144 Works

Population genomics of a predatory mammal reveals patterns of decline and impacts of exposure to toxic toads

Brenton Von Takach
Mammal declines across northern Australia are one of the major biodiversity loss events occurring globally. There has been no regional assessment of the implications of these species declines for genomic diversity. To address this, we conducted a species-wide assessment of genomic diversity in the northern quoll (Dasyurus hallucatus), an Endangered marsupial carnivore. We used next-generation sequencing methods to genotype 10,191 SNPs in 352 individuals from across a 3220 km length of the continent, investigating patterns...

Data from: Resistance and resilience to changing climate and fire regime depend on plant functional traits

Neal J. Enright, Joseph B. Fontaine, Byron B. Lamont, Ben P. Miller & Vanessa C. Westcott
Changing disturbance-climate interactions will drive shifts in plant communities: these effects are not adequately quantified by environmental niche models used to predict future species distributions. We quantified the effects of more frequent fire and lower rainfall - as projected to occur under a warming and drying climate - on population responses of shrub species in biodiverse Mediterranean-climate type shrublands near Eneabba, southwestern Australia. Using experimental fires, we measured the density of all shrub species for...

Data from: An assessment of ancient DNA preservation in Holocene-Pleistocene fossil bone excavated from the world heritage Naracoorte Caves, South Australia

Alicia Grealy, Amy Macken, Morten E. Allentoft, Nicolas J. Rawlence, Elizabeth Reed & Michael Bunce
Although there is a long history of research into the fossil deposits of the Naracoorte Caves (South Australia), ancient DNA (aDNA) has not been integrated into any palaeontological study from this World Heritage site. Here, we provide the first evidence of aDNA preservation in Holocene- and Pleistocene-aged fossil bone from a deposit inside Robertson Cave. Using a combination of metabarcoding and shotgun next-generation sequencing approaches, we demonstrate that aDNA from diverse taxa can be retrieved...

Data from: Combined DNA, toxicological and heavy metal analyses provides an auditing toolkit to improve pharmacovigilance of traditional Chinese medicine (TCM).

Megan L. Coghlan, Garth Maker, Elly Crighton, James Haile, Dáithí C. Murray, Nicole E. White, Roger W. Byard, Matthew I. Bellgard, Ian Mullaney, Robert Trengove, Richard J. N. Allcock, Christine Nash, Claire Hoban, Kevin Jarrett, Ross Edwards, Ian F. Musgrave & Michael Bunce
Globally, there has been an increase in the use of herbal remedies including traditional Chinese medicine (TCM). There is a perception that products are natural, safe and effectively regulated, however, regulatory agencies are hampered by a lack of a toolkit to audit ingredient lists, adulterants and constituent active compounds. Here, for the first time, a multidisciplinary approach to assessing the molecular content of 26 TCMs is described. Next generation DNA sequencing is combined with toxicological...

Data from: Vocalisations of killer whales (Orcinus orca) in the Bremer Canyon, Western Australia

Rebecca Wellard, Christine Erbe, Leila Fouda & Michelle Blewitt
To date, there has been no dedicated study in Australian waters on the acoustics of killer whales. Hence no information has been published on the sounds produced by killer whales from this region. Here we present the first acoustical analysis of recordings collected off the Western Australian coast. Underwater sounds produced by Australian killer whales were recorded during the months of February and March 2014 and 2015 in the Bremer Canyon in Western Australia. Vocalisations...

Data from: From benchtop to desktop: important considerations when designing amplicon sequencing workflows

Dáithí C. Murray, Megan L. Coghlan & Michael Bunce
Amplicon sequencing has been the method of choice in many high-throughput DNA sequencing (HTS) applications. To date there has been a heavy focus on the means by which to analyse the burgeoning amount of data afforded by HTS. In contrast, there has been a distinct lack of attention paid to considerations surrounding the importance of sample preparation and the fidelity of library generation. No amount of high-end bioinformatics can compensate for poorly prepared samples and...

