Simon Neil Jarman

Simon Neil Jarman
Curtin University · Molecular and Life Sciences

PhD

About

309
Publications
54,048
Reads
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7,413
Citations
Citations since 2016
98 Research Items
4984 Citations
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Introduction
I am a molecular ecologist. I originally trained in genetics at the University of Aberdeen, Scotland. I studied for my PhD on Antarctic krill genetics at the University of Tasmania. I have spent the past fourteen years working on expanding the field of molecular ecology, particularly in the use of molecular biological methods to study animal age and diet.
Additional affiliations
October 2017 - November 2017
Curtin University
Position
  • Professor
September 2002 - April 2016
Australian Antarctic Division
Position
  • Group Leader
September 2001 - present
Australian Antarctic Division
Position
  • Senior Researcher
Description
  • Postgraduate supervision. I have supervised 11 PhD students and three Masters students from a variety of institutions in Australia and Europe.
Education
September 1996 - September 2001
University of Tasmania
Field of study
  • Genetics of Antarctic krill
September 1992 - September 1995
University of Aberdeen
Field of study
  • Genetics

Publications

Publications (309)
Preprint
Full-text available
Lifespan is a key attribute of a species’ life cycle and varies extensively among major lineages of animals. In fish, lifespan varies by several orders of magnitude, with reported values ranging from less than one year to approximately 400 years. Lifespan information is particularly useful for species management, as it can be used to estimate invas...
Article
Full-text available
Coral reefs are biodiversity hotspots, places of high endemicity and provide essential services to billions of people globally. With increasing threats to these reefs worldwide, there is a need to implement faster, more efficient ways to monitor spatial and temporal patterns of biodiversity. Environmental DNA (eDNA) metabarcoding offers a promising...
Article
Full-text available
Abstract Reptile populations are in decline globally, with total reptile abundance halving in the past half century, and approximately a fifth of species currently threatened with extinction. Research on reptile distributions, population trends, and trophic interactions can greatly improve the accuracy of conservation listings and planning for spec...
Article
Full-text available
Age is a fundamental life history attribute that is used to understand the dynamics of wild animal populations. Unfortunately, most animals do not have a practical or non‐lethal method to determine age. This makes it difficult for wildlife managers to carry out population assessments, particularly for elusive and long‐lived fauna such as marine tur...
Article
Population genetic data can provide valuable information on the demography of a species. For rare and elusive marine megafauna, samples for generating the data are traditionally obtained from tissue biopsies, which can be logistically difficult and expensive to collect and require invasive sampling techniques. Analysis of environmental DNA (eDNA) o...
Article
Full-text available
The age, sex, and sexual maturity of individual animals are key parameters in assessing wild populations and informing conservation management strategies. These parameters represent the reproductive potential of a population and can indicate recovery rates or vulnerabilities. Natural populations of wild animals are difficult to study; logistically,...
Preprint
Passive collection is an emerging sampling method for environmental DNA (eDNA) in aquatic systems. Passive eDNA collection is inexpensive, efficient, and requires minimal equipment, making it suited to high density sampling and remote deployment. Here, we compare the effectiveness of nine membrane materials for passively collecting fish eDNA from a...
Article
Full-text available
We have developed two epigenetic clocks for ageing three threatened fish species. These epigenetic clocks can be applied non-lethally using fin clips taken from fish. Our approach transferred age-associated CpG sites characterized previously in a model species, the zebrafish, to deeply phylogenetically divergent fish species: The Australian lungfis...
Article
Full-text available
Age is a fundamental parameter in wildlife management as it is used to determine the risk of extinction, manage invasive species, and regulate sustainable harvest. In a broad variety of vertebrates species, age can be determined by measuring DNA methylation. Animals with known ages are initially required during development, calibration, and validat...
Article
Full-text available
Introduction DNA methylation data facilitate the development of accurate molecular estimators of chronological age, or ‘epigenetic clocks.’ We present a robust epigenetic clock for the beluga whale, Delphinapterus leucas, developed for an endangered population in Cook Inlet, Alaska, USA. Methods and Results We used a custom methylation array to me...
Article
Full-text available
The need for efficient and more accurate ways of monitoring threatened ecosystems is becoming increasingly urgent as climate change intensifies. Coral reefs are an example of an ecosystem in crisis, with widespread declines in coral cover and diversity documented over recent decades. Novel molecular approaches such as biomonitoring using environmen...
Article
Full-text available
Changes in DNA methylation at specific CpG sites have been used to build predictive models to estimate animal age, predominantly in mammals. Little testing for this effect has been conducted in other vertebrate groups, such as bony fish, the largest vertebrate class. The development of most age-predictive models has relied on a genome-wide sequenci...
