25 Works

Data from: Bacterial epibiont communities of panmictic Antarctic krill are spatially structured

Laurence Clarke, Leonie Suter, Rob King, Andrew Bissett, Sophie Bestley & Bruce Deagle
Antarctic krill (Euphausia superba) are amongst the most abundant animals on Earth, with a circumpolar distribution in the Southern Ocean. Genetic and genomic studies have failed to detect any population structure for the species, suggesting a single panmictic population. However, the hyper-abundance of krill slows the rate of genetic differentiation, masking potential underlying structure. Here we use high-throughput sequencing of bacterial 16S rRNA genes to show that krill bacterial epibiont communities exhibit spatial structuring, driven...

Data from: Adélie penguin population diet monitoring by analysis of food DNA in scats

Simon N. Jarman, Julie C. McInnes, Cassandra Faux, Andrea M. Polanowski, James Marthick, Bruce E. Deagle, Colin Southwell & Louise Emmerson
The Adélie penguin is the most important animal currently used for ecosystem monitoring in the Southern Ocean. The diet of this species is generally studied by visual analysis of stomach contents; or ratios of isotopes of carbon and nitrogen incorporated into the penguin from its food. There are significant limitations to the information that can be gained from these methods. We evaluated population diet assessment by analysis of food DNA in scats as an alternative...

Data from: Genetic monitoring of open ocean biodiversity: an evaluation of DNA metabarcoding for processing continuous plankton recorder samples

Bruce E. Deagle, Laurence J. Clarke, John A. Kitchener, Andrea M. Polanowski & Andrew T. Davidson
DNA metabarcoding is an efficient method for measuring biodiversity, but the process of initiating long-term DNA-based monitoring programs, or integrating with conventional programs, is only starting. In marine ecosystems, plankton surveys using the continuous plankton recorder (CPR) have characterised biodiversity along transects covering millions of kilometres with time-series spanning decades. We investigated the potential for use of metabarcoding in CPR surveys. Samples (n= 53) were collected in two Southern Ocean transects and metazoans identified using...

Data from: Phylogenomic resolution of the cetacean tree of life using target sequence capture

Michael McGowen, Georgia Tsagkogeorga, Sandra Álvarez-Carretero, Mario Dos Reis, Monika Struebig, Rob Deaville, Paul Jepson, Simon Jarman, Andrea Polanowski, Phillip Morin & Stephen Rossiter
The evolution of the 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 include the oceanic dolphins (37 spp.), which have experienced a recent rapid radiation, and the beaked whales (22 spp.), which have not been investigated in detail using...

Data from: Improving accuracy of DNA diet estimates using food tissue control materials and an evaluation of proxies for digestion bias

Austen C. Thomas, Simon N. Jarman, Katherine H. Haman, Andrew W. Trites & Bruce E. Deagle
Ecologists are increasingly interested in quantifying consumer diets based on food DNA in dietary samples and high-throughput sequencing of marker genes. It is tempting to assume that food DNA sequence proportions recovered from diet samples are representative of consumer's diet proportions, despite the fact that captive feeding studies do not support that assumption. Here, we examine the idea of sequencing control materials of known composition along with dietary samples in order to correct for technical...

Landfast ice: a major driver of reproductive success in a polar seabird

Sara Labrousse, Alexander D. Fraser, Michael Sumner, Frédéric Le Manach, Christophe Sauser, Isabella Horstmann, Eileen Devane, Karine Delord, Stéphanie Jenouvrier & Christophe Barbraud
In a fast-changing world, polar ecosystems are threatened by climate variability. Understanding the roles of fine-scale processes, and linear and nonlinear effects of climate factors on the demography of polar species is crucial for anticipating the future state of these fragile ecosystems. While the effects of sea ice on polar marine top predators are increasingly being studied, little is known about the impacts of landfast ice (LFI) on this species community. Based on a unique...

Data from: A phylogenomic analysis of the role and timing of molecular adaptation in the aquatic transition of cetartiodactyl mammals

Georgia Tsagkogeorga, Michael R. McGowen, Kalina T. J. Davies, Simon Jarman, Andrea Polanowski, Mads F. Bertelsen & Stephen J. Rossiter
Recent studies have reported multiple cases of molecular adaptation in cetaceans related to their aquatic abilities. However, none of these has included the hippopotamus, precluding an understanding of whether molecular adaptations in cetaceans occurred before or after they split from their semi-aquatic sister taxa. Here, we obtained new transcriptomes from the hippopotamus and humpback whale, and analysed these together with available data from eight other cetaceans. We identified more than 11 000 orthologous genes and...