Data from: Isolation by resistance across a complex coral reef seascape

Luke Thomas, W. Jason Kennington, Michael Stat, Shaun P. Wilkinson, Jonathan T. Kool & Gary A. Kendrick
A detailed understanding of the genetic structure of populations and an accurate interpretation of processes driving contemporary patterns of gene flow are fundamental to successful spatial conservation management. The field of seascape genetics seeks to incorporate environmental variables and processes into analyses of population genetic data to improve our understanding of forces driving genetic divergence in the marine environment. Information about barriers to gene flow (such as ocean currents) is used to define a resistance...

Data from: Directional selection for flowering time leads to adaptive evolution in Raphanus raphanistrum (Wild radish)

Michael B. Ashworth, Michael J. Walsh, Kenneth C. Flower, Martin M. Vila-Aiub, Stephen B. Powles & Ken C. Flower
Herbicides have been the primary tool for controlling large populations of yield depleting weeds from agro-ecosystems, resulting in the evolution of widespread herbicide resistance. In response, nonherbicidal techniques have been developed which intercept weed seeds at harvest before they enter the soil seed bank. However, the efficiency of these techniques allows an intense selection for any trait that enables weeds to evade collection, with early-flowering ecotypes considered likely to result in early seed shedding. Using...

Data from: It is premature to regard the ego-depletion effect as ‘too incredible’

Martin S. Hagger & Nikos L. D. Chatzisarantis
The ‘strength’ model conceptualizes self-control as a limited resource (Baumeister et al., 1998). Individuals are able to exert self-control, but only for a limited period after which capacity declines leading to reduced self-control capacity; a state known as ego-depletion. The model has generated a sizable literature confirming the ego-depletion effect in multiple spheres. Our meta-analysis of published ego-depletion studies computed a medium-sized effect (d=0.62) across 198 tests (Hagger et al., 2010). Carter and McCullough (2013)...

Data from: Effects of gear restriction on the abundance of juvenile fishes along sandy beaches in Hawai'i

Mary K. Donovan, Alan M. Friedlander, Paolo Usseglio, Whitney Goodell, Ily Iglesias, Eva M. Schemmel, Kostantinos A. Stamoulis, Filous Alexander, Jonatha Giddens, Keith Kamikawa, Haruko Koike, Kaylyn McCoy, Christopher B. Wall & Alexander Filous
In 2007, due to growing concerns of declines in nearshore fisheries in Hawai‘i, a ban on gillnets was implemented in designated areas around the island of O‘ahu in the main Hawaiian Islands. Utilizing a 17 year time-series of juvenile fish abundance beginning prior to the implementation of the gillnet ban, we examined the effects of the ban on the abundance of juveniles of soft-bottom associated fish species. Using a Before-After-Control-Impact (BACI) sampling design, we compared...

Data from: Assessing the spatial ecology and resource use of a mobile and endangered species in an urbanized landscape using satellite telemetry and DNA faecal metabarcoding

Christine Groom, Nicole E. White, Nicola Mitchell, J. Dale Roberts & Peter Mawson
The conservation of highly mobile species presents challenges to managers for assessment of threats to survival, given the difficulties in locating and observing such species. Here we evaluate satellite telemetry, DNA faecal metabarcoding and traditional field observations as three complementary techniques to acquire critical management information for an endangered species, Carnaby's Cockatoo Calyptorhynchus latirostris. Satellite telemetry of 23 birds resulted in 6026 location fixes accurate to within 500 m, and combined with extensive field observations...

Data from: Tropical ancient DNA from bulk archaeological fish bone reveals the subsistence practices of a historic coastal community in southwest Madagascar

Alicia Grealy, Kristina Douglass, James Haile, Chriselle Bruwer, Charlotte Gough & Michael Bunce
Taxonomic identification of archaeological fish bones provides important insights into the subsistence practices of ancient coastal peoples. However, it can be difficult to execute robust morphological identification of fish bones from species-rich fossil assemblages, especially from post-cranial material with few distinguishing features. Fragmentation, weathering and burning further impede taxonomic identification, resulting in large numbers of unidentifiable bones from archaeological sites. This limitation can be somewhat mitigated by taking an ancient DNA (aDNA) bulk-bone metabarcoding (BBM)...

