480 Works

Data from: Determinants of male floating behaviour and floater reproduction in a threatened population of the hihi (Notiomystis cincta)

Patricia Brekke, John G. Ewen, Gemma Clucas & Anna W. Santure
Floating males are usually thought of as non-breeders. However, some floating individuals are able to reproduce through extra-pair copulations. Floater reproductive success can impact breeders’ sex-ratio, reproductive variance, multiple paternity and inbreeding, particularly in small populations. Changes in reproductive variance alter the rate of genetic drift and loss of genetic diversity. Therefore, genetic management of threatened species requires an understanding of floater reproduction and determinants of floating behaviour to effectively conserve species. Here, we used...

Data from: Cost effectiveness of the New Zealand diabetes in pregnancy guideline screening recommendations

Catherine Coop, Richard Edlin, Julie Brown & Cynthia Farquhar
Objective: To compare the cost-effectiveness of 2 possible screening strategies for gestational diabetes mellitus (GDM) from the perspective of the New Zealand health system, developed as part of a gestational diabetes guideline. Design: A decision analytic model was built comparing 2-step screening (glycated haemoglobin (HbA1c) test at first booking and a 2 h 75 g oral glucose tolerance test (OGTT) as a single test at 24–28 weeks) with 3-step screening (HbA1c test at first booking...

Data from: An invasive non-native mammal population conserves genetic diversity lost from its native range

Andrew J. Veale, Olivia J. Holland, Robbie A. McDonald, Mick N. Clout, Dianne Gleeson & D.M. Gleeson
Invasive, non-native species are one of the major causes of global biodiversity loss. Although they are, by definition, successful in their non-native range, their populations generally show major reductions in their genetic diversity during the demographic bottleneck they experience during colonization. By investigating the mitochondrial genetic diversity of an invasive non-native species, the stoat Mustela erminea, in New Zealand and comparing it to diversity in the species’ native range in Great Britain, we reveal the...

Data from: Tracing the trans-Pacific evolutionary history of a domesticated seaweed (Gracilaria chilensis) with archaeological and genetic data

Marie-Laure Guillemin, Myriam Valero, Sylvain Faugeron, Wendy Nelson & Christophe Destombe
The history of a domesticated marine macroalga is studied using archaeological, phylogeographic and population genetic tools. Phylogeographic and population genetic analyses demonstrated that the cultivated red alga Gracilaria chilensis colonised the Chilean coast from New Zealand. Combining archaeological observations with phylogeographic data provided evidence that exchanges between New Zealand and Chile have occurred at least before the Holocene, likely at the end of the Last Glacial Maximum (LGM) and we suggest that migration probably occurred...

Data from: Sequence-based association analysis reveals an MGST1 eQTL with pleiotropic effects on bovine milk composition

Mathew D. Littlejohn, Kathryn Tiplady, Tania A. Fink, Klaus Lehnert, Thomas Lopdell, Thomas Johnson, Christine Couldrey, Michael D. Keehan, Richard G. Sherlock, Chad Harland, Andrew Scott, Russell G. Snell, Stephen R. Davis & Richard J. Spelman
GWAS_pop_dataChromosome 5 Illumina BovineHD genotypes and phenotypes for the milk fat percentage GWAS population.RNAseq_pop_imputed_seq_dataChromsome 5 imputed sequence and gene expression data used for eQTL mappingRNAseq_pop_imputed_seq_data_with_gap_varsChromsome 5 imputed sequence and gene expression data used for eQTL mapping - with reference gap variantsLarge_pop_imputed_seqChromsome 5 imputed sequence and phenotype data used for milk composition association mappingRNAseq_pop_del_haplotypeGene expression (phenotypes), pedigree, and diplotype (haplotype pair) data for analysis of the CNV-proxy haplotypeZipped library of Supplementary files 1-12A zipped collection of...

Data from: Genetic diversity loss in a biodiversity hotspot: ancient DNA quantifies genetic decline and former connectivity in a critically endangered marsupial.

