87 Works

Data from: Limited scope for latitudinal extension of reef corals

Paul R. Muir, Carden C. Wallace, Terence Done & J. David Aguirre
An analysis of present-day global depth distributions of reef-building corals and underlying environmental drivers contradicts a commonly held belief that ocean warming will promote tropical coral expansion into temperate latitudes. Using a global data set of a major group of reef corals, we found that corals were confined to shallower depths at higher latitudes (up to 0.6 meters of predicted shallowing per additional degree of latitude). Latitudinal attenuation of the most important driver of this...

Data from: Temperate marine protected area provides recruitment subsidies to local fisheries

Agnes Le Port, John C. Montgomery, Adam N.H. Smith, Adrian E. Croucher, Ian M. McLeod, Shane D. Lavery & A. N. H. Smith
The utility of marine protected areas (MPAs) as a means of protecting exploited species and conserving biodiversity within MPA boundaries is supported by strong empirical evidence. However, the potential contribution of MPAs to fished populations beyond their boundaries is still highly controversial; empirical measures are scarce and modelling studies have produced a range of predictions, including both positive and negative effects. Using a combination of genetic parentage and relatedness analysis, we measured larval subsidies to...

Data from: Subtle individual variation in indeterminate growth leads to major variation in survival and lifetime reproductive output in a long-lived reptile

Doug P. Armstrong, Matthew G. Keevil, Njal Rollinson & Ronald J. Brooks
1. The consequences of individual variation in life-history traits have been well studied due to their importance in evolutionary ecology. However, a trait that has received little empirical attention is the rate of indeterminate growth. In long-lived ectotherms, subtle variation in growth after maturity could have major effects over the animals’ lifetimes. 2. These effects are difficult to measure due to the challenges involved in reliably estimating individual variation in the face of environmental stochasticity,...

Data from: Identification of chloroplast genome loci suitable for high-resolution phylogeographic studies of Colocasia esculenta (L.) Schott (Araceae) and closely related taxa

Ibrar Ahmed, Peter J. Matthews, Patrick J. Biggs, Muhammad Naeem, Patricia A. McLenachan & Peter J. Lockhart
Recently, we reported the chloroplast genome-wide association of oligonucleotide repeats, indels and nucleotide substitutions in aroid chloroplast genomes. We hypothesized that the distribution of oligonucleotide repeat sequences in a single representative genome can be used to identify mutational hotspots and loci suitable for population genetic, phylogenetic and phylogeographic studies. Using information on the location of oligonucleotide repeats in the chloroplast genome of taro (Colocasia esculenta), we designed 30 primer pairs to amplify and sequence polymorphic...

Spatial and temporal variation in prey colour patterns for background-matching across a continuous heterogeneous environment

Marleen Baling, Devi Stuart-Fox, Dianne H. Brunton & James Dale
In heterogeneous habitats, camouflage via background-matching can be challenging because visual characteristics can vary dramatically across small spatial scales. Additionally, temporal variation in signalling functions of colouration can affect crypsis, especially when animals use colouration seasonally for intraspecific signalling (e.g. mate selection). We currently have a poor understanding of how wild prey optimise background-matching within continuously heterogeneous habitats, and whether this is affected by requirements of intraspecific signalling across biological seasons. Here, we quantified colour...

Data from: Phylogenetic measures reveal eco-evolutionary drivers of biodiversity along a depth gradient

David Eme, Marti Anderson, Elisabeth Myers, Clive Roberts & Libby Liggins
Energy and environmental stability are positively correlated with species richness along broad-scale spatial gradients in terrestrial ecosystems, so their relative importance in generating and preserving diversity cannot be readily disentangled. This study seeks to exploit the negative correlation between energy and stability along the oceanic depth gradient to better understand their relative contribution in shaping broadscale biodiversity patterns. We develop a conceptual framework by simulating speciation and extinction along energy and stability gradients to generate...

Changes in key traits versus depth and latitude suggest energy-efficient locomotion, opportunistic feeding and light lead to adaptive morphologies of marine fishes.

