Simon Neil Jarman

Curtin University · Molecular and Life Sciences

Animal age at maturity can be used as a universal and simple predictor of species extinction risk. At present, methods to estimate age at maturity are typically species-specific, limiting comparisons among species or are infeasible to do practical constraints. To overcome this, we developed a universal predictor of vertebrate species age at maturit...

Global biodiversity is declining at an ever-increasing rate. Yet effective policies to mitigate or reverse these declines require ecosystem condition data that are rarely available. Morphology-based bioassessment methods are difficult to scale, limited in scope, suffer prohibitive costs, require skilled taxonomists, and can be applied inconsistentl...

Age at sexual maturity is a key life history trait that can be used to predict population growth rates and develop life history models. In many wild animal species, the age at sexual maturity is not accurately quantified. This results in a reduced ability to accurately model demography of wild populations. Recent studies have indicated the potentia...

Conservation translocations require robust post‐release monitoring to evaluate their success, which can be challenging to implement and maintain. Monitoring techniques that can account for the dispersal and cryptic nature of translocated animals are necessary to provide critical information on persistence and distribution. In this study, we develop...

DNA collected from the environment (eDNA) can provide valuable understanding of ecological patterns and processes. eDNA is highly physically heterogeneous, but this has not been well‐characterized, so most eDNA sampling strategies do not target any particular physical fraction. Consequently, we have limited evidence to understand and interpret the...

Animal age data are valuable for management of wildlife populations. Yet, for most species, there is no practical method for determining the age of unknown individuals. However, epigenetic clocks, a molecular‐based method, are capable of age prediction by sampling specific tissue types and measuring DNA methylation levels at specific loci. Developi...

Aim To use a long‐term collection of bulk plankton samples to test the capacity of DNA metabarcoding to characterize the spatial and seasonal patterns found within a range of zooplankton communities, and investigate links with concurrent abiotic data collected as part of Australia's Integrated Marine Observing System (IMOS) programme. Location Sam...

Antarctic krill (Euphausia superba) is Earth's most abundant wild animal, and its enormous biomass is vital to the Southern Ocean ecosystem. Here, we report a 48.01-Gb chromosome-level Antarctic krill genome, whose large genome size appears to have resulted from inter-genic transposable element expansions. Our assembly reveals the molecular archite...

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...

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...

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...

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...

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...

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...

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,...

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...

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...

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...

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...

Environmental DNA (eDNA) metabarcoding is a sensitive and widely used approach for species detection and biodiversity assessment. The most common eDNA collection method in aquatic systems is actively filtering water through a membrane, which is time consuming and requires specialized equipment. Ecological studies investigating species abundance or...

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...

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...

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,...

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...

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...

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...

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...

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...

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...

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...

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...

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...

Number of Echinodermata detections in Rottnest Island zooplankton samples by each assay. (PDF)

Number of other Animalia taxa detections in Rottnest Island zooplankton samples by each assay. (PDF)

Pairwise analysis of seasonal OTU richness & assemblage, t statistics included for significant results (t)—PERMANOVA+[7]. (PDF)

Indicator species analysis for 17-month heatwave variation—Indval [8]. (PDF)

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...

Number of Arthropoda detections in Rottnest Island zooplankton samples by each assay. (PDF)

Indicator species analysis for seasonal variation—Indval [8]. (PDF)

Indicator species analysis for five-month heatwave variation—Indval [8]. (PDF)

Number of Chordata detections in Rottnest Island zooplankton samples by each assay. (PDF)

Number of Cnidaria detections in Rottnest Island zooplankton samples by each assay. (PDF)

Pairwise analysis of yearly OTU richness & assemblage, t statistics included for significant results (t)—PERMANOVA+[7]. (PDF)

Indicator species analysis for yearly variation—Indval [8]. (PDF)

Metabarcoding PCR assays developed and tested for this study. (PDF)

Example of typical rarefaction curves. These were produced, using all eight assays, from a single sample taken on May 23 2012 (EPS)

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)

References used for supporting information. (PDF)

The metabarcoding PCR assays used in this study. (PDF)

Number of Mollusca detections in Rottnest Island zooplankton samples by each assay. (PDF)

Pairwise analysis of the OTU richness & assemblage between before, during and after the heatwaves, t statistics included for significant results (t)—PERMANOVA+[7]. (PDF)