Carlo Pacioni, Helen Hunt, Morten E. Allentoft, Timothy G. Vaughan, Adrian F. Wayne, Alexander Baynes, Dalal Haouchar, Joe Dortch & Michael Bunce
The extent of genetic diversity loss and former connectivity between fragmented populations are often unknown factors when studying endangered species. While genetic techniques are commonly applied in extant populations to assess temporal and spatial demographic changes, it is no substitute for directly measuring past diversity using ancient DNA (aDNA). We analysed both mitochondrial DNA (mtDNA) and nuclear microsatellite loci from 64 historical fossil and skin samples of the critically endangered Western Australian woylie (Bettongia penicillata...

Data from: An integrated approach to historical population assessment of the great whales: case of the New Zealand southern right whale

Jennifer A. Jackson, Emma L. Carroll, Tim D. Smith, Alex N. Zerbini, Nathalie J. Patenaude & C. Scott Baker
Accurate estimation of historical abundance provides an essential baseline for judging the recovery of the great whales. This is particularly challenging for whales hunted prior to twentieth century modern whaling, as population-level catch records are often incomplete. Assessments of whale recovery using pre-modern exploitation indices are therefore rare, despite the intensive, global nature of nineteenth century whaling. Right whales (Eubalaena spp.) were particularly exploited: slow swimmers with strong fidelity to sheltered calving bays, the species...

Data from: Triggerfish uses chromaticity and lightness for object segregation

Karen L. Cheney, N. Justin Marshall, Fabio Cortesi, Laurie Mitchell & Misha Vorobyev
Humans group components of visual patterns according to their colour, and perceive colours separately from shape. This property of human visual perception is the basis behind the Ishihara test for colour deficiency, where an observer is asked to detect a pattern made up of dots of similar colour with variable lightness against a background of dots made from different colour(s) and lightness. To find out if fish use colour for object segregation in a similar...

Data from: The genomic ancestry, landscape genetics, and invasion history of introduced mice in New Zealand

Andrew J. Veale, James C. Russell & Carolyn M. King
The house mouse (Mus musculus) provides a fascinating system for studying both the genomic basis of reproductive isolation, and the patterns of human- mediated dispersal. New Zealand has a complex history of mouse invasions, and the living descendants of these invaders have genetic ancestry from all three subspecies, although most are primarily descended from M. m. domesticus. We used the GigaMUGA genotyping array (~135,000 loci) to describe the genomic ancestry of 161 mice, sampled from...

Data from: Genetic kinship analyses reveal that Gray's beaked whales strand in unrelated groups

Selina Patel, Kirsten F. Thompson, Anna W. Santure, Rochelle Constantine & Craig D. Millar
Some marine mammals are so rarely seen that their life history and social structure remain a mystery. Around New Zealand, Gray’s beaked whales (Mesoplodon grayi) are almost never seen alive, yet they are a commonly stranded species. Gray’s are unique among the beaked whales in that they frequently strand in groups, providing an opportunity to investigate their social organization. We examined group composition and genetic kinship in 113 Gray’s beaked whales with samples collected over...

Data from: Exotic species enhance response diversity to land-use change but modify functional composition

Jamie R. Stavert, David E. Pattemore, Anne C. Gaskett, Jacqueline R. Beggs & Ignasi Bartomeus
Two main mechanisms may buffer ecosystem functions despite biodiversity loss. First, multiple species could share similar ecological roles, thus providing functional redundancy. Second, species may respond differently to environmental change (response diversity). However, ecosystem function would be best protected when functionally redundant species also show response diversity. This linkage has not been studied directly, so we investigated whether native and exotic pollinator species with similar traits (functional redundancy) differed in abundance (response diversity) across an...

Data from: Widespread gene flow between oceans in a pelagic seabird species complex

Claire Raisin, Deborah A. Dawson, Helen Hipperson, Gavin J. Horsburgh, Jim J. Groombridge, Stefanie M.H. Ismar, Paul Sweet, Carl G. Jones, Vikash Tatayah, Kevin Ruhomaun, Norris Ken, Katherine A. Booth Jones, Malcolm A.C. Nicoll, Malcolm A. C. Nicoll, Ken Norris & Stefanie M. H. Ismar
Global-scale gene flow is an important concern in conservation biology as it has the potential to either increase or decrease genetic diversity in species and populations. Although many studies focus on the gene flow between different populations of a single species, the potential for gene flow and introgression between species is understudied, particularly in seabirds. The only well-studied example of a mixed-species, hybridizing population of petrels exists on Round Island, in the Indian Ocean. Previous...

