78 Works

Data from: Genomic evidence for the parallel evolution of coastal forms in the Senecio lautus complex

Federico Roda, Luke Ambrose, Gregory M. Walter, Huanle L. Liu, Andrea Schaul, Andrew Lowe, Pieter B. Pelser, Peter Prentis, Loren H. Rieseberg & Daniel Ortiz-Barrientos
Instances of parallel ecotypic divergence where adaptation to similar conditions repeatedly cause similar phenotypic changes in closely related organisms are useful for studying the role of ecological selection in speciation. Here we used a combination of traditional and next generation genotyping techniques to test for the parallel divergence of plants from the Senecio lautus complex, a phenotypically variable groundsel that has adapted to disparate environments in the South Pacific. Phylogenetic analysis of a broad selection...

Data from: Anomalous unrooted gene trees

James H. Degnan
The coalescent and multispecies coalescent model rooted genealogies backward through time. Often, the direction of time is unknown in trees estimated from molecular sequences due to reversible mutation models, absence of an appropriate outgroup, and the absence of the molecular clock. In this paper, probabilities of unrooted gene-tree topologies under the multispecies coalescent are considered. The main result is that for any species-tree topology with 7 or more taxa, there exist branch lengths such that...

Data from: Genomic diversity of a nectar yeast clusters into metabolically, but not geographically, distinct lineages

Manpreet K. Dhami, Thomas Hartwig, Andrew D. Letten, Michael Banf & Tadashi Fukami
Both dispersal limitation and environmental sorting can affect genetic variation in populations, but their contribution remains unclear, particularly in microbes. We sought to determine the contribution of geographic distance (as a proxy for dispersal limitation) and phenotypic traits (as a proxy for environmental sorting), including morphology, metabolic ability, and interspecific competitiveness, to the genotypic diversity in a nectar yeast species, Metschnikowia reukaufii. To measure genotypic diversity, we sequenced the genomes of 102 strains of M....

Data from: Contemporary ecological interactions improve models of past trait evolution

Matthew C. Hutchinson, Marilia P. Gaiarsa & Daniel B. Stouffer
Despite the fact that natural selection underlies both traits and interactions, evolutionary models often neglect that ecological interactions may, and in many cases do, influence the evolution of traits. Here, we explore the interdependence of ecological interactions and functional traits in the pollination associations of hawkmoths and flowering plants. Specifically, we develop an adaptation of the Ornstein-Uhlenbeck model of trait evolution that allows us to study the influence of plant corolla depth and observed hawkmoth-plant...

Data from: Higher-order interactions capture unexplained complexity in diverse communities

Margaret Mayfield & Daniel Stouffer
Natural communities are well known to be maintained by many complex processes. Despite this, the practical aspects of studying them often require some simplification, such as the widespread assumption that direct, additive competition captures the important details about how interactions between species impact community diversity. On the other hand, more complex non-additive ‘higher-order’ interactions, are assumed to be negligible or absent. Notably, these assumptions are poorly supported and have major consequences for the accuracy with...

Data from: Cophylogenetic signal is detectable in pollination interactions across ecological scales

Matthew C. Hutchinson, Edgar Fernando Cagua & Daniel B. Stouffer
That evolutionary history can influence the way that species interact is a basic tenet of evolutionary ecology. However, when the role of evolution in determining ecological interactions is investigated, focus typically centers on just one side of the interaction. A cophylogenetic signal, the congruence of evolutionary history across both sides of an ecological interaction, extends these previous explorations and provides a more complete picture of how evolutionary patterns influence the way species interact. To date,...

Data from: Reciprocal translocation of small numbers of inbred individuals rescues immunogenetic diversity

Catherine E. Grueber, Jolene T. Sutton, Sol Heber, James V. Briskie, Ian G. Jamieson & Bruce C. Robertson
Genetic rescue can reduce inbreeding depression and increase fitness of small populations, even when the donor populations are highly inbred. In a recent experiment involving two inbred island populations of the South Island robin, Petroica australis, reciprocal translocations improved microsatellite diversity and individual fitness. While microsatellite loci may reflect patterns of genome-wide diversity, they generally do not indicate the specific genetic regions responsible for increased fitness. We tested the effectiveness of this reciprocal translocation for...