Data from: Antarctic krill population genomics: apparent panmixia, but genome complexity and large population size muddies the water

Bruce E. Deagle, Cassandra Faux, So Kawaguchi, Bettina Meyer & Simon N. Jarman
Antarctic krill (Euphausia superba; hereafter krill) are an incredibly abundant pelagic crustacean which has a wide, but patchy, distribution in the Southern Ocean. Several studies have examined the potential for population genetic structuring in krill, but DNA-based analyses have focused on a limited number of markers and have covered only part of their circum-Antarctic range. We used mitochondrial DNA and restriction site-associated DNA sequencing (RAD-seq) to investigate genetic differences between krill from five sites, including...

Data from: Epigenetic estimation of age in humpback whales

Andrea M. Polanowski, Jooke Robbins, David Chandler & Simon N. Jarman
Age is a fundamental aspect of animal ecology, but is difficult to determine in many species. Humpback whales exemplify this as they have a lifespan comparable to humans, mature sexually as early as four years and have no reliable visual age indicators after their first year. Current methods for estimating humpback age cannot be applied to all individuals and populations. Assays for human age have recently been developed recently based on age-induced changes in DNA...

Data from: Smooth brome invasion increases rare soil bacterial species prevalence and alters soil bacterial community composition

Candace L. Piper, Steven D. Siciliano, Tristrom Winsley & Eric G. Lamb
Plant and soil communities are tightly linked, but the mechanisms by which the invasion of an exotic plant and the resulting shifts in plant diversity and productivity influence soil bacterial community structure remain poorly understood. We investigated the effects of invasive smooth brome (Bromus inermis) on grassland soil bacterial community structure using massively-parallel sequencing of the 16S rRNA gene to determine bacterial community richness, evenness, composition, and beta diversity (UniFrac indices) of soils collected along...

Data from: Analysis of Australian fur seal diet by pyrosequencing prey DNA in faeces

Bruce E. Deagle, Roger Kirkwood & Simon N. Jarman
DNA-based techniques have proven useful for defining trophic links in a variety of ecosystems and recently developed sequencing technologies provide new opportunities for dietary studies. We investigated the diet of Australian fur seals (Arctocephalus pusillus doriferus) by pyrosequencing prey DNA from faeces collected at three breeding colonies across the seals’ range. DNA from 270 faecal samples was amplified with four polymerase chain reaction primer sets and a blocking primer was used to limit amplification of...

Self-organization and information transfer in Antarctic krill swarms

Ashley Ward, Alicia Burns, Timothy Schaerf, Joseph Lizier, So Kawaguchi, Martin Cox, Rob King & Jens Krause
Antarctic krill swarms are one of the largest known animal aggregations, and yet, despite being the keystone species of the Southern Ocean, little is known about how swarms are formed and maintained. Understanding the local interactions between individuals that provide the basis for these swarms is fundamental to knowing how swarms arise in nature, and what potential factors might lead to their breakdown. Here we analyzed the trajectories of captive, wild-caught krill in 3D to...

Data from: Paternity assignment and demographic closure in the New Zealand southern right whale

Emma L. Carroll, Simon J. Childerhouse, Mark Christie, Shane Lavery, Nathalie Patenaude, Alana Alexander, Rochelle Constantine, Debbie Steel, Laura Boren & Charles Scott Baker
The identification and characterisation of reproductively isolated subpopulations or ‘stocks’ is essential for effective conservation and management decisions. This can be difficult in vagile marine species like marine mammals. We used paternity assignment and ‘gametic recapture’ to examine the reproductive autonomy of southern right whales (Eubalaena australis) on their New Zealand (NZ) calving grounds. We derived DNA profiles for 34 mother-calf pairs from skin biopsy samples, using sex-specific markers, 13 microsatellite loci and mtDNA haplotypes....

