192 Works

Data from: Multiple Quaternary refugia in the eastern Guiana Shield revealed by comparative phylogeography of 12 frog species

Antoine Fouquet, Brice P. Noonan, Miguel T. Rodrigues, Nicolas Pech, André Gilles & Neil J. Gemmell
The Guiana Shield is one of the most pristine regions of Amazonia and biologically one of the richest areas on Earth. How and when the massive diversity of life that exists in Amazonia arose remains the subject of considerable debate. The prevailing hypothesis of Quaternary glacial refugia suggests that a part of the eastern Guiana Shield, among other areas in Amazonia, served as stable, forested refugia during periods of aridity. However, the recently proposed Disturbance-Vicariance...

Data from: Swimming against the current: genetic structure, host mobility and the drift paradox in trematode parasites

Isabel Blasco-Costa, Jonathan M. Waters & Robert Poulin
Life cycle characteristics and habitat processes can potentially interact to determine gene flow and genetic structuring of parasitic species. In this comparative study, we analysed the genetic structure of two freshwater trematode species with different life histories using cytochrome c oxidase I gene (COI) sequences and examined the effect of a unidirectional river current on their genetic diversity at 10 sites along the river. We found moderate genetic structure consistent with an isolation by distance...

Data from: Phylogenetic signal in module composition and species connectivity in compartmentalized host-parasite networks

Boris R. Krasnov, Miguel A. Fortuna, David Mouillot, Irina S. Khokhlova, Georgy I. Shenbrot & Robert Poulin
Across different taxa, networks of mutualistic or antagonistic interactions show consistent architecture. Most networks are modular, with modules being distinct species subsets connected mainly with each other and having few connections to other modules. We investigate the phylogenetic relatedness of species within modules and whether a phylogenetic signal is detectable in the within- and among module connectivity of species using 27 mammal-flea networks from the Palaearctic. In the 24 networks that were modular, closely-related hosts...

Data from: Parallel tagged next-generation sequencing on pooled samples – a new approach for population genetics in ecology and conservation

Monika Zavodna, Catherine E. Grueber & Neil J. Gemmell
Next-generation sequencing (NGS) on pooled samples has already been broadly applied in human medical diagnostics and plant and animal breeding. However, thus far it has been only sparingly employed in ecology and conservation, where it may serve as a useful diagnostic tool for rapid assessment of species genetic diversity and structure at the population level. Here we undertake a comprehensive evaluation of the accuracy, practicality and limitations of parallel tagged amplicon NGS on pooled population...

Data from: PopART: full-feature software for haplotype network construction

Jessica W. Leigh & David Bryant
1. Haplotype networks are an intuitive method for visualising relationships between individual genotypes at the population level. 2. Here, we present popart, an integrated software package that provides a comprehensive implementation of haplotype network methods, phylogeographic visualisation tools and standard statistical tests, together with publication-ready figure production. 3. popart also provides a platform for the implementation and distribution of new network-based methods – we describe one such new method, integer neighbour-joining. 4. The software is...

Data from: Bottom-up regulation of parasite population densities in freshwater ecosystems

Clément Lagrue & Robert Poulin
Theory predicts the bottom–up coupling of resource and consumer densities, and epidemiological models make the same prediction for host–parasite interactions. Empirical evidence that spatial variation in local host density drives parasite population density remains scarce, however. We test the coupling of consumer (parasite) and resource (host) populations using data from 310 populations of metazoan parasites infecting invertebrates and fish in New Zealand lakes, spanning a range of transmission modes. Both parasite density (no. parasites per...

Data from: The linking of plate tectonics and evolutionary divergences

Matthew J. Phillips, Timothy J. Page, Mark De Bruyn, Joel A. Huey, William F. Humphreys, Jane M. Hughes, Scott R. Santos, Daniel J. Schmidt & Jonathan M. Waters
It is exciting to be living at a time when the big questions in biology can be investigated using modern genetics and computing. Bauzà-Ribot et al. take on one of the fundamental drivers of biodiversity, the effect of continental drift in the formation of the world’s biota, employing next-generation sequencing of whole mitochondrial genomes and modern Bayesian relaxed molecular clock analysis. Bauzà-Ribot et al. conclude that vicariance via plate tectonics best explains the genetic divergence...