Elisabeth Myers, Marti Anderson, David Eme, Libby Liggins & Clive Roberts
1. Understanding patterns and processes governing biodiversity along broad-scale environmental gradients, such as depth or latitude, requires an assessment of not just taxonomic richness, but also morphological and functional traits of organisms. Studies of traits can help to identify major selective forces acting on morphology. Currently, little is known regarding patterns of variation in the traits of fishes at broad spatial scales. 2. The aims of this study were: (i) to identify a suite of...

Environment dependent costs and benefits of recombination in independently evolved populations of Escherichia coli

Tim Cooper & Yinhua Wang
Understanding of the causes by which reproductive isolation arises remains limited. We examine the role of adaptation in driving reproductive isolation among 12 Escherichia coli populations evolved in two different environments. We found that, regardless of whether parents were selected in the same or different environments, the average fitness of recombinants was lower than the expected, consistent with a prevailing influence of incompatibility between independently accumulated mutations. Exceptions to this pattern occurred among recombinants of...

Data from: Comparing biocontrol and herbicide for managing an invasive non-native plant species: efficacy, non-target effects and secondary invasion

Paul Peterson, Merilyn Merrett, Simon Fowler, Paul Barrett & Quentin Paynter
1. Globally, invasive non-native plants are an increasing threat to indigenous biodiversity and ecosystems, but management can be compromised by poor efficacy of control methods, harmful non-target effects or secondary invasions by other non-native plant species. 2. A 5-year field trial compared two stakeholder-selected control methods for heather, a European plant invading native ecosystems in and adjoining Tongariro National Park in New Zealand. The control methods were a selective herbicide (Pasture Kleen®; 2,4-D ester) and...

DNA sequences for six chloroplast loci concatenated, representing haplotypes found in Colocasia esculenta, and closely related Araceae

Peter J. Matthews, Ibrar Ahmed, Peter J. Lockhart, Esperanza Maribel G. Agoo, Kyaw W. Naing, Dzu V. Nguyen & Dilip K. Medhi
As an ancient clonal root and leaf crop, taro (Colocasia esculenta) is highly polymorphic with uncertain genetic and geographic origins. We explored chloroplast DNA variation in wild and cultivated taros and other Colocasia species, and found cultivated taro to be polyphyletic, with tropical and temperate clades originating in Southeast Asia. A third clade was found exclusively in wild populations from Southeast Asia to Australia and Papua New Guinea. Our findings do not support the hypothesis...

Analytic dataset informing prediction of subterranean cave and mine ambient temperatures

Meredith McClure, Daniel Crowley, Catherine Haase, Liam McGuire, Nathan Fuller, David Hayman, Cori Lausen, Raina Plowright, Brett Dickson & Sarah Olson
Caves and other subterranean features provide unique environments for many species. The importance of cave microclimate is particularly relevant at temperate latitudes where bats make seasonal use of caves for hibernation. White-nose syndrome (WNS), a fungal disease that has devastated populations of hibernating bats across eastern and central North America, has brought renewed interest in bat hibernation and hibernaculum conditions. A recent review synthesized current understanding of cave climatology, exploring the qualitative relationship between cave...

Capturing the dynamics of small populations: A retrospective assessment using long-term data for an island reintroduction

Doug Armstrong, Elizabeth Parlato, Barbara Egli, Wendy Dimond, Åsa Berggren, Mhairi McCready, Kevin Parker & John Ewen
1. The art of population modelling is to incorporate factors essential for capturing a population’s dynamics while otherwise keeping the model as simple as possible. However, it is unclear how optimal model complexity should be assessed, and whether this optimal complexity has been affected by recent advances in modelling methodology. This issue is particularly relevant to small populations because they are subject to complex dynamics but inferences about those dynamics are often constrained by small...