Data from: Comparative population genomics reveals key barriers to dispersal in Southern Ocean penguins

Gemma V. Clucas, Jane L. Younger, Damian Kao, Louise Emmerson, Colin Southwell, Barbara Wienecke, Alex D. Rogers, Charles-Andre Bost, Gary D. Miller, Michael J. Polito, Patrick Lelliot, Jonathan Handley, Sarah Crofts, Richard A. Phillips, Michael J. Dunn, Karen J. Miller, Tom Hart & Patrick Lelliott
The mechanisms that determine patterns of species dispersal are important factors in the production and maintenance of biodiversity. Understanding these mechanisms helps to forecast the responses of species to environmental change. Here we used a comparative framework and genome-wide data obtained through RAD-seq to compare the patterns of connectivity among breeding colonies for five penguin species with shared ancestry, overlapping distributions, and differing ecological niches, allowing an examination of the intrinsic and extrinsic barriers governing...

Hull fouling marine invasive species pose a very low, but plausible, risk of introduction to East Antarctica in climate change scenarios

Oakes Holland, Justine Shaw, Jonathan Stark & Kerrie Wilson
Aims: To identify potential hull fouling marine invasive species that could survive in East Antarctica presently and in the future. Location: Australia's Antarctic continental stations: Davis, Mawson and Casey, East Antarctica; and subantarctic islands: Macquarie Island and Heard and McDonald Islands. Methods: Our study uses a novel machine-learning algorithm to predict which currently known hull fouling MIS could survive in shallow benthic ecosystems adjacent to Australian Antarctic research stations and subantarctic islands, where ship traffic...

Data from: Capturing open ocean biodiversity: comparing environmental DNA metabarcoding to the continuous plankton recorder

Leonie Suter, Andrea Polanowski, Laurence Clarke, John Kitchener & Bruce Deagle
Environmental DNA (eDNA) metabarcoding is emerging as a novel, objective tool for monitoring marine metazoan biodiversity. Zooplankton biodiversity in the vast and important open ocean is currently monitored through continuous plankton recorder (CPR) surveys, using ship-based bulk plankton sampling and morphological identification. We assessed whether eDNA metabarcoding (2 L filtered seawater) could capture similar Southern Ocean biodiversity as conventional CPR bulk sampling (~1500 L filtered seawater per CPR sample). We directly compared eDNA metabarcoding with...

Taxonomy based on limited genomic markers may underestimates species diversity of rockhopper penguins and threaten their conservation

María José Frugone, Theresa Cole, María Eugenia López, Gemma Clucas, Pável Matos-Maraví, Nicolás Lois, Pierre Pistorius, Francesco Bonadonna, Phil Trathan, Andrea Polanowski, Barbara Wienecke, Andrea Raya-Rey, Klemens Pütz, Antje Steinfurth, Ke Bi, Cynthia Wang-Claypool, Rauri C. K. Bowie, Jonathan Waters, Elie Poulin & Juliana Vianna
Delimiting recently diverged species is challenging. During speciation, genetic differentiation may be distributed unevenly across the genome, as different genomic regions can be subject to different selective pressures and evolutionary histories. Reliance on limited numbers of genetic markers that may be underpowered can make species delimitation even more challenging, potentially resulting in taxonomic inconsistencies. Rockhopper penguins of the genus Eudyptes comprise three broadly recognized taxa: northern (E. moseleyi), southern (E. chrysocome), and eastern rockhopper (E....

Data from: Pyrosequencing of prey DNA in reptile faeces: analysis of earthworm consumption by slow worms

David S. Brown, Simon N. Jarman & William O.C. Symondson
Little quantitative ecological information exists on the diets of most invertebrate feeding reptiles, particularly nocturnal or elusive species that are difficult to observe. In the UK and elsewhere, reptiles are legally required to be relocated before land development can proceed, but without knowledge of their dietary requirements the suitability of receptor sites cannot be known. Here we tested the ability of non-invasive DNA-based molecular diagnostics (454 pyrosequencing) to analyse reptile diets, with the specific aims...

Data from: Quantifying sequence proportions in a DNA-based diet study using Ion Torrent amplicon sequencing: which counts count?