Data from: DNA metabarcoding for diet analysis and biodiversity: A case study using the endangered Australian sea lion (Neophoca cinerea)

Tina E. Berry, Sylvia K. Osterrieder, Dáithí C. Murray, Megan L. Coghlan, Anthony J. Richardson, Alicia K. Grealy, Michael Stat, Lars Bejder & Michael Bunce
The analysis of apex predator diet has the ability to deliver valuable insights into ecosystem health, and the potential impacts a predator might have on commercially relevant species. The Australian sea lion (Neophoca cinerea) is an endemic apex predator and one of the world's most endangered pinnipeds. Given that prey availability is vital to the survival of top predators, this study set out to understand what dietary information DNA metabarcoding could yield from 36 sea...

Data from: Ecosystem biomonitoring with eDNA: metabarcoding across the tree of life in a tropical marine environment

Michael Stat, Megan J. Huggett, Rachele Bernasconi, Joseph D. DiBattista, Tina E. Berry, Stephen J. Newman, Euan S. Harvey & Michael Bunce
Effective marine management requires comprehensive data on the status of marine biodiversity. However, efficient methods that can document biodiversity in our oceans are currently lacking. Environmental DNA (eDNA) sourced from seawater offers a new avenue for investigating the biota in marine ecosystems. Here, we investigated the potential of eDNA to inform on the breadth of biodiversity present in a tropical marine environment. Directly sequencing eDNA from seawater using a shotgun approach resulted in only 0.34%...

Data from: High intra-ocean, but limited inter-ocean genetic connectivity in populations of the deep-water oblique-banded snapper Pristipomoides zonatus (Pisces: Lutjanidae)

W. Jason Kennington, Peter W. Keron, Euan S. Harvey, Corey B. Wakefield, Ashley J. Williams, Tuikolongahau Halafihi & Stephen J. Newman
While many studies have investigated connectivity and subdivision in marine fish occupying tropical, shallow water reef habitats, relatively few have been conducted on commercially important deep-water species in the Indo-Pacific region. Here, we examine spatial and temporal genetic variation in the deep-water oblique-banded snapper Pristipomoides zonatus, collected from eight locations across the Indian and Pacific Oceans. A total of 292 individuals were screened for genetic variation at six nuclear microsatellite loci and the cytochrome c...

Data from: The behavioural response of migrating humpback whales to a full seismic air gun array

Rebecca A. Dunlop, Michael J. Noad, Robert D. McCauley, Eric Kniest, Robert Slade, David Paton & Douglas H. Cato
Despite concerns on the effects of noise from seismic survey air guns on marine organisms, there remains uncertainty in the biological significance of any response. This study quantifies and interprets the response of migrating humpback whales (Megaptera novaeangliae) to a 3130 cui (51.3l) commercial air gun array. We compare the behavioural responses to active trials (array operational; n = 34 whale groups), with responses to control trials (source vessel towing the array while silent; n...

Data from: Genetic signatures through space, time and multiple disturbances in a ubiquitous brooding coral

Jim N. Underwood, Zoe T. Richards, Karen J. Miller, Marji L. Puotinen & James P. Gilmour
The predominance of self-recruitment in many reef-building corals has fundamental and complex consequences for their genetic diversity, population persistence and responses to climate change. Knowledge of genetic structure over local scales needs to be placed within a broad spatial context, and also integrated with genetic monitoring through time to disentangle these consequences. Here, we examined patterns of genetic diversity over multiple spatio-temporal scales across tropical Australia in the ubiquitous brooding coral, Seriatopora hystrix. We also...