Data from: Progressive genome-wide introgression in agricultural Campylobacter coli

Samuel K. Sheppard, Xavier Didelot, Keith A. Jolley, Aaron E. Darling, David J. Kelly, Alison Cody, Frances M. Colles, Norval J.C. Strachan, Iain D. Ogden, Ken Forbes, Nigel P. French, Philip Carter, William G. Miller, Noel D. McCarthy, Robert Owen, Eva Litrup, Michael Egholm, Stephen D. Bentley, Julian Parkhill, Martin C. J. Maiden, Daniel Falush, Jason P. Affourtit, Norval J. C. Strachan, Ben Pascoe & Guillaume Meric
Hybridization between distantly related organisms can facilitate rapid adaptation to novel environments, but is potentially constrained by epistatic fitness interactions among cell components. The zoonotic pathogens Campylobacter coli and C. jejuni differ from each other by around 15% at the nucleotide level, corresponding to an average of nearly 40 amino acids per protein-coding gene. Using whole genome sequencing, we show that a single C. coli lineage, which has successfully colonized an agricultural niche, has been...

Data from: The root of flowering plants and total evidence

Vadim V. Goremykin, Svetlana V. Nikiforova, Duccio Cavalieri, Massimo Pindo & Peter Lockhart
Support for Amborella as the sole survivor of an evolutionary lineage that is sister to all other angiosperms comes from positions in DNA multiple-sequence alignments that have a poor fit to time-reversible substitution models. These sites exhibit significant levels of homoplasy, compositional heterogeneity, and strong heterotachy. We report phylogenetic analyses with observed, randomized, and simulated data which show there is little or no expectation that these sites provide useful information for understanding relationships among basal...

Data from: Genetic admixture predicts parasite intensity: evidence for increased hybrid performance in Darwin’s tree finches

Katharina J. Peters, Christine Evans, J. David Aguirre & Sonia Kleindorfer
Hybridisation can increase adaptive potential when enhanced genetic diversity or novel genetic combinations confer a fitness advantage, such as in the evolution of anti-parasitic mechanisms. Island systems are especially susceptible to invasive parasites due to the lack of defence mechanisms that usually coevolve in long-standing host-parasite relationships. We test if host genetic admixture affects parasite numbers in a novel host-parasite association on the Galápagos Islands. Specifically, we compare the number of Philornis downsi in nests...

Data from: Manipulating the appearance of a badge of status causes changes in true badge expression

Cody J. Dey, James Dale & James S. Quinn
Signals of dominance and fighting ability (i.e. status signals) are found in a wide range of taxa and are used to settle disputes between competitive rivals. Most previous research has considered status-signal phenotype as an attribute of the individual; however, it is more likely that signal expression is an emergent property that also incorporates aspects of the social environment. Furthermore, because an individual's signal phenotype is likely to influence its social interactions, the relationships between...

Species-level coral bleaching data for Maldives and GBR

Paul Muir, Terence Done & David Aguirre
Response to coral bleaching for 7368 coral colonies exposed to similar levels of temperature stress at a similar depth of occurrence and similar subsequent mortality. Collected in situ following moderate thermal bleaching events in the GBR in 2002 and the Maldives in 2016. Data gives species, site, depth of occurence and bleaching response which was scored by tissue colour.

Data from: Individual repeatability in laying behaviour does not support the migratory carry-over effect hypothesis of egg-size dimorphism in Eudyptes penguins

Kyle W. Morrison
Penguins of the genus Eudyptes are unique among birds in that their first-laid A-egg is 54–85% the mass of their second-laid B-egg. Although the degree of intra-clutch egg-size dimorphism varies greatly among the seven species of the genus, obligate brood reduction is typical of each, with most fledged chicks resulting from the larger B-egg. Many authors have speculated upon why Eudyptes penguins have evolved and maintained a highly dimorphic 2-egg clutch, and why it is...

Data from: Do cryptic species matter in macroecology? Sequencing European groundwater crustaceans yields smaller ranges but does not challenge biodiversity determinants

David Eme, Maja Zagmajster, Teo Delić, Cene Fiser, Jean-François Flot, Lara Konecny-Dupré, Snaebjorn Palsson, Fabio Stoch, Valerija Zakšek, Christophe J. Douady & Florian Malard
Ecologists increasingly rely on molecular delimitation methods (MMs) to identify species boundaries, thereby potentially increasing the number of putative species because of the presence of morphologically cryptic species. It has been argued that cryptic species could challenge our understanding of what determine large-scale biodiversity patterns which have traditionally been documented from morphology alone. Here, we used morphology and three MMs to derive four different sets of putative species among the European groundwater crustaceans. Then, we...