Data from: Sexual conflict in action: an antagonistic relationship between maternal and paternal sex allocation in the tammar wallaby, Notamacropus eugenii

Amy M. Edwards, Elissa Z. Cameron, Janine E. Deakin, Tariq Ezaz, Jorge C. Pereira, Malcolm A. Ferguson-Smith & Kylie A. Robert
Sex ratio biases are often inconsistent, both among and within species and populations. While some of these inconsistencies may be due to experimental design, much of the variation remains inexplicable. Recent research suggests that an exclusive focus on mothers may account for some of the inconsistency, with an increasing number of studies showing variation in sperm sex ratios and seminal fluids. Using fluorescent in-situ hybridization we show a significant population level Y-chromosome bias in the...

Data from: Between-year changes in community composition shape species' roles in an Arctic plant-pollinator network

Alyssa R. Cirtwill, Tomas Roslin, Claus Rasmussen, Jens Mogens Olesen & Daniel B. Stouffer
Inter-annual turnover in community composition can affect the richness and functioning of ecological communities. If incoming and outgoing species do not interact with the same partners, ecological functions such as pollination may be disrupted. Here, we explore the extent to which turnover affects species' roles --as defined based on their participation in different motifs positions-- in a series of temporally replicated plant-pollinator networks from high-Arctic Zackenberg, Greenland. We observed substantial turnover in the plant and...

Data from: Designing monitoring protocols to measure population trends of threatened insects: a case study of the cryptic, flightless grasshopper Brachaspis robustus

Jennifer C. Schori, Tammy E. Steeves & Tara J. Murray
Statistically robust monitoring of threatened populations is essential for effective conservation management because the population trend data that monitoring generates is often used to make decisions about when and how to take action. Despite representing the highest proportion of threatened animals globally, the development of best practice methods for monitoring populations of threatened insects is relatively uncommon. Traditionally, population trend data for the Nationally Endangered New Zealand grasshopper Brachaspis robustus has been determined by counting...

Exotic plants accumulate and share herbivores yet dominate communities via rapid growth

Warwick Allen
Manuscript abstract: Herbivores may facilitate or impede exotic plant invasion, depending on their direct and indirect interactions with exotic plants relative to co-occuring natives. However, previous studies investigating direct effects have mostly used pairwise native-exotic comparisons with few enemies, reached conflicting conclusions, and largely overlooked indirect interactions such as apparent competition. Here we ask whether native and exotic plants differ in their interactions with invertebrate herbivores. We manipulate and measure plant-herbivore and plant-soil biota interactions...

Patterns of plant naturalization show that facultative mycorrhizal plants are more likely to succeed outside their native Eurasian ranges

Jaime Moyano, Ian Dickie, Mariano Rodriguez Cabal & Martin Nuñez
The naturalization of an introduced species is a key stage during the invasion process. Therefore, identifying the traits that favor the naturalization of non-native species can help understand why some species are more successful when introduced to new regions. The ability and the requirement of a plant species to form a mutualism with mycorrhizal fungi, together with the types of associations formed may play a central role in the naturalization success of different plant species....

Community-level direct and indirect impacts of an invasive plant favour exotic over native species

Warwick Allen, Ralph Wainer, Jason Tylianakis, Barbara Barratt, Marcus-Rongowhitiao Shadbolt, Lauren Waller & Ian Dickie
1. Indirect interactions mediated by shared enemies or mutualists (i.e., apparent competition) can influence whether invasive plants harm or benefit co-occurring species. However, studies to date have largely examined single pairwise interactions, limiting our understanding of the interplay among different types of interactions and whether indirect impacts systematically favour native or exotic species. Predicting indirect interaction strength has also proven challenging, and it remains unclear whether the strengths of different indirect interactions are correlated. 2....

