64 Works

Data from: Outlier SNPs enable food traceability of the southern rock lobster, Jasus edwardsii

Cecilia Villacorta-Rath, Irina Ilyushkina, Jan M. Strugnell, Bridget S. Green, Nicholas P. Murphy, Stephen R. Doyle, Nathan E. Hall, Andrew J. Robinson & James J. Bell
Recent advances in next-generation sequencing have enhanced the resolution of population genetic studies of non-model organisms through increased marker generation and sample throughput. Using double digest restriction site-associated DNA sequencing (ddRADseq), we investigated the population structure of the commercially important southern rock lobster, Jasus edwardsii, in Australia and New Zealand with the aim of identifying a panel of SNP markers that could be used to trace country of origin. Four ddRADseq libraries comprising a total...

Data from: Testing the consistency of connectivity patterns for a widely dispersing marine species

Luke Thomas & James J. Bell
Connectivity is widely recognised as an important component in developing effective management and conservation strategies. While managers are generally most interested in demographic, rather than genetic connectivity, new analytic approaches are able to provide estimates of both demographic and genetic connectivity measures from genetic data. Combining such genetic data with mathematical models represents a powerful approach for accurately determining patterns of population connectivity. Here, we use microsatellite markers to investigate the genetic population structure of...

How functionally diverse are fish in the deep? A comparison of fish communities in deep and shallow‐water systems

Victoria Grace Carrington, Yvan Papa, Jessica Hall, Monique A. Ladds, Alice Rogers, Peter Horn, Raphaël Covain & Chelsey M. Beese
Aim: Functional diversity metrics inform how species’ traits relate to ecosystem functions, useful for quantifying how exploitation and disturbance impact ecosystems. We compare the functional diversity of entire fish communities in a shallow-water region with a deep-sea region for further insight into the differences between these ecosystem types. Location: The regions compared in this study were selected to represent a shallow-water coastal region, Tasman and Golden Bays (TBGB), and a deep-sea region, Chatham Rise (CR),...

Data from: Ocean acidification during pre-fertilization chemical communication affects sperm success

Rowan Lymbery, Jason Kennington, Christopher Cornwall & Jonathan Evans
Ocean acidification (OA) poses a major threat to marine organisms, particularly during reproduction when externally shed gametes are vulnerable to changes in seawater pH. Accordingly, several studies on OA have focused on how changes in seawater pH influence sperm behaviour and/or rates of in vitro fertilization. By contrast, few studies have examined how pH influences pre-fertilization gamete interactions, which are crucial during natural spawning events in most externally fertilizing taxa. One mechanism of gamete interaction...

Data from: Koe: Web-based software to classify acoustic units and analyse sequence structure in animal vocalisations

Yukio Fukuzawa, Wesley H. Webb, Michelle M. Roper, Stephen Marsland, Dianne H. Brunton, Andrew Gilman & Matthew D. M. Pawley
1. Classifying acoustic units is often a key step in studying repertoires and sequence structure in animal communication. Manual classification by eye and ear remains the primary method, but new tools and techniques are urgently needed to expedite the process for large, diverse datasets. 2. Here we introduce Koe, an application for classifying and analysing animal vocalisations. Koe offers bulk-labelling of units via interactive ordination plots and unit tables, as well as visualisation and playback,...

Wavelet filters for automated recognition of birdsong in long-time field recordings

Nirosha Priyadarshani, Stephen Marsland, Julius Juodakis, Isabel Castro & Virginia Listanti
1. Ecoacoustics has the potential to provide a large amount of information about the abundance of many animal species at a relatively low cost. Acoustic recording units are widely used in field data collection, but the facilities to reliably process the data recorded -- recognising calls that are relatively infrequent, and often significantly degraded by noise and distance to the microphone -- are not well developed yet. 2. We propose a call detection method for...

Data from: Dermal denticle assemblages in coral reef sediments correlate with conventional shark surveys

Erin Dillon, Kevin Lafferty, Douglas McCauley, Darcy Bradley, Richard Norris, Jennifer Caselle, Graziella DiRenzo, Jonathan Gardner & Aaron O'Dea
It is challenging to assess long-term trends in mobile, long-lived, and relatively rare species such as sharks. Despite ongoing declines in many coastal shark populations, conventional surveys might be too fleeting and too recent to describe population trends over decades to millennia. Placing recent shark declines into historical context should improve management efforts as well as our understanding of past ecosystem dynamics. A new paleoecological approach for surveying shark abundance on coral reefs is to...