Data from: Evolution of vertebrate postcranial complexity: axial skeleton regionalization and paired appendages in a Devonian jawless fish

Marion Chevrinais, Zerina Johanson, Kate Trinajstic, John Long, Catherine Morel, Claude B. Renaud & Richard Cloutier
One of the major events in vertebrate evolution involves the transition from jawless (agnathan) to jawed (gnathostome) vertebrates, including a variety of cranial and postcranial innovations. It has long been assumed that characters such as the pelvic girdles and fins, male intromittent organs independent from the pelvic girdles, as well as a regionalized axial skeleton first appeared in various basal gnathostome groups if not at the origin of gnathostomes. Here we describe the first occurrence...

Data from: Avian mitochondrial genomes retrieved from museum eggshell

Alicia Grealy, Michael Bunce & Clare Holleley
Avian eggshell is a bio-ceramic material with exceptional properties for preserving DNA within its crystalline structure, presenting an opportunity to retrieve genomic information from extinct or historic populations of birds. However, intracrystalline DNA has only been recovered from the large, thick eggshell of palaeognaths; members of their more-diverse sister group (neognaths) lay smaller, thinner eggs that may not exhibit the same propensity for DNA preservation. Here, we use three 40-60 year-old museum eggshell specimens of...

Data from: Optimized fishing through periodically harvested closures

Paul G. Carvalho, Stacy D. Jupiter, Fraser A. Januchowski-Hartley, Jordan Goetze, Joachim Claudet, Rebecca Weeks, Austin Humphries & Crow White
1. Periodically harvested closures are a widespread, centuries-old form of fisheries management that protects fish between pulse harvests and can generate high harvest efficiency by reducing fish wariness of fishing gear. However, the ability for periodic closures to also support high fisheries yields and healthy marine ecosystems is uncertain, despite increased promotion of periodic closures for managing fisheries and conserving ecosystems in the Indo-Pacific. 2. We developed a bioeconomic fisheries model that considers changes in...

Effect of in-situ mineral dissolution on high salinity of flowback water during hydraulic fracturing in shales

Lingping Zeng, Nathan Reid, Yunhu Lu, Mofazzal Hossain, Ali Saeedi & Quan Xie
Hydraulic fracturing has been widely implemented to enhance hydrocarbon production from shale reservoirs. However, one of the main challenges during hydraulic fracturing is to understand the high salinity of flowback water (up to 300,000 mg/L). While several mechanisms have been proposed to explain the controlling factor behind this phenomenon, less attention has been paid to quantify the contribution of fluid-shale interactions such as mineral dissolution and surface complexation on fluid salinity. We thus conducted spontaneous...

Cold call: the acoustic repertoire of Ross Sea killer whales (Orcinus orca, Type C) in McMurdo Sound, Antarctica

Rebecca Wellard, Robert Pitman, John Durban & Christine Erbe
Killer whales (Orcinus orca) are top marine predators occurring globally. In Antarctic waters, five ecotypes have been described, with Type C being the smallest form of killer whale known. Acoustic recordings of nine encounters of Type C killer whales were collected in 2012 and 2013 in McMurdo Sound, Ross Sea. In a combined 3.5 hours of recordings, 6386 killer whale vocalisations were detected and graded based on their signal-to-noise ratio. Spectrograms of the highest-quality calls...

Nalanthamala psidii supplementary data

, Anita Severn-Ellis, Maritha Schoeman, Philipp Bayer, James K. Hane, Jasper G. Rees, Dave Edwards & Jacqueline Batley

Environmental DNA reveals a multi-taxa biogeographic break across the Arabian Sea and Sea of Oman

Joseph DiBattista, Michael Berumen, Mark Priest, Maarten De Brauwer, Darren Coker, Tane Sinclair-Taylor, Amanda Hay, Gerd Bruss, Shawky Mansour, Michael Bunce, Christopher Goatley, Matthew Power & Alyssa Marshell
Environmental DNA (eDNA) is increasingly being used to assess community composition in marine ecosystems. Applying eDNA approaches across broad spatial scales now provide the potential to inform biogeographic analyses. However, to date, few studies have employed this technique to assess broad biogeographic patterns across multiple taxonomic groups. Here, we compare eDNA-derived communities of bony fishes and invertebrates, including corals and sponges, from 15 locations spanning the entire length of the Omani coast. This survey includes...

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