Alternative linear models for Assemblage and Richness. (PDF)

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)

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

Regression plots for gene set 1 CpG loci in feather (A. tenuirostris). (PDF)

Python script used for calculating methylation proportion of specific CpG sites. (PY)

R script that does linear regression for each CpG site and uses the package ‘glmnet’ for lasso predictor selection. (R)

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...

qPCR sexing assay of A. tenuirostris. DNA blood stored on FTA cards was used to amplify a small amplicon in the CHD1 gene. Melt curve analysis reveals a double peak for females (n = 4, green) and a single peak for males (n = 7, red). A NTC (n = 1, blue) shows no contamination. A third primer dimer peak is also seen for female samples at approximate...

Bisulphite converted PCR. A serial dilution of bisulphite converted DNA isolated from a plucked breast feather. In this example a 243 bp target region of the predicted ASPA gene in the shearwater was amplified using bisulphite specific primers. 100 ng of genomic DNA was bisulphite converted and eluted in 10 μL of elution buffer. At an approximate o...

Regression plots for gene set 1 CpG loci in blood (A. tenuirostris). (PDF)

Proportion data for gene set 1 CpG loci in blood (A. tenuirostris). (XLSX)

Proportion data for gene set 1 CpG loci in feather (A. tenuirostris). (XLSX)

Proportion data for gene set 2 CpG loci in feather (A. tenuirostris). (XLSX)

Isolated DNA from blood and feather of A. tenuirostris. A QC gel indicating the isolation of high quality genomic DNA from shearwater tissue samples. FTA: DNA isolated from blood stored on FTA cards, FPa: plucked breast feather from adult, FPc: plucked breast feather from chick. Approximately 50 ng of DNA was loaded into a 1% agarose gel and run at...

Age distribution of A. tenuirostris used in this study. The known ages of all birds used in this study are shown split into those used for feather quill tip (FP) and whole blood (FTA) methylation analysis. (TIFF)

Editable excel spreadsheet of all supporting tables mentioned in text. (XLSX)

Regression plots for gene set 2 CpG loci in blood (A. tenuirostris). (PDF)

Regression plots for gene set 2 CpG loci in feather (A. tenuirostris). (PDF)

Proportion data for gene set 2 CpG loci in blood (A. tenuirostris). (XLSX)

A dominant Antarctic ecological paradigm suggests that winter sea ice is generally the main feeding ground for krill larvae. Observations from our winter cruise to the southwest Atlantic sector of the Southern Ocean contradict this view and present the first evidence that the pack-ice zone is a food-poor habitat for larval development. In contrast,...

The use of metabarcoding has grown exponentially in the study of animals’ diets. The accuracy and detail of this technique is invaluable for a better understanding of biotic interactions characterizing natural and human-dominated ecosystems, and thus to their conservation and sustainable use. However it has seldom been applied to passerine birds, t...

Almost all of the world's fisheries overlap spatially and temporally with foraging seabirds, with impacts that range from food supplementation (through scavenging behind vessels), to resource competition and incidental mortality. The nature and extent of interactions between seabirds and fisheries vary, as does the level and efficacy of management...

DNA methylation (DNAm) is a key mechanism for regulating gene expression in animals and levels are known to change with age. Recent studies have used DNAm changes as a biomarker to estimate chronological age in humans and these techniques are now also being applied to domestic and wild animals. Animal age is widely used to track ongoing changes in...

Gelatinous zooplankton are a large component of the animal biomass in all marine environments, but are considered to be uncommon in the diet of most marine top predators. However, the diets of key predator groups like seabirds have conventionally been assessed from stomach content analyses, which cannot detect most gelatinous prey. As marine top pr...

Antarctic pack ice serves as habitat for microalgae which contribute to Southern Ocean primary production and serve as important food source for pelagic herbivores. Ice algal biomass is highly patchy, and remains severely undersampled by classical methods such as spatially restricted ice-coring surveys. Here we provide an unprecedented view of ice...

Environmental DNA (eDNA) and metabarcoding are potentially useful tools for monitoring water ecological status and detect rare species, including threatened and recently introduced species. While it is now clear these tools have the ability to generate important data to inform managers, its widespread application has been hindered by the lack of st...