Data from: Identification and independence morphometrics of Cenozoic New Zealand Spissatella and Eucrassatella (Bivalvia, Crassatellidae)

Katie S. Collins, James S. Crampton & Michael Hannah
Fossil bivalve shells are well-suited for landmark/semilandmark morphometric analysis because they preserve both traces of the internal anatomy and the whole shell outline. Utilizing landmarks and semilandmarks, we have characterized internal and external shape variation in a monophyletic clade of Cenozoic New Zealand and Australian crassatellid bivalves, to test the contiguity in morphospace of species-level taxa and to quantitatively examine the "Concept of Independent Entities" of Yonge (1953). Thirteen species from two genera (Spissatella Finlay...

Data from: Anchors and snorkels: heterochrony, development and form in functionally-constrained fossil crassatellid bivalves

Katie S. Collins, James S. Crampton, Helen L. Neil, Euan G. C. Smith, Michael F. Gazley & Michael Hannah
New growth-rate estimates for nine species from three genera of New Zealand Crassatellidae (Mollusca; Bivalvia), combined with existing morphometric ontogenetic descriptions, allow identification of heterochronic processes in the evolution of these genera. Both paedomorphosis (progenesis and neoteny) and peramorphosis (hypermorphosis and acceleration) have occurred within the clade. Overall, morphological variability and response to environmental pressure in this non-siphonate group is restricted by the interplay of anatomical and life-habit constraints. Stability in the substrate, predator avoidance,...

Data from: Optimal nutrient exchange and immune responses operate in partner specificity in the cnidarian-dinoflagellate symbiosis

Jennifer L. Matthews, Camerron M. Crowder, Clinton A. Oakley, Adrian Lutz, Ute Roessner, Eli Meyer, Arthur R. Grossman, Virginia M. Weis & Simon K. Davy
The relationship between reef-building corals and phototrophic dinoflagellates of the genus Symbiodinium is fundamental to the functioning of coral reef ecosystems. It has been suggested that reef corals may adapt to climate change by changing their dominant symbiont type to a more thermally tolerant one, although the capacity for such a community shift is potentially hindered by the compatibility of different host-symbiont pairings. Here we combined transcriptomic and metabolomic analyses to characterize the molecular, cellular,...

Data from: Efficiency of ddRAD target enriched sequencing across spiny rock lobster species (Palinuridae: Jasus)

Carla A. Souza, Nicholas Murphy, Cecilia Villacorta-Rath, Laura N. Woodings, Irina Ilyushkina, Cristian E. Hernandez, Bridget S. Green, James J. Bell & Jan M. Strugnell
Double digest restriction site-associated DNA sequencing (ddRADseq) and target capture sequencing methods are used to explore population and phylogenetic questions in non-model organisms. ddRADseq offers a simple and reliable protocol for population genomic studies, however it can result in a large amount of missing data due to allelic dropout. Target capture sequencing offers an opportunity to increase sequencing coverage with little missing data and consistent orthologous loci across samples, although this approach has generally been...

Data from: Pathogen shifts in a honey bee predator following arrival of the Varroa mite

Kevin J. Loope, James W. Baty, Phil J. Lester & Erin E. Wilson Rankin
Emerging infectious diseases (EIDs) are a global threat to honey bees, and spillover from managed bees threaten wider insect populations. Deformed wing virus (DWV), a widespread virus that has become emergent in conjunction with the spread of the mite Varroa destructor, is thought to be partly responsible for global colony losses. The arrival of Varroa in honey bee populations causes a dramatic loss of viral genotypic diversity, favoring a few virulent strains. Here, we investigate...

Data from: Multiple anthropogenic interventions drive puma survival following wolf recovery in the Greater Yellowstone Ecosystem

L. Mark Elbroch, Lucile Marescot, Howard Quigley, Derek Craighead & Heiko U. Wittmer
Humans are primary drivers of declining abundances and extirpation of large carnivores worldwide. Management interventions to restore biodiversity patterns, however, include carnivore reintroductions, despite the many unresolved ecological consequences associated with such efforts. Using multistate capture-mark-recapture models, we explored age-specific survival and cause-specific mortality rates for 134 pumas (Puma concolor) monitored in the Greater Yellowstone Ecosystem during gray wolf (Canis lupus) recovery. We identified two top models explaining differences in puma survivorship, and our results...

