Kor-jent Van Dijk

Kor-jent Van Dijk
University of Adelaide · School of Biological Sciences

PhD
NGS, Hybrid Capture, population genetics

About

61
Publications
11,406
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Introduction
I am a research associate in Prof. Michelle Waycott research group. I am leading research into population genetics and evolution of plants, and specialised seagrasses. I utilise molecular genetic techniques– traditional and NGS– to establish the relationship among species, populations and genetic individuals. In the recent years we have been developing Hybrid Capture methods (OzBaits) to assess phylogenetic and phylogeographic relationships among plants using dozens of nuclear and plastid loci.
Additional affiliations
September 2012 - present
University of Adelaide
Position
  • Researcher
March 2009 - August 2010
James Cook University
Position
  • PostDoc Position
Description
  • I have been actively involved in 2nd and 3d year genetics courses, overseeing the practical coursework of both and presenting lectures. BZ2420/BZ5420 Genetics for Biology BZ3450/BZ5450 Ecological and Conservation Genetics
February 2009 - August 2012
James Cook University
Position
  • PostDoc Position

Publications

Publications (61)
Article
Full-text available
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 samples relies on the ability to match unknown sequences to known reference libraries. Without comprehensive reference databases, species can go...
Preprint
Full-text available
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 samples relies on the ability to match unknown sequences to known reference libraries. Without comprehensive reference databases, species can go...
Article
Full-text available
Halophila johnsonii is an endangered seagrass species that is restricted to the southeast coast of Florida, United States. Its taxonomic status has been called into question, in particular, given the close morphological and genetic similarity of H. johnsonii and the widely distributed and morphologically variable Halophila ovalis, which is largely...
Article
Full-text available
Metabarcoding of plant DNA recovered from environmental samples, termed environmental DNA (eDNA), has been used to detect invasive species, track biodiversity changes, and reconstruct past ecosystems. The P6 loop of the trnL intron is the most widely utilised gene region for metabarcoding plants due to the short fragment length and subsequent ease...
Preprint
A proliferation in environmental DNA (eDNA) research has increased the reliance on reference sequence databases to assign unknown DNA sequences to known taxa. Without comprehensive reference databases, DNA extracted from environmental samples cannot be correctly assigned to taxa, limiting the use of this genetic information to identify organisms in...
Preprint
Full-text available
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 (OzBa...
Preprint
Full-text available
Metabarcoding of plant DNA recovered from environmental samples, termed environmental DNA (eDNA), has been used to detect invasive species, track biodiversity changes and reconstruct past ecosystems. The P6 loop of the trnL intron is the most widely utilized gene region for metabarcoding plants due to the short fragment length and subsequent ease o...
Article
The spatial genetic structure of marine organisms is related to dispersal and life-history traits, historical processes, current oceanographic connectivity and habitat features. Here, we assessed the relative importance of these factors for the genetic structure of a broad range of marine species in the Indo Australian Archipelago (IAA). We collate...
Article
Full-text available
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.
Article
Full-text available
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 suggestion...
Article
Seagrasses are important habitats providing many ecological services. Most species have broad distributions with maximum dispersal distances of 100's of kms, however there is limited understanding of dispersal distances of colonising species like Halodule uninervis. It commonly grows in disturbed environments and could disperse to other meadows via...
Article
Full-text available
Seagrasses are important marine ecosystems situated throughout the world’s coastlines. They are facing declines around the world due to global and local threats such as rising ocean temperatures, coastal development and pollution from sewage outfalls and agriculture. Efforts have been made to reduce seagrass loss through reducing local and regional...
Article
Full-text available
The genetic population structure of Halodule wrightii at locations in Florida, North Carolina, and Bermuda was investigated using 11 polymorphic microsatellite loci on samples representing 15 sites. We measured allelic diversity and genotypic richness and determined population differentiation and gene flow using principal components and k-means pop...
Article
Novel single nucleotide polymorphism loci were identified for teak (Tectona grandis Linn. f.) using a combined Next Generation Sequencing approach on the Illumina MiSeq system with genotyping on the Agena MassARRAY iPLEX™ platform. Three hundred and forty four putative loci were identified through sequencing of DNA fragments following a modified do...
Article
Full-text available