Data from: Trophic partitioning and feeding capacity in Permian bryozoan faunas of Gondwana

Catherine Reid & Yuta Tamberg
Bryozoans are epibenthic suspension-feeders and use their ciliated tentacles to generate feeding currents. Modern bryozoan mouth size limits the size of the particles that can be ingested, and lophophore diameter is linked to water pumping rates. In fossil bryozoans these soft parts are absent, however, mouth and lophophore dimensions can be inferred from preserved skeletons. Gondwanan Permian palaeostomate bryozoans show distinct order-level trophic partitioning across warm to cold-water faunas. In diverse warm-water faunas of southern...

Latitudinal influences on bryozoan calcification through the Paleozoic

Catherine Reid, Patrick N Wyse Jackson &
Bryozoans are active non-phototrophic biomineralizers that precipitate their calcareous skeletons in sea-water. Carbonate saturation states vary temporally and spatially in Paleozoic oceans, and we used the Bryozoan Skeletal Index (BSI) to investigate whether bryozoan calcification is controlled by seawater chemistry in Paleozoic trepostome and cryptostome bryozoans. Our results show that cryptostome bryozoan genera are influenced by ocean chemistry throughout the Paleozoic and precipitate the most calcite per autozooid at lower latitudes, where carbonate saturation states...

Plant Respiration Modelling with JULES for a changing climate (1860-2100)

C. Huntingford, O.K. Atkin, A. Martinez-De La Torre, L.M. Mercado, M.A. Heskel, A.B. Harper, K.J. Bloomfield, O.S. O'Sullivan, P.B. Reich, K.R. Wythers, E.E. Butler, M. Chen, K.L. Griffin, P. Meir, M.G. Tjoelker, M.H. Turnbull, S. Sitch, A. Wiltshire & Y. Malhi
The dataset contains annual global plant respiration (and related diagnostics, such as Net Primary Productivity, Gross Primary Productivity and soil respiration), applicable for pre-industrial times (taken as year 1860) through to the end of the 21st Century (year 2100). The spatial resolution of the data is 2.5 degrees latitude x 3.75 degrees longitude. These diagnostics are outputs from the Joint UK Land Environment Simulator (JULES land surface model) under four different approaches to calcluate leaf...

Data from: Inferring predator-prey interactions in food webs

Justin Page Pomeranz, Ross M. Thompson, Timothée Poisot, Jon S. Harding & Justin P. F. Pomeranz
1. Food webs are a powerful way to represent the diversity, structure, and function of ecological systems. However, the accurate description of food webs requires significant effort in time and resources, limiting their widespread use in ecological studies. Newly published methods allow for the inference of feeding interactions using proxy variables. Here, we compare the accuracy of two recently described methods, as well as describe a composite model of the two, for the inference of...

Data from: Mechanisms of trophic niche compression: evidence from landscape disturbance

Francis J. Burdon, Angus R. McIntosh & Jon S. Harding
1. Natural and anthropogenic disturbances commonly alter patterns of biodiversity and ecosystem functioning. However, how networks of interacting species respond to these changes remains poorly understood. We described aquatic food webs using invertebrate and fish community composition, functional traits, and stable isotopes from twelve agricultural streams along a landscape disturbance gradient. 2. We predicted that excessive deposition of fine inorganic sediment (sedimentation) associated with agricultural activities would negatively influence aquatic trophic diversity (e.g., reduced vertical...

The population genomics of repeated freshwater colonizations by Gulf Pipefish

Sarah Flanagan, Emily Rose & Adam Jones
How organisms adapt to the novel challenges imposed by the colonization of a new habitat has long been a central question in evolutionary biology. When multiple populations of the same species independently adapt to similar environmental challenges, the question becomes whether the populations have arrived at their adaptations through the same genetic mechanisms. In recent years, genetic techniques have been used to tackle these questions by investigating the genome‐level changes underlying local adaptation. Here, we...

