ORCID Profile
0000-0002-6521-2843
Current Organisation
University of Adelaide
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Publisher: MDPI AG
Date: 13-01-2023
DOI: 10.3390/D15010111
Abstract: A molecular genetic approach was used to elucidate the phylogeographic relationships of the clover grass (Halophila baillonii Asch.) from three key regions within its current distributional range. Halophila baillonii is a small seagrass that has historically been only found in a few locations in the Caribbean and Atlantic coast of Brazil. In the past few decades H. baillonii has also been observed in the Eastern Tropical Pacific (ETP). Very little is known about the relationship between the ETP populations and the Caribbean and Atlantic ones. To study their relationship, we used a hybrid capture approach targeting chloroplast loci on s les from Belize, Brazil, and the Pacific coast of Costa Rica. Phylogenetic analyses resolved H. baillonii as monophyletic and placed the s les from Belize and Costa Rica in a clade sister to the Brazilian ones. The results clearly indicate that the ETP s les are very closely related to Belize and that the most likely explanation of its occurrence in the ETP is a recent introduction, possibly as a consequence of the opening of the Panama Canal.
Publisher: MDPI AG
Date: 10-12-2020
DOI: 10.3390/D12120468
Abstract: A hybrid origin for a conservation listed taxon will influence its status and management options. Here, we investigate the genetic origins of a nationally endangered listed taxon—Eucalyptus paludicola—a tree that is restricted to the Fleurieu Peninsula and Kangaroo Island of South Australia. Since its description in 1995, there have been suggestions that this taxon may potentially be a stable hybrid species. Using a high throughput sequencing approach, we developed a panel of polymorphic loci that were screened across E. paludicola and its putative parental species E. cosmophylla and E. ovata. Bayesian clustering of the genotype data identified separate groups comprising E. ovata and E. cosmophylla while E. paludicola in iduals were admixed between these two, consistent with a hybrid origin. Hybrid class assignment tests indicate that the majority of E. paludicola in iduals (~70%) are F1 hybrids with a low incidence of backcrossing. Most of the post-F1 hybrids were associated with revegetation sites suggesting they may be maladapted and rarely reach maturity under natural conditions. These data support the hypothesis that E. paludicola is a transient hybrid entity rather than a distinct hybrid species. We briefly discuss the conservation implications of our findings.
Publisher: Elsevier BV
Date: 09-2021
Publisher: Wiley
Date: 04-2022
DOI: 10.1002/ECE3.8816
Abstract: Metabarcoding has improved the way we understand plants within our environment, from their ecology and conservation to invasive species management. The notion of identifying plant taxa within environmental s les relies on the ability to match unknown sequences to known reference libraries. Without comprehensive reference databases, species can go undetected or be incorrectly assigned, leading to false‐positive and false‐negative detections. To improve our ability to generate reference sequence databases, we developed a targeted capture approach using the OZBaits_CP V1.0 set, designed to capture chloroplast gene regions across the entirety of flowering plant ersity. We focused on generating a reference database for coastal temperate plant species given the lack of reference sequences for these taxa. Our approach was successful across all specimens with a target gene recovery rate of 92%, which was achieved in a single assay (i.e., s les were pooled), thus making this approach much faster and more efficient than standard barcoding. Further testing of this database highlighted 80% of all s les could be discriminated to family level across all gene regions with some genes achieving greater resolution than others—which was also dependent on the taxon of interest. Thus, we demonstrate the importance of generating reference sequences across multiple chloroplast gene regions as no single loci are sufficient to discriminate across all plant groups. The targeted capture approach outlined in this study provides a way forward to achieve this.
Publisher: Wiley
Date: 2021
DOI: 10.1111/EMR.12452
Abstract: Three case studies involving two temperate Australian seagrass species – Pondweed ( Ruppia tuberosa ) and Ribbon Weed ( Posidonia australis ) – highlight different approaches to their restoration. Seeds and rhizomes were used in three collaborative programmes to promote new approaches to scale up restoration outcomes.