Worldwide evidence of a unimodal relationship between productivity and plant species richness

Lauchlan H. Fraser, Jason Pither, Anke Jentsch, Marcelo Sternberg, Martin Zobel, Diana Askarizadeh, Sandor Bartha, Carl Beierkuhnlein, Jonathan A. Bennett, Alex Bittel, Bazartseren Boldgiv, Ilsi I. Boldrini, Edward Bork, Leslie Brown, Marcelo Cabido, James Cahill, Cameron N. Carlyle, Giandiego Campetella, Stefano Chelli, Ofer Cohen, Anna-Maria Csergo, Sandra Diaz, Lucas Enrico, David Ensing, Alessandra Fidelis … & Szilárd Szentes
The search for predictions of species diversity across environmental gradients has challenged ecologists for decades. The humped-back model (HBM) suggests that plant diversity peaks at intermediate productivity; at low productivity few species can tolerate the environmental stresses, and at high productivity a few highly competitive species dominate. Over time the HBM has become increasingly controversial, and recent studies claim to have refuted it. Here, by using data from coordinated surveys conducted throughout grasslands worldwide and...

Data from: Building strong relationships between conservation genetics and primary industry leads to mutually beneficial genomic advances

Stephanie J. Galla, Thomas R. Buckley, Rob Elshire, Marie L. Hale, Michael Knapp, John McCallum, Roger Moraga, Anna W. Santure, Phillip Wilcox & Tammy E. Steeves
Several reviews in the past decade have heralded the benefits of embracing high-throughput sequencing technologies to inform conservation policy and the management of threatened species, but few have offered practical advice on how to expedite the transition from conservation genetics to conservation genomics. Here, we argue that an effective and efficient way to navigate this transition is to capitalize on emerging synergies between conservation genetics and primary industry (e.g., agriculture, fisheries, forestry and horticulture). Here,...

Data from: Low spatial genetic differentiation associated with rapid recolonization in the New Zealand fur seal Arctocephalus forsteri

Nicolas Dussex, Bruce C. Robertson, Alexander T. Salis, Aleksandr Kalinin, Hugh Best & Neil J. Gemmell
Population declines resulting from anthropogenic activities are of major consequence for the long-term survival of species because the resulting loss of genetic diversity can lead to extinction via the effects of inbreeding depression, fixation of deleterious mutations, and loss of adaptive potential. Otariid pinnipeds have been exploited commercially to near extinction with some species showing higher demographic resilience and recolonization potential than others. The New Zealand fur seal (NZFS) was heavily impacted by commercial sealing...

Data from: The Trojan Female Technique for pest control: a candidate mitochondrial mutation confers low male fertility across diverse nuclear backgrounds in Drosophila melanogaster

Damian K. Dowling, Daniel M. Tompkins & Neil J. Gemmell
Pest species represent a major ongoing threat to global biodiversity. Effective management approaches are required that regulate pest numbers, while minimizing collateral damage to nontarget species. The Trojan Female Technique (TFT) was recently proposed as a prospective approach to biological pest control. The TFT draws on the evolutionary hypothesis that maternally inherited mitochondrial genomes are prone to the accumulation of male, but not female, harming mutations. These mutations could be harnessed to provide trans-generational fertility-based...

Data from: Population characteristics, mechanisms of primary care and premature mortality in England: a cross-sectional study

Richard Baker, Kate Honeyford, Louis S. Levene, , David R. Jones, M. John Bankart & Tim Stokes
Objectives. Health systems with strong primary care tend to have better population outcomes, but in many countries demand for care is growing. We sought to identify mechanisms of primary care that influence premature mortality. Design. We developed a conceptual model of the mechanisms by which primary care influences premature mortality, and undertook a cross-sectional study in which population and primary care variables reflecting the model were used to explain variations in mortality under aged 75...