Data from: Analyses of phenotypic differentiations among South Georgian Diving Petrel (Pelecanoides georgicus) populations reveal an undescribed and highly endangered species from New Zealand

Johannes H. Fischer, Igor Debski, Colin M. Miskelly, Charles A. Bost, Aymeric Fromant, Alan J. D. Tennyson, Jake Tessler, Rosalind Cole, Johanna H. Hiscock, Graeme A. Taylor & Heiko U. Wittmer
Unresolved taxonomy of threatened species is problematic for conservation as the field relies on species being distinct taxonomic units. Differences in breeding habitat and results from a preliminary molecular analysis indicated that the New Zealand population of the South Georgian Diving Petrel (Pelecanoides georgicus) was a distinct, yet undescribed, species. We measured 11 biometric characters and scored eight plumage characters in 143 live birds and 64 study skins originating from most populations of P. georgicus,...

Data from: Genetic consequences of a century of protection: serial founder events and survival of the little spotted kiwi (Apteryx owenii)

Kristina M. Ramstad, Rogan M. Colbourne, Hugh A. Robertson, Fred W. Allendorf & Charles H. Daugherty
We present the outcome of a century of post-bottleneck isolation of a long-lived species, the little spotted kiwi (Apteryx owenii, LSK) and demonstrate that profound genetic consequences can result from protecting few individuals in isolation. LSK were saved from extinction by translocation of five birds from South Island, New Zealand to Kapiti Island 100 years ago. The Kapiti population now numbers some 1200 birds and provides founders for new populations. We used 15 microsatellite loci...

Data from: Toxicity and utilization of chemical weapons: does toxicity and venom utilization contribute to the formation of species communities?

Fabian L. Westermann, Iain S. McPherson, Tappy H. Jones, Lesley Milicich, Phillip J. Lester, Philip J. Lester & Tappey H. Jones
Toxicity and the utilization of venom are essential features in the ecology of many animal species and have been hypothesized to be important factors contributing to the assembly of communities through competitive interactions. Ants of the genus Monomorium utilize a variety of venom compositions, which have been reported to give them a competitive advantage. Here, we investigate two pairs of Monomorium species, which differ in the structural compositions of their venom and their co-occurrence patterns...

Data from: Table scraps: inter-trophic food provisioning by pumas

L. Mark Elbroch & Heiko U. Wittmer
Large carnivores perform keystone ecological functions through direct predation, or indirectly, through food subsidies to scavengers or trophic cascades driven by their influence on the distributions of their prey. Pumas (Puma concolor) are an elusive, cryptic species difficult to study, and little is known about their inter-trophic level interactions in natural communities. Using new GPS technology, we discovered that pumas in Patagonia provided 232 ± 31 kg of edible meat/month/100 km2 to near-threatened Andean condors...

Data from: Fitness and microbial networks of the common wasp, Vespula vulgaris (Hymenoptera: Vespidae), in its native and introduced range

Monica A. M. Gruber, Oliver Quinn, James W. Baty, Jana Dobelmann, John Haywood, T. Wenseleers & Philip J. Lester
1. Variation in microbial communities between populations is increasingly hypothesized to affect animal fitness and performance, including for invasive species. Pathogenic species may be lost during the introduction process, enhancing invader fitness and abundance. 2. We assessed fitness, immune gene expression, and microbial network complexity of invasive common wasps, Vespula vulgaris. Microbial networks were assayed using 16S and 18S sequencing and gene expression arrays in the native (Belgium) and introduced range (New Zealand). We examined...