Article
Full-text available
Environmental DNA (eDNA) metabarcoding, where specific DNA markers (barcodes) are purified from the environment, sequenced, and used to identify organisms, is revolutionizing biodiversity science. Researchers, industry, and governments are increasingly incorporating eDNA surveys into their toolkits for biomonitoring because of their high accuracy,...
Preprint
Full-text available
Introduction DNA methylation data facilitate the development of accurate molecular estimators of chronological age, or ‘epigenetic clocks.’ We present a robust epigenetic clock for the beluga whale, Delphinapterus leucas, developed for an endangered population in Cook Inlet, Alaska, USA. Methods and Results We used a custom methylation array to me...
Article
Full-text available
Maximum lifespan for most animal species is difficult to define. This is challenging for wildlife management as it is critical for estimating important aspects of population biology such as mortality rate, population viability, and period of reproductive potential. Recently, it has been shown cytosine-phosphate-guanine (CpG) density is predictive o...
Article
Full-text available
Detecting changes in marine food webs is challenging, but top predators can provide information on lower trophic levels. However, many commonly measured predator responses can be decoupled from prey availability by plasticity in predator foraging effort. This can be overcome by directly measuring foraging effort and success and integrating these in...
Article
Full-text available
Lutjanus erythropterus and L. malabaricus are sympatric, sister taxa that are important to fisheries throughout the Indo-Pacific. Their juveniles are morphologically indistinguishable (i.e. cryptic). A DNA metabarcoding dietary study was undertaken to assess the diet composition and partitioning between the juvenile and adult life history stages of...
Article
Full-text available
Fish biodiversity can be measured by capturing and then sequencing free DNA present in water. Such environmental DNA (eDNA) methods offer an effective, noninvasive tool for species diversity measurement, although standardized protocols are not yet developed. We investigate how metrics of fish biodiversity revealed through eDNA analysis of water are...
Article
Full-text available
Biological ageing and its mechanistic underpinnings are of immense biomedical and ecological significance. Ageing involves the decline of diverse biological functions and places a limit on a species’ maximum lifespan. Ageing is associated with epigenetic changes involving DNA methylation. Furthermore, an analysis of mammals showed that the density...
Article
Full-text available
The evolution of cetaceans, from their early transition to an aquatic lifestyle to their subsequent diversification, has been the subject of numerous studies. However, while the higher-level relationships among cetacean families have been largely settled, several aspects of the systematics within these groups remain unresolved. Problematic clades i...
Article
Full-text available
The application of DNA metabarcoding to dietary analysis of trophic generalists requires using multiple markers in order to overcome problems of primer specificity and bias. However, limited attention has been given to the integration of information from multiple markers, particularly when they partly overlap in the taxa amplified, and vary in taxo...
Article
Full-text available
Marine ecosystems are changing rapidly as the oceans warm and become more acidic. The physical factors and the changes to ocean chemistry that they drive can all be measured with great precision. Changes in the biological composition of communities in different ocean regions are far more challenging to measure because most biological monitoring met...
Data
Number of Echinodermata detections in Rottnest Island zooplankton samples by each assay. (PDF)
Data
Number of other Animalia taxa detections in Rottnest Island zooplankton samples by each assay. (PDF)
Data
Pairwise analysis of seasonal OTU richness & assemblage, t statistics included for significant results (t)—PERMANOVA+[7]. (PDF)
Data
Indicator species analysis for 17-month heatwave variation—Indval [8]. (PDF)
Data
Number of sequences (beige—right axis) and number of OTUs (red—left axis), per sample, for each assay. The assays showed a range of correlations between sequencing depth and the number of OTUs produced. No correlation was detected in the 18S and Crustacea 16S assays, while the Fish 16S showed a weak but non-significant correlation. The COI assays a...
Data
Number of Arthropoda detections in Rottnest Island zooplankton samples by each assay. (PDF)
Data
Indicator species analysis for seasonal variation—Indval [8]. (PDF)
Data
Indicator species analysis for five-month heatwave variation—Indval [8]. (PDF)
Data
Number of Chordata detections in Rottnest Island zooplankton samples by each assay. (PDF)
Data
Number of Cnidaria detections in Rottnest Island zooplankton samples by each assay. (PDF)
Data
Pairwise analysis of yearly OTU richness & assemblage, t statistics included for significant results (t)—PERMANOVA+[7]. (PDF)
Data
Indicator species analysis for yearly variation—Indval [8]. (PDF)
Data
Metabarcoding PCR assays developed and tested for this study. (PDF)
Data
Example of typical rarefaction curves. These were produced, using all eight assays, from a single sample taken on May 23 2012 (EPS)
Data
Example of a consensus alignment used to create the assays used in this study. This COI alignment resulted in the Copepod 3 assay [10]. (EPS)
Data
References used for supporting information. (PDF)
Data
The metabarcoding PCR assays used in this study. (PDF)