Data from: Cryptic female choice enhances fertilization success and embryo survival in chinook salmon

Patrice Rosengrave, Robert Montgomerie & Neil Gemmell
In this study we investigated two potentially important intersexual postcopulatory gametic interactions in a population of chinook salmon (Oncorhynchus tshawytscha): (i) the effect of female ovarian fluid (OF) on the behaviour of spermatozoa during fertilisation, and (ii) the effects of multilocus heterozygosity (as an index of male quality) and female-male genetic relatedness on sperm behaviour and male fertilisation success when there is sperm competition in the presence of that ovarian fluid. To do this, we...

Data from: Reduced representation sequencing detects only subtle regional structure in a heavily exploited and rapidly recolonizing marine mammal species

Nicolas Dussex, Helen R. Taylor, Willam R. Stovall, Kim Rutherford, Ken G. Dodds, Shannon M. Clarke & Neil J. Gemmell
Next‐generation reduced representation sequencing (RRS) approaches show great potential for resolving the structure of wild populations. However, the population structure of species that have shown rapid demographic recovery following severe population bottlenecks may still prove difficult to resolve due to high gene flow between subpopulations. Here, we tested the effectiveness of the RRS method Genotyping‐By‐Sequencing (GBS) for describing the population structure of the New Zealand fur seal (NZFS, Arctocephalus forsteri), a species that was heavily...

Data from: Evidence that fertility trades off with early offspring fitness as males age

Sheri L. Johnson, Sylvia Zellhuber-McMillan, Joanne Gillum, Jessica Dunleavy, Jonathan P. Evans, Shinichi Nakagawa & Neil J. Gemmell
Models of aging predict that sperm function and fertility should decline with age as sperm are exposed to free radical damage and mutation accumulation. However, theory also suggests that mating with older males should be beneficial for females because survival to old age is a demonstration of a male’s high genetic and/or phenotypic quality. Consequently, declines in sperm fitness may be offset by indirect fitness benefits exhibited in offspring. While numerous studies have investigated age-based...

Data from: Comparative tests of the role of dewlap size in Anolis lizard speciation

Travis Ingram, Alexis Harrison, D. Luke Mahler, María Del Rosario Castañeda, Richard E. Glor, Anthony Herrel, Yoel E. Stuart & Jonathan B. Losos
Phenotypic traits may be linked to speciation in two distinct ways: character values may influence the rate of speciation or diversification in the trait may be associated with speciation events. Traits involved in signal transmission, such as the dewlap of Anolis lizards, are often involved in the speciation process. The dewlap is an important visual signal with roles in species recognition and sexual selection, and dewlaps vary among species in relative size as well as...

Data from: Are 2D space-use analyses adapted to animals living in 3D environments? A case study on a fish shoal

Aurélien Vivancos, Gerry Closs & Cédric Tentelier
Methodologies enabling the monitoring of animal movement and behavior in 3-dimensions (3D; x, y, z, the latter accounting for the vertical dimension) are becoming increasingly accessible and can be deployed on entire groups of animals inhabiting 3D habitats. When 2-dimensional (2D; x, y) space-use analyses are used on such groups, their spatial organization is represented as a planar projection of individuals’ space-use. Movement on the vertical dimension is ignored and could biased ecological inference made...

Data from: Global analysis reveals that cryptic diversity is linked with habitat but not mode of life

Robert Poulin & Gerardo Perez-Ponce De Leon
The ubiquity of genetically distinct, cryptic species is limiting any attempt to estimate local or global biodiversity as well as impeding efforts to conserve species or control pests and diseases. Environmental factors or biological traits promoting rapid diversification into morphologically similar species remain unclear. Here, using a meta-analysis of 1230 studies using DNA sequences to search for cryptic diversity in metazoan taxa, we test two hypotheses regarding the frequency of cryptic taxa based on mode...

Data from: Logging increases the functional and phylogenetic dispersion of understorey plant communities in tropical lowland rainforest

Timm F. Döbert, Bruce L. Webber, John B. Sugau, Katharine J. M. Dickinson & Raphael K. Didham
1. Logging is a major driver of tropical forest degradation, with severe impacts on plant richness and composition. Rarely have these effects been considered in terms of their impact on the functional and phylogenetic diversity of understorey plant communities, despite the direct relevance to community reassembly trajectories. Here, we test the effects of logging on functional traits and evolutionary relatedness, over and above effects that can be explained by changes in species richness alone. We...

