismatches are not correctable by consistent scaling factors, but instead are context-dependent on the other species present in a s le. Together, our results show that metabarcoding is largely robust for determining pollen presence/absence but that sequence reads should not be used to infer relative abundance of pollen grains.
Publisher: Coleopterists Society
Date: 03-2008
DOI: 10.1649/984.1
Publisher: Wiley
Date: 11-2021
DOI: 10.1002/ECE3.8281
Abstract: Molecular identification of mixed‐species pollen s les has a range of applications in various fields of research. To date, such molecular identification has primarily been carried out via licon sequencing, but whole‐genome shotgun (WGS) sequencing of pollen DNA has potential advantages, including (1) more genetic information per s le and (2) the potential for better quantitative matching. In this study, we tested the performance of WGS sequencing methodology and publicly available reference sequences in identifying species and quantifying their relative abundance in pollen mock communities. Using mock communities previously analyzed with DNA metabarcoding, we sequenced approximately 200Mbp for each s le using Illumina HiSeq and MiSeq. Taxonomic identifications were based on the Kraken k ‐mer identification method with reference libraries constructed from full‐genome and short read archive data from the NCBI database. We found WGS to be a reliable method for taxonomic identification of pollen with near 100% identification of species in mixtures but generating higher rates of false positives (reads not identified to the correct taxon at the required taxonomic level) relative to rbcL and ITS2 licon sequencing. For quantification of relative species abundance, WGS data provided a stronger correlation between pollen grain proportion and sequence read proportion, but erged more from a 1:1 relationship, likely due to the higher rate of false positives. Currently, a limitation of WGS‐based pollen identification is the lack of representation of plant ersity in publicly available genome databases. As databases improve and costs drop, we expect that eventually genomics methods will become the methods of choice for species identification and quantification of mixed‐species pollen s les.
Publisher: Wiley
Date: 06-2017
DOI: 10.3732/APPS.1600124
Publisher: Elsevier BV
Date: 05-2003
Publisher: Wiley
Date: 02-2009
Publisher: No publisher found
Date: 2014
Publisher: Wiley
Date: 05-10-2023
DOI: 10.1002/EDN3.471
Publisher: Wiley
Date: 27-04-2008
Publisher: Oxford University Press (OUP)
Date: 26-03-2012
Publisher: Wiley
Date: 22-04-2013
DOI: 10.1111/JBI.12102
Publisher: Public Library of Science (PLoS)
Date: 04-2015
Publisher: Wiley
Date: 22-01-2022
DOI: 10.1111/AEC.13143
Abstract: The little red flying‐fox ( Pteropus scapulatus, Pteropodidae) is the most widely distributed of the four Australian mainland flying‐fox ( Pteropus ) species. They move very large distances following foraging resources and congregate in large numbers which often causes human‐animal conflict. To better understand the resources that drive these movements and aggregations, we investigated the diet of the little red flying‐fox using data from five sources: (i) faecal eDNA metabarcoding of field s led little red flying‐foxes (ii) identification of foraging locations through satellite tracking (iii) a literature search (iv) a search of online databases and (v) an expert survey. Our sources revealed a specialist nectarivore diet containing 204 species, dominated by floral products from the plant family Myrtaceae. We consider a small number of widely occurring and structurally dominant Myrtaceae, particularly from the genera Corymbia , Eucalyptus and Melaleuca , as major diet species that regularly drive mass aggregations. In addition, we consider a moderate number of species dominated by the Myrtaceae as important diet species and a large number of species from erse taxa as supplementary diet species. Fruit represents approximately 5% of the diet suggesting that the little red flying‐fox is unlikely to be a major pest of horticultural crops or disperser of weeds. The combination of long‐distance movement and a wide range of diet species results in a long‐distance pollination service to many plant species which likely promotes genetic mixing between isolated populations of plants. Our understanding of the little red flying‐fox diet allows us to better predict mass migrations and aggregations at a continental scale and allows us to clearly identify key foraging habitat so that informed management decisions can be made.
Publisher: Elsevier BV
Date: 04-2004
Publisher: Elsevier BV
Date: 05-2011
Location: Australia
No related grants have been discovered for Karen Bell.