Data from: Carotenoid-based bill coloration functions as a social, not sexual, signal in songbirds (Aves: Passeriformes)

Cody J. Dey, Mihai Valcu, Bart Kempenaers & James Dale
Many animals use coloration to communicate with other individuals. While the signalling role of avian plumage colour is relatively well studied, there has been much less research on coloration in avian bare parts. However, bare parts could be highly informative signals as they can show rapid changes in coloration. We measured bill colour (a ubiquitous bare part) in over 1600 passerine species and tested whether interspecific variation in carotenoid-based coloration is consistent with signalling to...

Data from: Decoupled responses of soil bacteria and their invertebrate consumer to warming, but not freeze-thaw cycles, in the Antarctic Dry Valleys

Matthew A. Knox, Walter S. Andriuzzi, Heather N. Buelow, Cristina Takacs-Vesbach, Byron J. Adams & Diana H. Wall
Altered temperature profiles resulting in increased warming and freeze–thaw cycle (FTC) frequency pose great ecological challenges to organisms in alpine and polar ecosystems. We performed a laboratory microcosm experiment to investigate how temperature variability affects soil bacterial cell numbers, and abundance and traits of soil microfauna (the microbivorous nematode Scottnema lindsayae) from McMurdo Dry Valleys, Antarctica. FTCs and constant freezing shifted nematode body size distribution towards large individuals, driven by higher mortality among smaller individuals....

Data from: Species identity and depth predict bleaching severity in reef building corals: shall the deep inherit the reef?

Paul R. Muir, Paul A. Marshall, Ameer Abdulla & J. David Aguirre
Mass bleaching associated with unusually high sea temperatures represents one of the greatest threats to corals and coral reef ecosystems. Deeper reef areas are hypothesized as potential refugia, but the susceptibility of Scleractinian species over depth has not been quantified. During the most severe bleaching event on record, we found up to 83% of coral cover severely affected on Maldivian reefs at a depth of 3–5 m, but significantly reduced effects at 24–30 m. Analysis...

Data from: Explaining large mitochondrial sequence differences within a population sample

Mary Morgan-Richards, Mariana Bulgarella, Louisa Sivyer, Edwina J. Dowle, Marie Hale, Rachael Van Heugten, Natasha E. McKean & Steven A. Trewick
Mitochondrial DNA sequence is frequently used to infer species' boundaries, as divergence is relatively rapid when populations are reproductively isolated. However, the shared history of a non-recombining gene naturally leads to correlation of pairwise differences, resulting in mtDNA clusters that might be mistaken for evidence of multiple species. There are four distinct processes that can explain high levels of mtDNA sequence difference within a single sample. Here, we examine one case in detail as an...

Data from: Flirtation reduces males’ fecundity but not longevity

Kambiz Esfandi, Xiong Zhao He & Qiao Wang
Theory predicts that due to limited resources males should strategically adjust their investment in reproduction and survival. Based on different conceptual framework, experimental designs and study species, many studies support while others contradict this general prediction. Using a moth Ephestia kuehniella whose adults do not feed and thus have fixed resources for their lifetime fitness, we investigated whether males adjusted their investment in various life activities under dynamic socio-sexual environment. We allowed focal males to...

Data from: Long-lasting modification of soil fungal diversity associated with the introduction of rabbits to a remote sub-Antarctic archipelago

Johan Pansu, Richard C. Winkworth, Françoise Hennion, Ludovic Gielly, Pierre Taberlet & Philippe Choler
During the late nineteenth century, Europeans introduced rabbits to many of the sub-Antarctic islands, environments that prior to this had been devoid of mammalian herbivores. The impacts of rabbits on indigenous ecosystems are well studied; notably, they cause dramatic changes in plant communities and promote soil erosion. However, the responses of fungal communities to such biotic disturbances remain unexplored. We used metabarcoding of soil extracellular DNA to assess the diversity of plant and fungal communities...

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