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: Microbiome symbionts and diet diversity incur costs on the immune system of insect larvae

Indrikis Krams, Sanita Kecko, Priit Jõers, Giedrius Trakimas, Didzis Elferts, Ronalds Krams, Severi Luoto, Markus J. Rantala, Inna Inashkina, Dita Gudrā, Dāvids Fridmanis, Jorge Contreras-Garduño, Lelde Grantiņa-Ieviņa & Tatjana Krama
Communities of symbiotic microorganisms that colonize the gastrointestinal tract play an important role in food digestion and protection against opportunistic microbes. Diet diversity increases the number of symbionts in the intestines, a benefit that is considered to impose no cost for the host organism. However, less is known about the possible immunological investments that hosts have to make in order to control the infections caused by symbiont populations that increase due to diet diversity. By...

Data from: Patterns of phenotypic plasticity and local adaptation in the wide elevation range of the alpine plant Arabis alpina

Pierre De Villemereuil, Médéric Mouterde, Oscar E. Gaggiotti & Irène Till-Bottraud
Local adaptation and phenotypic plasticity are two important characteristics of alpine plants to overcome the threats caused by global changes. Among alpine species, Arabis alpina is characterised by an unusually wide altitudinal amplitude, ranging from 800 to 3,100 m of elevation in the French Alps. Two non‐exclusive hypotheses can explain the presence of A. alpina across this broad ecological gradient: adaptive phenotypic plasticity or local adaptation, making this species especially useful to better understand these...

Data from: A high density SNP chip for genotyping great tit (Parus major) populations and its application to studying the genetic architecture of exploration behaviour

Jun-Mo Kim, Anna W. Santure, Henry J. Barton, John L. Quinn, Eleanor F. Cole, Marcel E. Visser, Ben C. Sheldon, Martien A.M. Groenen, Kees Van Oers, Jon Slate & J.-M. Kim
High density SNP microarrays (‘SNP chips’) are a rapid, accurate and efficient method for genotyping several hundred thousand polymorphisms in large numbers of individuals. While SNP chips are routinely used in human genetics and in animal and plant breeding, they are less widely used in evolutionary and ecological research. In this paper we describe the development and application of a high density Affymetrix Axiom chip with around 500 000 SNPs, designed to perform genomics studies...

Data from: Model selection and parameter inference in phylogenetics using nested sampling

Patricio Maturana Russel, Brendon J. Brewer, Steffen Klaere & Remco R. Bouckaert
Bayesian inference methods rely on numerical algorithms for both model selection and parameter inference. In general, these algorithms require a high computational effort to yield reliable estimates. One of the major challenges in phylogenetics is the estimation of the marginal likelihood. This quantity is commonly used for comparing different evolutionary models, but its calculation, even for simple models, incurs high computational cost. Another interesting challenge relates to the estimation of the posterior distribution. Often, long...

Data from: Exaggerated male legs increase mating success by reducing disturbance to females in the cave wētā Pachyrhamma waitomoensis

Murray Fea & Gregory I. Holwell
Mate guarding is a widespread behaviour resulting from sperm competition and conflict over optimal remating rates. It is a key way in which males exhibit differential mating investment, and represents a complex interplay between mating effort, intrasexual competition, opportunity costs and sexual conflict. Nevertheless, although there are many examples of exaggerated male structures used to fight rivals, few animals have developed specialised male morphological adaptations for directly sheltering females from disturbance by non-rivals. Here we...

Data from: Effects of mis-alignment between dispersal traits and landscape structure on dispersal success in fragmented landscapes

Justine A. Atkins, George L. W. Perry & Todd E. Dennis
Dispersal is fundamental to population dynamics and hence extinction risk. The dispersal success of animals depends on the biophysical structure of their environments and their biological traits; however, comparatively little is known about how evolutionary trade-offs among suites of biological traits affect dispersal potential. We developed a spatially explicit agent-based simulation model to evaluate the influence of trade-offs among a suite of biological traits on the dispersal success of vagile animals in fragmented landscapes. We...

