89 Works

Data from: The molecular biogeography of the Indo-Pacific: testing hypotheses with multispecies genetic patterns

Eric D. Crandall, Cynthia Riginos, Chris E. Bird, Libby Liggins, Eric Treml, Maria Beger, Paul H. Barber, Sean R. Connolly, Peter F. Cowman, Joseph D. Dibattista, Jeff A. Eble, Sharon F. Magnuson, John B. Horne, Marc Kochzius, Harilaos A. Lessios, Shang Yin Vanson Liu, William B. Ludt, Hawis Madduppa, John M. Pandolfi, Robert R. Toonen, Contributing Members Of Diversity Of The Indo-Pacific Network & Michelle R. Gaither
Aim: To test hypothesized biogeographic partitions of the tropical Indo-Pacific Ocean with phylogeographic data from 56 taxa, and to evaluate the strength and nature of barriers emerging from this test. Location: The Indo-Pacific Ocean. Time Period: Pliocene through the Holocene. Major Taxa Studied: 56 marine species. Methods: We tested eight biogeographic hypotheses for partitioning of the Indo-Pacific using a novel modification to analysis of molecular variance. Putative barriers to gene flow emerging from this analysis...

Data from: Tuatara and a new morphometric dataset for Rhynchocephalia: comments on Herrera‐Flores et al

Felix Vaux, Mary Morgan-Richards, Elizabeth E. Daly & Steven A. Trewick
It has recently been suggested that a ‘living fossil’ can be identified because it is both morphologically conservative and exhibits a significantly slower rate of morphological evolution compared to related lineages (Herrera-Flores et al. 2017). As an exemplar, variation among known rhynchocephalians was investigated, and it was concluded that the New Zealand tuatara Sphenodon punctatus Gray, 1831 is a living fossil species (Herrera-Flores et al. 2017). In addition to the dubious biological meaning and basis...

Data from: Natural variation in GL1 and its effects on trichome density in Arabidopsis thaliana

Rebecca H. Bloomer, Thomas E. Juenger & Vaughan V. Symonds
The ultimate understanding of how biological diversity arises, is maintained, and lost depends on identifying the genes responsible. Although a good deal has been discovered about gene function over the past few decades, far less is understood about gene effects; i.e., how natural variation in a gene contributes to natural variation in phenotypes. Trichome density in Arabidopsis thaliana is an ideal trait for studies of natural molecular and phenotypic variation, as trichome initiation is genetically...

Data from: A missense mutation in AGTPBP1 was identified in sheep with a lower motor neuron disease

Dorian J. Garrick, Xia Zhao, Suneel K. Onteru, Keren E. Dittmer, Kathleen Parton, Hugh T. Blair & M. F. Rothschild
A type of lower motor neuron (LMN) disease inherited as autosomal recessive in Romney sheep was characterized with normal appearance at birth, but with progressive weakness and tetraparesis after the first week of life. Here, we carried out genome-wide homozygosity mapping using Illumina Ovine SNP50 BeadChips on lambs descended from one carrier ram, including 19 sheep diagnosed as affected and 11 of their parents that were therefore known carriers. A homozygous region of 136 consecutive...

Genome-wide association analysis reveals QTL and candidate mutations involved in white spotting in cattle

Swati Jivanji, Gemma Worth, Thomas J. Lopdell, Anna Yeates, Christine Couldrey, Edwardo Reynolds, Kathryn Tiplady, Lorna McNaughton, Thomas J.J. Johnson, Stephen R Davis, Bevin Harris, Richard Spelman, Russell G Snell, Dorian Garrick & Mathew D. Littlejohn
Background White spotting of the coat is a characteristic trait of various domestic species including cattle and other mammals. It is a hallmark of Holstein-Friesian cattle, and several previous studies have detected genetic loci with major effects for white spotting in animals with Holstein-Friesian ancestry. Here, our aim was to better understand the underlying genetic and molecular mechanisms of white spotting, by conducting the largest mapping study for this trait in cattle, to date. Results...

Data from: Non-additive association analysis using proxy phenotypes identifies novel cattle sydromes

Edwardo Reynolds & Mathew Littlejohn
Mammalian species carry ~100 loss-of-function variants per individual, where ~1-5 of these impact essential genes and cause embryonic lethality or severe disease when homozygous. The functions of the remainder are more difficult to resolve, though are assumed to impact fitness in less manifest ways. Here, we present data behind one of the largest sequence-resolution screens of cattle to date, targeting discovery and validation of non-additive effects in 130,725 animals. We highlight six novel recessive loci...