Cascading impacts of earthquakes and extreme heatwaves have destroyed populations of an iconic marine foundation species

Mads Thomsen
Aim: Ecologists traditionally study how contemporary local processes, such as biological interactions and physical stressors, affect the distribution and abundance of organisms. By comparison, biogeographers study the distribution of the same organisms, but focus on historic, larger-scale processes that can cause mass mortalities, such as earthquakes. Here we document cascading effects of rare biogeographical (seismic) and more common ecological (temperature-related) processes on the distribution and abundances of coastal foundation species. Location: Intertidal wave-exposed rocky reefs...

Pieces in a global puzzle: Population genetics at two whale shark aggregations in the western Indian Ocean

Royale Hardenstine, Song He, Jesse Cochran, Camrin Braun, E. Fernando Cagua, Simon Pierce, Clare Prebble, Christoph Rohner, Pablo Saenz-Agudelo, Tane Sinclair-Taylor, Gregory Skomal, Simon Thorrold, Alexandra Watts, Casey Zakroff & Michael Berumen
The whale shark Rhincodon typus is found throughout the world’s tropical and warm-temperate ocean basins. Despite their broad physical distribution, research on the species has been concentrated at a few aggregation sites. Comparing DNA sequences from sharks at different sites can provide a demographically neutral understanding of the whale shark’s global ecology. Here, we created genetic profiles for 84 whale sharks from the Saudi Arabian Red Sea and 72 individuals from the coast of Tanzania...

Data from: Blood-red colour as a prey-choice cue for mosquito specialist predators

Lisa Taylor, Fiona Cross & Robert Jackson
Specialist predators are innately and distinctively proficient at targeting specific prey types. This is enabled by behavioural, perceptual, and cognitive mechanisms that can only be understood using carefully-designed experiments. Evarcha culicivora is an East African jumping spider that feeds on vertebrate blood acquired indirectly by actively targeting blood-carrying female mosquitoes as preferred prey. Here we asked whether these spiders use the colour red to locate this prey. In Objective 1, we used spectrophotometry to document...

Data for: Density dependence and spatial heterogeneity limit the population growth rate of invasive pines at the landscape scale

Rowan Sprague, Philip Hulme, Elena Moltchanova & William Godsoe
Determining population growth across large scales is difficult because it is often impractical to collect data at large scales and over long timespans. Instead, the growth of a population is often only measured at a small, plot-level scale and then extrapolated to derive a mean field estimate. However, this approach is prone to error since it simplifies spatial processes such as the neighbourhood effects of density and dispersal. We present a novel approach that estimates...

Data from: Genotype matching in a parasitoid-host genotypic food web: an approach for measuring effects of environmental change

Blas Lavandero & Jason M. Tylianakis
Food webs typically quantify interactions between species, whereas evolution operates through the success of alleles within populations of a single species. To bridge this gap, we quantify genotypic interaction networks among individuals of a single specialized parasitoid species and its obligately to cyclically parthenogenetic aphid host along a climatic gradient. As a case study for the kinds of questions genotype food webs could be used to answer, we show that genetically-similar parasitoids became more likely...

Data from: Organic farming promotes biotic resistance to food-borne human pathogens

Matthew S. Jones, Zhen Fu, John P. Reganold, Daniel S. Karp, Thomas E. Besser, Jason M. Tylianakis & William E. Snyder
Farmland biodiversity benefits pollination, biological control and other key ecosystem services. Food safety has been seen as an exception to this broader pattern, as diverse farmlands attract wildlife that vector foodborne human pathogens. Resulting mitigation efforts thus often seek to deter wildlife by removing natural habitats, while also excluding vertebrate livestock. However, surprising recent evidence suggests that farm simplification actually increases the likelihood that produce will be contaminated with human pathogens. Here, we consider the...

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