15 Works

Data from: Bucking the trend: genetic analysis reveals high diversity, large population size and low differentiation in a deep ocean cetacean

Craig Millar, Kirsten Thompson, Selina Patel, Scott Baker & Rochelle Constantine
Understanding the genetic structure of a population is essential to its conservation and management. We report the level of genetic diversity and determine the population structure of a cryptic deep ocean cetacean, the Gray’s beaked whale (Mesoplodon grayi). We analysed 530 bp of mitochondrial control region and 12 microsatellite loci from 94 individuals stranded around New Zealand and Australia. The samples cover a large area of the species distribution (~6000 km) and were collected over...

Data from: Cultural traditions across a migratory network shape the genetic structure of southern right whales around Australia and New Zealand

E. L. Carroll, C. S. Baker, M. Watson, R. Alderman, J. Bannister, O. E. Gaggiotti, D. R. Gröcke, N. Patenaude & R. Harcourt
Fidelity to migratory destinations is an important driver of connectivity in marine and avian species. Here we assess the role of maternally directed learning of migratory habitats, or migratory culture, on the population structure of the endangered Australian and New Zealand southern right whale. Using DNA profiles, comprising mitochondrial DNA (mtDNA) haplotypes (500 bp), microsatellite genotypes (17 loci) and sex from 128 individually-identified whales, we find significant differentiation among winter calving grounds based on both...

Data from: Intrauterine insemination: a UK survey on the adherence to NICE clinical guidelines by fertility clinics

Dongah Kim, Tim Child & Cynthia Farquhar
Objective: To evaluate the awareness and response of fertility clinics in the UK to the National Institute for Health and Care Excellence (NICE) guideline recommendation that intrauterine insemination (IUI) should not be offered routinely, in order to report on current practice in the UK. Design: Online questionnaire survey of fertility clinics in the UK regarding their current clinical practice of IUI, formal discussion of the guideline recommendations, and any alterations made since the recommendations. Setting:...

Data from: Preschool children’s vision screening in New Zealand: a retrospective evaluation of referral accuracy

Miriam A. Langeslag-Smith, Alain C. Vandal, Vincent Briane, Benjamin Thompson & Nicola S. Anstice
Objectives: To assess the accuracy of preschool vision screening in a large, ethnically diverse, urban population in South Auckland, New Zealand. Design: Retrospective longitudinal study. Methods: B4 School Check vision screening records (n=5572) were compared with hospital eye department data for children referred from screening due to impaired acuity in one or both eyes who attended a referral appointment (n=556). False positive screens were identified by comparing screening data from the eyes that failed screening...

Data from: Moa diet fits the bill: virtual reconstruction incorporating mummified remains and prediction of biomechanical performance in avian giants

Marie R. G. Attard, Laura A. B. Wilson, Trevor H. Worthy, Paul Scofield, Peter Johnston, William C. H. Parr & Stephen Wroe
The moa (Dinornithiformes) are large to gigantic extinct terrestrial birds of New Zealand. Knowledge about niche partitioning, feeding mode and preference among moa species is limited, hampering palaeoecological reconstruction and evaluation of the impacts of their extinction on remnant native biota, or the viability of exotic species as proposed ecological ‘surrogates'. Here we apply three-dimensional finite-element analysis to compare the biomechanical performance of skulls from five of the six moa genera, and two extant ratites,...

Data from: No evidence for MHC class I based disassortative mating in a wild population of great tits

Irem Sepil, Reinder Radersma, Anna W. Santure, Isabelle De Cauwer, Jon Slate & Ben C. Sheldon
Genes of the major histocompatibility complex (MHC) are regarded as a potentially important target of mate choice due to the fitness benefits that may be conferred to the offspring. According to the complementary genes hypothesis, females mate with MHC dissimilar males to enhance the immunocompetence of their offspring or to avoid inbreeding depression. Here, we investigate whether selection favours a preference for maximally dissimilar or optimally dissimilar MHC class I types, based on MHC genotypes,...

Data from: Computational performance and statistical accuracy of *BEAST and comparisons with other methods

Huw A. Ogilvie, Joseph Heled, Dong Xie & Alexei J. Drummond
Under the multispecies coalescent model of molecular evolution, gene trees have independent evolutionary histories within a shared species tree. In comparison, supermatrix concatenation methods assume that gene trees share a single common genealogical history, thereby equating gene coalescence with species divergence. The multispecies coalescent is supported by previous studies which found that its predicted distributions fit empirical data, and that concatenation is not a consistent estimator of the species tree. *BEAST, a fully Bayesian implementation...

Data from: Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations

Anna W. Santure, Jocelyn Poissant, Isabelle De Cauwer, Kees Van Oers, Matthew R. Robinson, John L. Quinn, Martien A. M. Groenen, Marcel E. Visser, Ben C. Sheldon & Jon Slate
Currently there is much debate on the genetic architecture of quantitative traits in wild populations. Is trait variation influenced by many genes of small effect or by a few genes of major effect? Where is additive genetic variation located in the genome? Do the same loci cause similar phenotypic variation in different populations? Great tits (Parus major) have been studied extensively in long-term studies across Europe, and consequently are considered an ecological 'model organism'. Recently,...

Data from: Targeted gene enrichment and high-throughput sequencing for environmental biomonitoring: a case study using freshwater macroinvertebrates

Eddy J. Dowle, Xavier Pochon, Jonathan C. Banks, Karen Shearer & Susanna A. Wood
Recent studies have advocated biomonitoring using DNA techniques. In this study, two high-throughput sequencing (HTS)-based methods were evaluated: amplicon metabarcoding of the cytochrome C oxidase subunit I (COI) mitochondrial gene and gene enrichment using MYbaits (targeting nine different genes including COI). The gene-enrichment method does not require PCR amplification and thus avoids biases associated with universal primers. Macroinvertebrate samples were collected from 12 New Zealand rivers. Macroinvertebrates were morphologically identified and enumerated, and their biomass...

Data from: The influence of nonrandom extra-pair paternity on heritability estimates derived from wild pedigrees

Josh A. Firth, Jarrod D. Hadfield, Anna W. Santure, Jon Slate & Ben C. Sheldon
Quantitative genetic analysis is often fundamental for understanding evolutionary processes in wild populations. Avian populations provide a model system due to the relative ease of inferring relatedness amongst individuals through observation. However, extra-pair paternity (EPP) creates erroneous links within the social pedigree. Previous work has suggested this causes minor underestimation of heritability if paternal misassignment is random and hence not influenced by the trait being studied. Nevertheless, much literature suggests numerous traits are associated with...

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: 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: 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: 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...

Registration Year

  • 2015
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Resource Types

  • Dataset
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Affiliations

  • University of Auckland
    15
  • University of Oxford
    4
  • University of Sheffield
    4
  • Western Australian Museum
    2
  • University of Exeter
    2
  • Department of Primary Industries, Parks, Water and Environment
    1
  • Murdoch University
    1
  • University of Queensland
    1
  • Livestock Improvement Corporation
    1
  • University of Waikato
    1