Evaluating genetic diversity of seagrasses provides insight into reproductive mode and adaptation potential, and is therefore integral to broader conservation strategies for coastal ecosystems. In this study, we assessed genetic diversity, population structure and gene flow in an opportunistic seagrass, Syringodium filiforme, in the Florida Keys an...
Data
Pairwise genetic differentiation. FST values are provided to the left of the diagonal and Jost's D values are provided to the right of the diagonal. Bold text indicates significance based on non-overlapping confidence intervals. (DOCX)
Data
Principal components analysis (PCA) plot. Axis loading values are depicted for the two principle coordinate axes containing the greatest amount of variation, PC1 (18.3% variance) and PC2 (7.7% variance). Genotypes from each population group are distinguished by color and shape (Atlantic: blue circles, Gulf: orange triangles, Bermuda: yellow diamond...
Data
Sample site GPS coordinates. GPS coordinates mark the exact location of each sample site. Latitude and longitude are in decimal degrees. (DOCX)
Data
Values for relative magnitude and direction of gene flow. Values represent the relative amount of gene flow from populations in the first column to receiving populations identified in the first row. For example, the highest amount of gene flow (1.000) occurs from Carysfort to Davis, while the lowest amount of gene flow occurs from the Bahamas to Ke...
Article
Full-text available
Many marine species have widespread geographic ranges derived from their evolutionary and ecological history particularly their modes of dispersal. Seagrass (marine angiosperm) species have ranges that are unusually widespread, which is not unexpected following recent reviews of reproductive strategies demonstrating the potential for long‐distance...
Article
Building DNA barcode databases for plants has historically been ad hoc, and often with a relatively narrow taxonomic focus. To realise the full potential of DNA barcoding for plants, and particularly its application to metabarcoding for mixed-species environmental samples, systematic sequencing of reference collections is required using an augmente...
Chapter
Connectivity among populations influences resilience, genetic diversity , adaptation and speciation, so understanding this process is fundamental for conservation and management. This chapter summarises the main mechanisms of gene flow within and among seagrass meadows, and what we know about the spatial patterns of gene flow around Australia’s coa...
Article
The limited data available on the genetic diversity of the temperate seagrass Amphibolis antarctica indicate diversity may be extremely low. The available previous study was based on allozymes and restriction fragment length polymorphisms (RFLPs) as molecular markers. Numerous studies into other seagrass taxa have shown that these markers may not h...
Article
Full-text available
Clonality is common in many aquatic plant species, including seagrasses, where populations are maintained through a combination of asexual and sexual reproduction. One common measure used to describe the clonal structure of populations is clonal richness. Clonal richness is strongly dependent on the biological characteristics of the species, and ho...
Article
Seagrass species form important marine and estuarine habitats providing valuable ecosystem services and functions. Coastal zones that are increasingly impacted by anthropogenic development have experienced substantial declines in seagrass abundance around the world. Australia, which has some of the world’s largest seagrass meadows and is home to ov...
Article
Understanding spatial patterns of gene flow and genetic structure is essential for the conservation of marine ecosystems. Contemporary ocean currents and historical isolation due to Pleistocene sea-level fluctuations have been predicted to influence the genetic structure in marine populations. In the Indo-Australian Archipelago (IAA), the world's h...
Article
Next-generation sequencing (NGS) provides numerous tools for population and systematic studies. These tools are a boon to researchers working with non-model and poorly characterised organisms where little or no genomic resources exist. Several techniques have been developed to subsample the genomes of multiple individuals from related populations a...
Article
Phenetic analysis of morphological characters in different species of Onobrychis Miller sect. HymenobrychisDC.(Fabaceae),classi edthem in two main groups based on corolla features. To determine the phylogenetic relationships among the 13 species, chloroplast DNA sequences were used. Analysis of these data resulted in a well-resolved and well-suppor...
Data
Table S1. Current velocities at Back‐Reef and Mid‐Lagoon at Puerto Morelos reef lagoon during 2005, together with wind speed and direction. Table S2. Thalassia testudinum. Dispersal patterns of pollen with hydrodynamic parameters in the Puerto Morelos Reef Lagoon during pre‐trials in 2005. Table S3. Polymorphic microsatellite markers for Thalassi...
Article
Full-text available
The high prevalence of dioecy in marine angiosperms or seagrasses (>50% of all species) is thought to enforce cross-fertilization. However, seagrasses are clonal plants, and they may still be subject to sibling-mating or bi-parental inbreeding if the genetic neighborhood is smaller than the size of the genets. We tested this by determining the gene...
Article