Bruce E. Deagle, Austen C. Thomas, Amanda K. Shaffer, Andrew W. Trites & Simon N. Jarman
A goal of many environmental DNA barcoding studies is to infer quantitative information about relative abundances of different taxa based on sequence read proportions generated by high-throughput sequencing. However, potential biases associated with this approach are only beginning to be examined. We sequenced DNA amplified from faeces (scats) of captive harbour seals (Phoca vitulina) to investigate whether sequence counts could be used to quantify the seals’ diet. Seals were fed fish in fixed proportions, a...

Data from: Age estimation in a long-lived seabird (Ardenna tenuirostris) using DNA methylation-based biomarkers

Ricardo De Paoli-Iseppi, Bruce E. Deagle, Andrea M. Polanowski, Clive R. McMahon, Joanne L. Dickinson, Mark A. Hindell & Simon N. Jarman
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 labour intensive and expensive process. The estimation of chronological age using DNA methylation is emerging as a robust approach in mammals including humans, mice and some...

Data from: Counting with DNA in metabarcoding studies: how should we convert sequence reads to dietary data?

Bruce E. Deagle, Austen C. Thomas, Julie C. McInnes, Laurence J. Clarke, Eero J. Vesterinen, Elizabeth L. Clare, Tyler R. Kartzinel & J. Paige Eveson
Advances in DNA sequencing technology have revolutionised the field of molecular analysis of trophic interactions and it is now possible to recover counts of food DNA sequences from a wide range of dietary samples. But what do these counts mean? To obtain an accurate estimate of a consumer’s diet should we work strictly with datasets summarising frequency of occurrence of different food taxa, or is it possible to use relative number of sequences? Both approaches...

Data from: Fine-scale diet of the Australian sea lion (Neophoca cinerea) using DNA-based analysis of faeces.

Kristian J. Peters, Kathy Ophelkeller, Nathan J. Bott, Bruce E. Deagle, Simon N. Jarman & Simon D. Goldsworthy
We applied DNA-based faecal analysis to determine the diet of female Australian sea lions (n = 12) from two breeding colonies in South Australia. DNA dietary components of fish and cephalopods were amplified using the polymerase chain reaction and mitochondrial DNA primers targeting the short (~100 base pair) section of the 16S gene region. Prey diversity was determined by sequencing ~50 amplicons generated from clone libraries developed for each individual. Faecal DNA was also combined...

Implications for the mesopelagic microbial gardening hypothesis as determined by experimental fragmentation of Antarctic krill faecal pellets

Emma Cavan, So Kawaguchi & Philip Boyd
1. Detritivores need to upgrade their food to increase its nutritional value. One method is to fragment detritus promoting the colonisation­ of nutrient-rich microbes, which consumers then ingest along with the detritus; so-called microbial gardening. Observations and numerical models of the detritus-dominated ocean mesopelagic zone have suggested microbial gardening by zooplankton is a fundamental process in the ocean carbon cycle leading to increased respiration of carbon-rich detritus. However, no experimental evidence exists to demonstrate that...

Using seabird and whale distribution models to estimate spatial consumption of krill to inform fishery management

Victoria Warwick-Evans, Natalie Kelly, Luciano Dalla Rosa, Ari Friedlaender, Jefferson Hinke, Jeong-Hoon Kim, Nobuo Kokubun, Jarrod Santora, Eduardo Secchi, Elisa Seyboth & Philip Trathan
Ecosystem dynamics at the north-west Antarctic Peninsula are driven by interactions between physical and biological processes. For example, baleen whale populations are recovering from commercial harvesting against the backdrop of rapid climate change, including reduced sea-ice extent and changing ecosystem composition. Concurrently, the commercial harvesting of Antarctic krill is increasing, with the potential to increase the likelihood for competition with and between krill predators and the fishery. However, understanding the ecology, abundance, and spatial distribution...

Data from: Pyrosequencing of prey DNA in reptile faeces: analysis of earthworm consumption by slow worms

David S. Brown, Simon N. Jarman & William O.C. Symondson
Little quantitative ecological information exists on the diets of most invertebrate feeding reptiles, particularly nocturnal or elusive species that are difficult to observe. In the UK and elsewhere, reptiles are legally required to be relocated before land development can proceed, but without knowledge of their dietary requirements the suitability of receptor sites cannot be known. Here we tested the ability of non-invasive DNA-based molecular diagnostics (454 pyrosequencing) to analyse reptile diets, with the specific aims...

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