Explaining illness with evil: Pathogen prevalence fosters moral vitalism

Brock Bastian, Christin-Melanie Vauclair, Steve Loughnan, Paul Bain, Ashwini Ashokkumar, Maja Becker, Michal Bilewicz, Emma Collier-Baker, Carla Crespo, Paul W. Eastwick, Ronald Fischer, Malte Friese, Ángel Gómez, Valeschka M. Guerra, Jose Luis Castellanos Guevara, Katja Hanke, Nic Hooper, Li-Li Huang, Shi Junqi, Minoru Karasawa, Peter Kuppens, Siri Leknes, Müjde Peker, Cesar Pelay, Afoditi Pina … & William B. Swann
Pathogens represent a significant threat to human health leading to the emergence of strategies designed to help manage their negative impact. We examined how spiritual beliefs developed to explain and predict the devastating effects of pathogens and spread of infectious disease. Analysis of existing data in Studies 1 and 2 suggests that moral vitalism (beliefs about spiritual forces of evil) is higher in geographical regions characterized by historical higher levels of pathogens. Furthermore, drawing on...

A coralline alga gains tolerance to ocean acidification after multiple generations of exposure: data

Christopher Cornwall
Crustose coralline algae (CCA) play a crucial role in the building of reefs in the photic zones of nearshore ecosystems globally and are highly susceptible to ocean acidification. Yet the extent to which CCA can gain tolerance to ocean acidification over multiple generations of exposure is unknown. We show that while calcification of juvenile CCA is initially highly sensitive to ocean acidification, after 6 generations of exposure the effects of ocean acidification disappears. A reciprocal...

Data associated with: Going round the twist – An empirical analysis of shell coiling in helicospiral gastropods

Katie S. Collins, Roman Klapaukh, James S. Crampton, Michael F. Gazley, C. Ian Schipper, Anton Maksimenko & Benjamin R. Hines
The logarithmic helicospiral has been the most widely accepted model of regularly coiled mollusc form since it was proposed by Moseley (1838) and popularised by Thompson (1942) and Raup (1966). It is based on an explicit assumption that shells are isometric and grow exponentially, and an implicit assumption that the external form of the shell follows the internal shape, which implies that the parameters of the spiral could, theoretically, be reconstructed from the external whorl...

Reproductive maturity in boreal trees, Northwest Territories, Canada

Raquel Alfaro Sánchez, Jill F Johnstone, Steve G Cumming, Nicola Day, Michelle C Mack, Xanthe J Walker & Jennifer L Baltzer
In boreal North America, much of the landscape is covered by fire-adapted forests dominated by serotinous conifers. For these forests, reductions in fire return interval could limit reproductive success, owing to insufficient time for stands to reach reproductive maturity i.e., to initiate cone production. Improved understanding of the drivers of reproductive maturity can provide important information about the capacity of these forests to self-replace following fire. Here, we assessed the drivers of reproductive maturity in...

Reintroduced wolves and hunting limit the abundance of a subordinate apex predator in a multi-use landscape

L. Mark Elbroch, Jake Ferguson, Howard Quigley, Derek Craighead, Daniel Thompson & Heiko Wittmer
Top-down effects exhibited by apex predators are modulated by human impacts on community composition and species abundances. For these reasons, research supporting strong top-down effects of apex predators occurs almost entirely within protected areas rather than the much more common multi-use landscapes dominating modern ecosystems. Based on 16 years of monitoring, we developed an integrated population model to disentangle the concurrent contributions of a reintroduced apex predator, the gray wolf, human hunting, and prey abundances...

Lunar rhythms in growth of larval fish

Jeffrey S. Shima, Craig W. Osenberg, Erik G. Noonburg, Suzanne H. Alonzo & Stephen E. Swearer
Growth and survival of larval fishes is highly variable and unpredictable. Our limited understanding of this variation constrains our ability to forecast population dynamics and effectively manage fisheries. Here we show that daily growth rates of a coral reef fish (the sixbar wrasse, Thalassoma hardwicke) are strongly lunar-periodic and predicted by the timing of nocturnal brightness: growth was maximized when the first half of the night was dark and the second half of the night...

Data from: Decoding the dynamics of dental distributions: insights from shark demography and dispersal

Sora Kim, Justin Yeakel, Juergen Kriwet, Meghan Balk, Jaelyn Eberle, Sarah Zeichner & Dina Fieman
Shark teeth are the most abundant vertebrate fossil, and because tooth size generally correlates with body size, their accumulations document the size structure of populations. Understanding how ecological and environmental processes influence size structure, and how this extends to influence these dental distributions, may offer a window into the ecological and environmental dynamics of past and present shark populations. Here we examine the dental distributions of sand tigers, including extant Carcharias taurus and extinct Striatolamia...

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