182 SNP markers were developed for Ayous (Triplochiton scleroxylon K. Schum) by incorporating information from two next generation sequencing approaches (RADseq Floragenex and AFLPseq IonTorrent PGM) into a single genotyping panel for MassARRAY® iPLEX™. This set of markers was successfully used to genotype 753 individuals from 43 populations in fiv...
Article
Full-text available
Novel single nucleotide polymorphisms (SNPs) and insertion/deletions (INDELs) were identified for the Bigleaf maple (Acer macrophyllum Pursch) using a combined next generation sequencing approach on the Ion Torrent PGM system with genotyping on the MassARRAY® iPLEX™ platform. Five hundred and ninety-eight putative loci were identified through seque...
Article
A new subtribal classification of the Fabaceae-Caraganeae is presented informed by phylogenetic reconstruction using the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA (nr DNA) for 17 genera belonging to tribes Caraganeae, Galegeae and Astragaleae. Based on these results we propose to erect a new subtribe Chesneyinae Ranjbar,...
Article
Full-text available
A movement ecology framework is applied to enhance our understanding of the causes, mechanisms and consequences of movement in seagrasses: marine, clonal, flowering plants. Four life-history stages of seagrasses can move: pollen, sexual propagules, vegetative fragments and the spread of individuals through clonal growth. Movement occurs on the wate...
Article
Full-text available
• Premise of the study: New microsatellites were developed for the seagrass Thalassia hemprichii (Hydrocharitaceae), a long-lived seagrass species that is found throughout the shallow waters of tropical and subtropical Indo-West Pacific. Three multiplex PCR panels were designed utilizing new and previously developed markers, resulting in a toolkit...
Article
Full-text available
• Premise of the study: A total of 17 polymorphic microsatellite markers were developed for the tropical Atlantic seagrass Syringodium filiforme (Cymodoceaceae), enabling analysis of population genetic structure in this species for the first time. • Methods and Results: The 17 primers amplified di- and trinucleotide repeats revealing two to eight a...
Article
Full-text available
Halophytes, such as seagrasses, predominantly form habitats in coastal and estuarine areas. These habitats can be seasonally exposed to hypo-salinity events during watershed runoff exposing them to dramatic salinity shifts and osmotic shock. The manifestation of this osmotic shock on seagrass morphology and phenology was tested in three Indo-Pacifi...
Article
Full-text available
Global seagrass losses parallel significant declines observed in corals and mangroves over the past 50 years. These combined declines have resulted in accelerated global losses to ecosystem services in coastal waters. Seagrass meadows can be extensive (hundreds of square kilometers) and long-lived (thousands of years), with the meadows persisting p...
Article
Full-text available
The first microsatellite primers were developed for Solanum centrale, a native Australian species used in the bush foods industry. Existing markers developed for other Solanum species were also amplified. Using an enrichment cloning protocol, seven novel markers were developed, and 48 existing markers from other Solanum species were tested, resulti...
Article
The clonal structure of the tropical seagrass Thalassia testudinum was studied at 16 sites along the Mexican Atlantic coast, situated in back-reef, shallow coastal and lagoon habitats. Thalassia testudinum was highly clonal, with an overall average clonal richness (R) of 0.55. The largest genet found in this study extended throughout the sampling a...
Article
Full-text available
Marine ecosystems are traditionally considered to be highly connected, caused by long-distance movements of propagules in an open fluid medium. But this principle is not universal, and populations of many marine organisms have restricted gene-flow, including ones with drifting propagules. Direct tracking of marine free-floating propagules over larg...
Article
Passage of hurricane Wilma (October 2005, category 4, duration similar to 60 h) over Puerto Morelos, Mexican Caribbean, allowed verification of a previous experiment simulating hurricane-like impacts on the seagrass beds in its back-reef lagoon. At two mid-lagoon stations, numbers of the seagrass Syringodium filiforme and macro-algae Udotea spp., P...
Article
Estimates for the production of calcium carbonate by Halimeda spp. have been based on limited measures in small areas or over short periods, subsequently extrapolated over larger temporal and spatial scales. The accuracy of these extrapolations depends on the variations in time and space of the parameters used for the derivations of the production,...
Article
We isolated 14 polymorphic microsatellite loci for the western Atlantic tropical seagrass, Thalassia testudinum, using two different enrichment procedures. Polymorphism was screened among samples from Mexico and Panama. Allelic diversity varied between three and 17 alleles per locus, and expected heterozygosity ranged from 0.271 to 0.859.
Article
Full-text available
Halimeda incrassata is the most abundant of Halimeda species growing in the Puerto Morelos reef lagoon (Mexico). Somatic plus calcareous dry biomass was 120.32 g m2, 117.99 g m2 and 77.90 g m2 at the Reef-, Lagoon-, and Beach-station respectively. Growth was measured during a period of two weeks in the months November, December (1997) and January (...

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