Publisher: Authorea, Inc.
Date: 25-03-2022
DOI: 10.22541/AU.164823556.63225773/V1
Abstract: Metabarcoding has improved the way we understand plants within our environment, from their ecology and conservation to invasive species management. The notion of identifying plant taxa within environmental s les relies on the ability to match unknown sequences to known reference libraries. Without comprehensive reference databases, species can go undetected or be incorrectly assigned, leading to false positive and negative detections. To improve our ability to generate reference sequence databases we developed a targeted capture approach using the OZBaits_CP V1.0 set, designed to capture chloroplast gene regions across the entirety of flowering plant ersity. We focused on generating a reference database for coastal temperate plant species given the lack of reference sequences for these taxa. Our approach was successful across all specimens with a target gene recovery rate of 92% which was achieved in a single assay (i.e., s les were pooled), thus making this approach much faster and more efficient than standard barcoding. Further testing of this database highlighted 80% of all s les could be discriminated to family level across all gene regions with some genes achieving greater resolution than others – which was also dependant on the taxon of interest. Thus, we demonstrate the importance of generating reference sequences across multiple chloroplast gene regions as no single loci is sufficient to discriminate across all plant groups. The targeted capture approach outlined in this study provides a way forward to achieve this.
Publisher: Wiley
Date: 29-08-2018
DOI: 10.1002/ECE3.4443
Publisher: Cold Spring Harbor Laboratory
Date: 07-09-2021
DOI: 10.1101/2021.09.06.456727
Abstract: Novel multi-gene targeted capture probes have been developed with the objective of obtaining multi-locus high quality sequence reads across any angiosperm lineage. Using existing genomic and transcriptomic data, two independent single assay probe/bait sets have been developed, the first targeting conserved exons from 20 low copy nuclear genes (OzBaits_NR V1.0) and the second, 19 plastid gene regions (OZBaits_CP V1.0). These ‘universal’ bait sets can efficiently generate DNA sequence data that are suitable for systematics and evolutionary studies of flowering plants. The bait sets can be ordered as Daicel-Arbor Sciences custom myBaits. We demonstrate the utility of the bait set in consistently recovering the targeted genomic regions across an evolutionarily broad range of angiosperm taxa.
Publisher: Wiley
Date: 07-2023
DOI: 10.1002/ECE3.10257
Abstract: Understanding patterns of gene flow and processes driving genetic differentiation is important for a broad range of conservation practices. In marine organisms, genetic differentiation among populations is influenced by a range of spatial, oceanographic, and environmental factors that are attributed to the seascape. The relative influences of these factors may vary in different locations and can be measured using seascape genetic approaches. Here, we applied a seascape genetic approach to populations of the seagrass, Thalassia hemprichii , at a fine spatial scale (~80 km) in the Kimberley coast, western Australia, a complex seascape with strong, multidirectional currents greatly influenced by extreme tidal ranges (up to 11 m, the world's largest tropical tides). We incorporated genetic data from a panel of 16 microsatellite markers, overwater distance, oceanographic data derived from predicted passive dispersal on a 2 km‐resolution hydrodynamic model, and habitat characteristics from each meadow s led. We detected significant spatial genetic structure and asymmetric gene flow, in which meadows 12–14 km apart were less connected than ones 30–50 km apart. This pattern was explained by oceanographic connectivity and differences in habitat characteristics, suggesting a combined scenario of dispersal limitation and facilitation by ocean current with local adaptation. Our findings add to the growing evidence for the key role of seascape attributes in driving spatial patterns of gene flow. Despite the potential for long‐distance dispersal, there was significant genetic structuring over small spatial scales implicating dispersal and recruitment bottlenecks and highlighting the importance of implementing local‐scale conservation and management measures.
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.
No related grants have been discovered for Kor-jent van Dijk.