Climate and ice in the last glacial maximum explain patterns of isolation by distance inferred for alpine grasshoppers

David Carmelet-Rescan, Mary Morgan-Richards, Emily Koot & Steven Trewick
Aim: Cold-adapted species are likely to have had widespread ranges with greater connectivity of populations during the last glacial cycle. We sought evidence of this in the level and distribution of variation within one alpine insect species. Location: Southern Alps, New Zealand Taxon: The endemic, wingless, alpine grasshopper Sigaus australis (Orthoptera: Acrididae) Methods: The current fragmented alpine distribution of Sigaus australis was used to estimate its environmental envelope (niche) and this model was then used...

Analytic dataset informing modeling of winter species distributions of North American bat species

Sarah Olson, Meredith McClure, Catherine Haase, Carter Hranac, David Hayman, Brett Dickson, Liam McGuire, Daniel Crowley, Nathan Fuller, Cori Lausen & Raina Plowright
The fungal pathogen Pseudogymnoascus destructans and resultant white-nose syndrome (WNS) continues to advance across North America, infecting new bat populations, species, and hibernacula. Western North America hosts the highest bat diversity in the U.S. and Canada, yet little is known about hibernacula and hibernation behavior in this region. An improved understanding of where bats hibernate and the conditions that create suitable hibernacula is critical if land managers are to anticipate and address the conservation needs...

Data from: Are replication rates the same across academic fields? community forecasts from the DARPA SCORE program

Michael Gordon, Thomas Pfeiffer, Domenico Viganola, Michael Bishop, Yiling Chen, Anna Dreber, Brandon Goldfedder, Felix Holzmeister, Magnus Johannesson, Yang Liu, Charles Twardy & Juntao Wang
The DARPA program “Systematizing Confidence in Open Research and Evidence” (SCORE) aims to generate confidence scores for a large number of research claims from empirical studies in the social and behavioral sciences. The confidence scores will provide a quantitative assessment of how likely a claim will hold up in an independent replication. To create the scores we follow earlier approaches and use prediction markets and surveys to forecast replication outcomes. Based on an initial set...

Ancient crested penguin constrains timing of recruitment into seabird hotspot

Daniel Thomas, Alan Tennyson, R. Paul Scofield, Tracy Heath, Walker Pett & Daniel Ksepka
New Zealand is a globally significant hotspot for seabird diversity, but the sparse fossil record for most seabird lineages has impeded our understanding of how and when this hotspot developed. Here, we describe multiple exceptionally well-preserved specimens of a new species of penguin from tightly dated (3.36–3.06 Ma) Pliocene deposits in New Zealand. Bayesian and parsimony analyses place Eudyptes atatu sp. nov. as the sister species to all extant and recently extinct members of the...

Data from: Gaps, an elusive source of phylogenetic information

Kumar Saurabh, Barbara R. Holland, Gillian C. Gibb & David Penny
Morrison (2009) raises a very fundamental question, “Why would phylogeneticists ignore computerized sequence alignment?” While well aware of the difficulties, he considers the whole issue is a ‘gaping hole that needs to be filled’. Particularly with the expansion of genomic-scale data there are many advantages to using automated alignment for phylogenetic analyses, the most obvious being that it is much more efficient and potentially less prone to experimenter bias. So yes, it is obviously desirable...

Data from: Genetic structure and shell shape variation within a rocky shore whelk suggests both diverging and constraining selection with gene flow

Michael R. Gemmell, Steven A. Trewick, James S. Crampton, Felix Vaux, Simon F.K. Hills, Elizabeth E. Daly, Bruce A. Marshall, Alan G. Beu, Mary Morgan-Richards & Simon F K Hills
Variation in snail shell shape has provided evolutionary biologists with excellent material for the study of local adaptation to local environments. However, assuming shell shape variation is evidence of distinct lineages (species) may have led to taxonomic inflation within some gastropod lineages. Here we compare shell shape variation and genetic structure of two independent lineages of New Zealand rocky shore whelks in order to understand the process that lead to an unusual disjunct distribution. We...