Data from: An Ishihara-style test of animal colour vision

Karen L. Cheney, Naomi.F. Green, Alexander P. Vibert, Misha Vorobyev, Justin Marshall, Daniel C. Osorio & John A. Endler
Colour vision mediates ecologically relevant tasks for many animals, such as mate choice, foraging and predator avoidance. However, our understanding of animal colour perception is largely derived from human psychophysics, even though animal visual systems differ from our own. Behavioural tests of non-human animals are required to understand how colour signals are perceived by them. Here we introduce a novel test of colour vision in animals inspired by the Ishihara colour charts, which are widely...

ICD-1/BTF3 antagonizes SKN-1-mediated endoderm specification in Caenorhabditis elegans

Chee Kiang Ewe, Yamila N Torres Cleuren & Joel H Rothman
The entire C. elegans intestine is derived from a single endodermal progenitor cell (E), the posterior daughter arising from the asymmetric division of the EMS blastomere. During early embryonic development, maternally provided SKN-1/Nrf2 activates the mesendoderm gene regulatory network (GRN) in both E and its sister, MS. A triply redundant Wnt/MAPK/Src signaling system from the neighboring P2 blastomere polarizes EMS, resulting in activation of E fate on the side contacting it. In MS, and in...

Data from: Equivalent effect of UV coloration and vibratory signal on mating success in a jumping spider

Hua Zeng, Samantha S.E. Wee, Christina J. Painting, Shichang Zhang, Daiqin Li & Samantha S E Wee
Ultraviolet (UV; wavelengths: 280–400 nm) colouration has been shown to be an important visual signal but has not been studied in conjunction with other signals such as vibratory signals previously. Here we investigated multimodal signal function in the visual and substrate-borne vibratory modalities of the UV-ornamented jumping spider Cosmophasis umbratica, in which the importance of UV colouration in courtship displays has been demonstrated. We first described vibratory signals produced by courting males. We found that...

Cumulative stressors reduce the self-regulating capacity of coastal ecosystems

Simon Thrush
Marine ecosystems are prone to tipping points, particularly in coastal zones where dramatic changes are associated with interactions between cumulative stressors (e.g. shellfish harvesting, eutrophication and sediment inputs) and ecosystem functions. A common feature of many degraded estuaries is elevated turbidity that reduces incident light to the seafloor, resulting from multiple factors including changes in sediment loading, sea-level rise and increased water column algal biomass. To determine whether cumulative effects of elevated turbidity may result...

A genome-wide investigation of adaptations related to tool use behaviour in New Caledonian and Hawaiian crows

Nicolas Dussex, Verena E. Kutschera, R. Axel W. Wiberg, Darren Parker, Gavin Hunt, Russell D. Gray, Kim Rutherford, Abe Hideaki, Robert Fleischer, Christian Rutz, Michael G. Ritchie, Jochen B.W. Wolf & Neil J. Gemmell
GFF3 file with protein-coding gne predictions for the C. moneduloides de novo genome assembly (available at the National Center for Biotechnology Information (NCBI); assembly accession number: VRTO00000000), generated using the MAKER2 pipeline.

Genetic diversity and connectivity of southern right whales (Eubalaena australis) found in the Brazil and Chile–Peru wintering grounds and the South Georgia (Islas Georgias del Sur) feeding ground

Emma L Carroll, Paulo Ott, Louise McMillan, Bárbara Galletti Vernazzani, Petra Neveceralova, Els Vermeulen, Oscar Gaggiotti, Artur Andriolo, C. Scott Baker, Connor Bamford, Peter Best, Elsa Cabrera, Susannah Calderan, Andrea Chirife, Rachel M. Fewster, Paulo A. C. Flores, Timothy Frasier, Thales R. O. Freitas, Karina Groch, Pavel Hulva, Amy Kennedy, Russell Leaper, Mathew S. Leslie, Michael Moore, Larissa Oliviera … & Jennifer A Jackson
As species recover from exploitation, continued assessments of connectivity and population structure are warranted to provide information for conservation and management. This is particularly true in species with high dispersal capacity, such as migratory whales, where patterns of connectivity could change rapidly. Here we build on a previous long-term, large-scale collaboration on southern right whales (Eubalaena australis) to combine new (nnew) and published (npub) mitochondrial (mtDNA) and microsatellite genetic data from all major wintering grounds...

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