Data
Number of Mollusca detections in Rottnest Island zooplankton samples by each assay. (PDF)
Data
Pairwise analysis of the OTU richness & assemblage between before, during and after the heatwaves, t statistics included for significant results (t)—PERMANOVA+[7]. (PDF)
Data
Alternative linear models for Assemblage and Richness. (PDF)
Data
Annual sea surface temperature anomalies from 1900–2017. The 2011 and 2012 heatwave events produce the two highest peaks—Extracted from the Bureau of Meteorology time series graphs [9]. (PDF)
Article
Full-text available
Diet studies provide base understanding of trophic structure and are a valuable initial step for many fields of marine ecology, including conservation and fisheries biology. Considerable complexity in marine trophic structure can exist due to the presence of highly mobile species with long life spans. Mobula rays are highly mobile, large, planktivo...
Article
Full-text available
Age structure is a fundamental aspect of animal population biology. Age is strongly related to individual physiological condition, reproductive potential and mortality rate. Currently, there are no robust molecular methods for age estimation in birds. Instead, individuals must be ringed as chicks to establish known‐age populations, which is a labou...
Article
Full-text available
Effective biomonitoring is critical for driving management outcomes that ensure long‐term sustainability of the marine environment. In recent years environmental DNA (eDNA), coupled with metabarcoding methodologies, has emerged as a promising tool for generating biotic surveys of marine ecosystems, including those under anthropogenic pressure. Howe...
Article
Full-text available
The Sahara desert is the largest warm desert in the world and a poorly explored area. Small water-bodies occur across the desert and are crucial habitats for vertebrate biodiversity. Environmental DNA (eDNA) is a powerful tool for species detection and is being increasingly used to conduct biodiversity assessments. However, there are a number of di...
Technical Report
Full-text available
The overall goal of ERA Chair/EnvMetaGen project No 668981 is to expand the research and innovation potential of InBIO – Research network in Biodiversity and Evolutionary Biology, through the creation of an ERA Chair in Environmental Metagenomics. This field was selected as the focus of the ERA Chair, because Environmental DNA (eDNA) analysis is in...
Technical Report
Full-text available
The overall goal of ERA Chair/EnvMetaGen project No 668981 is to expand the research and innovation potential of InBIO – Research network in Biodiversity and Evolutionary Biology, through the creation of an ERA Chair in Environmental Metagenomics. This field was selected as the focus of the ERA Chair, because Environmental DNA (eDNA) analysis is in...
Technical Report
Full-text available
The overall goal of the EnvMetaGen project No 668981 is to expand the research and innovation potential of InBIO – Research network in Biodiversity and Evolutionary Biology - through the creation of an ERA Chair in Environmental Metagenomics. This field was selected as the focus of the ERA Chair, because Environmental DNA (eDNA) analysis is increas...
Technical Report
Full-text available
The overall goal of the EnvMetaGen project No 668981 is to expand the research and innovation potential of InBIO – Research network in Biodiversity and Evolutionary Biology, through the creation of an ERA Chair in Environmental Metagenomics. This field was selected as the focus of the ERA Chair, because Environmental DNA (eDNA) analysis is increasi...
Article
Full-text available
DNA metabarcoding is increasingly used in dietary studies to estimate diversity, composition, and frequency of occurrence of prey items. However, few studies have assessed how technical and biological replication affect the accuracy of diet estimates. This study addresses these issues using the European free‐tailed bat Tadarida teniotis, involving...
Article
Full-text available
Blue whales are little studied, face significant anthropogenic threats and within the Northern Indian Ocean, have a restricted range, making them an archetype for conservation needs of megafauna around the world. We studied feeding behavior of blue whales using dietary DNA metabarcoding of fecal samples. While globally blue whale populations feed p...
Article
Obtaining direct measurements to characterise ecosystem function can be hindered by remote or inaccessible regions. Next-generation satellite tags that inform increasingly sophisticated movement models, and the min-iaturisation of animal-borne loggers, have enabled the use of animals as tools to collect habitat data in remote environments, such as...
Article
Full-text available
Most seabirds do not have any outward identifiers of their chronological age, so estimation of seabird population age structure generally requires expensive, long-term banding studies. We investigated the potential to use a molecular age biomarker to estimate age in short-tailed shearwaters (Ardenna tenuirostris). We quantified DNA methylation in s...
Data
Regression plots for gene set 1 CpG loci in feather (A. tenuirostris). (PDF)
Data
Python script used for calculating methylation proportion of specific CpG sites. (PY)
Data
R script that does linear regression for each CpG site and uses the package ‘glmnet’ for lasso predictor selection. (R)
Data
ASPA sequence conservation in mammals and select bird species. A: 20 base pairs are shown for 3’ and 5’ directions around an age-related CpG loci (27K: cg02228185, in bold) in the ASPA gene in humans, mouse and birds. Following the methods described in text, this sequence was compared to the chicken and northern fulmar genomes. The resulting matche...