Data from: Quantifying apart what belongs together: a multi-state species distribution modeling framework for species using distinct habitats

Veronica F. Frans, Amélie A. Augé, Hendrik A. Edelhoff, Stefan Erasmi, Niko Balkenhol, Jan O. Engler & Hendrik Edelhoff
1. Species distribution models (SDMs) have been used to inform scientists and conservationists about the status and change of occurrence patterns in threatened species. Many mobile species use multiple functionally distinct habitats, and cannot occupy one habitat type without the other being within a reachable distance. For such species, classical applications of SDMs might lead to erroneous representations of habitat suitability, as the complex relationships between predictors are lost when merging occurrence information across multiple...

Data from: Rautangaroa, a new genus of feather star (Echinodermata: Crinoidea) from the Oligocene of New Zealand

Tomasz K. Baumiller & R. Ewan Fordyce
We describe a nearly complete, and thus extremely rare, featherstar (Crinoidea, Comatulida) from Oligocene strata of North Otago/South Canterbury, New Zealand. A detailed analysis of this specimen, as well as newly recovered material and previously described fragmentary remains from nearby contemporaneous sedimentary units, in addition to relevant historical specimens, lead us to conclude that it cannot be placed in any currently established genus. A new genus, Rautangaroa, is proposed to accommodate it. This intact specimen...

Persisting in a glaciated landscape: Pleistocene microrefugia evidenced by the tree wētā Hemideina maori in central South Island, New Zealand

Keith King, Debbie Lewis, Jonathan Waters & Graham Wallis
Aim: Repeated cycles of Pleistocene glaciation have influenced phylogeographic structure of taxa on New Zealand’s South Island. Many taxa became restricted to refugia at either end of the island during glaciation, resulting in an area of low endemicity in central South Island. This area of low endemism is typified by the so-called beech (or biotic) gap, where the absence of Nothofagus forest (and many other plant and invertebrate taxa) has been attributed to repeated glaciation....

Data from: Does migration promote or inhibit diversification? A case study involving the dominant radiation of temperate Southern Hemisphere freshwater fishes

Christopher Burridge & Jonathan M. Waters
While theory predicts that dispersal is a pivotal influence on speciation and extinction rates, it can have contradictory effects on each, such that empirical studies are needed to quantify its role. In many studies, dispersal reduction appears to promote diversification, although some analyses of migratory species suggest otherwise. Here we test for a relationship between migratory status and diversification rate within the dominant radiation of temperate Southern Hemisphere freshwater fishes, the Galaxiidae. We reconstructed a...

Data from: Subsistence practices, past biodiversity, and anthropogenic impacts revealed by New Zealand-wide ancient DNA survey

Frederik V. Seersholm, Theresa L. Cole, Alicia Grealy, Nicolas J. Rawlence, Karen Greig, Michael Knapp, Michael Stat, Anders J. Hansen, Luke J. Easton, Lara Shepherd, Alan J. D. Tennyson, R. Paul Scofield, Richard Walter & Michael Bunce
New Zealand’s geographic isolation, lack of native terrestrial mammals, and Gondwanan origins make it an ideal location to study evolutionary processes. However, since the archipelago was first settled by humans (c. 1280 AD), its unique biodiversity has been under pressure, and today an estimated 49% of the terrestrial avifauna is extinct. Current efforts to conserve the remaining fauna rely on a better understanding of the composition of past ecosystems, as well as the causes and...

Data from: Using molecular diet analysis to inform invasive species management: a case study of introduced rats consuming endemic New Zealand frogs

Bastian Egeter, Cailin Roe, Sara Peixoto, Pamela Puppo, Luke J. Easton, Joana Pinto, Phil J. Bishop & Bruce C. Robertson
The decline of amphibians has been of international concern for more than two decades and the global spread of introduced fauna is a major factor in this decline. Conservation management decisions to implement control of introduced fauna are often based on diet studies. One of the most common metrics to report in diet studies is Frequency of Occurrence (FO), but this can be difficult to interpret, as it does not include a temporal perspective. Here...

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