103 Works

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...

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...

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: 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: 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: 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: 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: 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...

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...

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...

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...

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...

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...

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...

Fitness of evolving bacterial populations is contingent on deep and shallow history but only shallow history creates predictable patterns

Timothy Cooper, Francisco Moore, Chelsea Smith & Adam Smith
Long term evolution experiments have tested the importance of genetic and environmental factors in influencing evolutionary outcomes. Differences in phylogenetic history, recent adaptation to distinct environments, and chance events all influence the fitness of a population. However, the interplay of these factors on a population's evolutionary potential remains relatively unexplored. We tracked the outcome of 2,000 generations of evolution of four natural isolates of Escherichia coli bacteria that were engineered to also create differences in...

Additional file 1 of Genome sequence of the entomopathogenic Serratia entomophila isolate 626 and characterisation of the species specific itaconate degradation pathway

Amy L. Vaughan, Eric Altermann, Travis R. Glare & Mark R. H. Hurst
Additional file 1. COG breakdown of Serratia entomophila 626 in comparison to the 5 selected Serratia species from Genbank. No. denotes number of COGs per isolate; % the percentage of the genome made up by this category.

Additional file 7 of The Venturia inaequalis effector repertoire is dominated by expanded families with predicted structural similarity, but unrelated sequence, to avirulence proteins from other plant-pathogenic fungi

Mercedes Rocafort, Joanna K. Bowen, Berit Hassing, Murray P. Cox, Brogan McGreal, Silvia de la Rosa, Kim M. Plummer, Rosie E. Bradshaw & Carl H. Mesarich
Additional file 7: Matrix amino acid identity of the effector candidate (EC) structural families (MAX, ToxA, LARS, FOLD).

Data from: The genetic covariance between life-cycle stages separated by metamorphosis.

J. David Aguirre, Mark W. Blows & Dustin J. Marshall
Metamorphosis is common in animals, yet the genetic associations between life cycle stages are poorly understood. Given the radical changes that occur at metamorphosis, selection may differ before and after metamorphosis, and the extent that genetic associations between pre- and post-metamorphic traits constrain evolutionary change is a subject of considerable interest. In some instances, metamorphosis may allow the genetic decoupling of life cycle stages, whereas in others, metamorphosis could allow complementary responses to selection across...

Data from: The evolutionary root of flowering plants

Vadim V. Goremykin, Svetlana V. Nikiforova, Patrick J. Biggs, Bojian Zhong, Peter DeLange, William Martin, Stefan Woetzel, Robin A. Atherton, Patricia McLenachan, Peter James Lockhart & Patricia A. Mclenachan
Correct rooting of the angiosperm radiation is both challenging and necessary for understanding the origins and evolution of physiological and phenotypic traits in flowering plants. The problem is known to be difficult due to the large genetic distance separating flowering plants from other seed plants and the sparse taxon sampling among basal angiosperms. Here we provide further evidence for concern over substitution model misspecification in analyses of chloroplast DNA sequences. We show that support for...

Data from: The role of a dominant predator in shaping biodiversity over space and time in a marine ecosystem

Kari Elsa Ellingsen, Marti J. Anderson, Nancy L. Shackell, Torkild Tveraa, Nigel G. Yoccoz & Kenneth T. Frank
1. Exploitation of living marine resources has resulted in major changes to populations of targeted species and functional groups of large-bodied species in the ocean. However, the effects of overfishing and collapse of large top predators on the broad-scale biodiversity of oceanic ecosystems remain largely unexplored. 2. Populations of the Atlantic cod (Gadus morhua) were overfished and several collapsed in the early 1990s across Atlantic Canada, providing a unique opportunity to study potential ecosystem-level effects...

Data from: Correlation of shell phenotype and local environment suggests a role for natural selection in the evolution of Placostylus snails

Eddy J. Dowle, Mary Morgan-Richards, Fabrice Brescia & Steve A. Trewick
The giant edible Placostylus snails of New Caledonia occur across a wide range of environmental conditions, from the dry southwest to the wetter central and northeastern regions. In large, slow-moving animals such as Placostylus, speciation could be assumed to be largely driven by allopatry and genetic drift as opposed to natural selection. We examined variation in shell morphology using geometric morphometrics and genetic structure within two species of Placostylus (P. fibratus, P. porphyrostomus), to determine...

Data from: Combining data‐derived priors with postrelease monitoring data to predict persistence of reintroduced populations

Faline M. Drummond, Tim G. Lovegrove & Doug P. Armstrong
Monitoring is an essential part of reintroduction programs, but many years of data may be needed to obtain reliable population projections. This duration can potentially be reduced by incorporating prior information on expected vital rates (survival and fecundity) when making inferences from monitoring data. The prior distributions for these parameters can be derived from data for previous reintroductions, but it is important to account for site‐to‐site variation. We evaluated whether such informative priors improved our...

Data from: Sticky genomes: using NGS evidence to test hybrid speciation hypotheses

Mary Morgan-Richards, Simon F. K. Hills, Patrick J. Biggs & Steven A. Trewick
Hypotheses of hybrid origin are common. Here we use next generation sequencing to test a hybrid hypothesis for a non-model insect with a large genome. We compared a putative hybrid triploid stick insect species (Acanthoxyla geisovii) with its putative paternal diploid taxon (Clitarchus hookeri), a relationship that provides clear predictions for the relative genetic diversity within each genome. The parental taxon is expected to have comparatively low allelic diversity that is nested within the diversity...

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