Temporal and sociocultural effects of human colonisation on native biodiversity: Filtering and rates of adaptation

Christophe Amiot, Christophe Amiot, Weihong Ji, Erle Ellis & Michael Anderson
Modern human societies have negatively impacted native species richness and their adaptive capacity on every continent, in clearly contrasting ways. We propose a general model to explain how the sequence, duration, and type of colonising society alter native species richness patterns through changes in evolutionary pressures. These changes cause different ‘filtering effects’ on native species, while simultaneously altering the capacity of surviving species to adapt to further anthropogenic pressures. This framework may better explain the...

Gaps in genetic knowledge affect conservation management of kiwi (Apteryx) species

Malin Undin, Isabel Castro, Simon Hills & Peter Lockhart
Worldwide, there is growing appreciation of the importance of integrating genetic information into conservation management. However, there are commonly occurring problems which impact on doing this successfully. This issue is well illustrated by kiwi Apteryx species. Like many endangered taxa, extant kiwi populations are small, fragmented and isolated, raising concerns of potential inbreeding depression. Accordingly, kiwi conservation includes discussion of genetic management and translocations. To date, kiwi taxa have been the subject of 41 genetic...

Recent extinctions among Little Spotted Kiwi (Apteryx owenii) and the origin of extant populations

Kristina Ramstad, Gillian Gibb, Hugh Robertson, Rogan Colbourne, Erin Doran & Lara Shepherd
Little Spotted Kiwi (LSK; Apteryx owenii) have the lowest genetic diversity of five currently recognised kiwi species apparently due to a bottleneck when at most five individuals were translocated to Kapiti Island in 1912. Ancient DNA analyses show that LSK also had the lowest genetic diversity of kiwi species historically, possibly due to population bottlenecks during Pleistocene glaciation. We compare genetic diversity between LSK from Kapiti Island (extant), D’Urville Island (extinct) and the South Island...

Male courtship reduces the risk of cannibalism in web-building spiders but varies in structure

Anne Wignall & Marie Herberstein
Male courtship serves multiple functions in addition to inducing females to accept them as a mate. In predatory species, male courtship can function to reduce the risk of sexual cannibalism. This is particularly important in web-building spiders in which males risk being mistaken for prey when they enter the female’s predatory trap – the web – in order to commence courtship. Male spiders generate vibrations by shuddering in the female’s web. Shudder vibrations can delay...

High functional diversity in deep-sea fish communities and increasing intra-specific trait variation with increasing latitude

Elisabeth Myers, Marti Anderson, Libby Liggins, Euan Harvey, Clive Roberts & David Eme
Variation in both inter- and intra-specific traits affect community dynamics, yet we know little regarding the relative importance of external environmental filters vs internal biotic interactions that shape the functional space of communities along broad-scale environmental gradients, such as latitude, elevation or depth. We examined changes in several key aspects of functional alpha-diversity for marine fishes along depth and latitude gradients by quantifying intra- and inter-specific richness, dispersion and regularity in functional trait space. We...

Global flyway evolution in red knots Calidris canutus and genetic evidence for a Nearctic refugium

Jesse Conklin, Yvonne Verkuil, Phil Battley, Chris Hassell, Job Ten Horn, James Johnson, Pavel Tomkovich, Allan Baker, Theunis Piersma & Michaël Fontaine
Present-day ecology and population structure are the legacies of past climate and habitat perturbations, and this is particularly true for species that are widely distributed at high latitudes. The red knot, Calidris canutus, is an arctic-breeding, long-distance migratory shorebird with six recognized subspecies defined by differences in morphology, migration behavior, and annual-cycle phenology, in a global distribution thought to have arisen just since the Last Glacial Maximum (LGM). We used nextRAD sequencing of 10,881 single-nucleotide...

Diversity in lac Operon Regulation among Diverse Escherichia coli Isolates Depends on the Broader Genetic Background but Is Not Explained by Genetic Relatedness

Tim Cooper, Kelly Phillips, Scott Widmann, Jennifer Nguyen, Christian Ray, Gabor Balazsi & Huei-Yi Lai
Transcription of bacterial genes is controlled by the coordinated action of cis- and trans-acting regulators. The activity and mode of action of these regulators can reflect different requirements for gene products in different environments. A well-studied example is the regulatory function that integrates the environmental availability of glucose and lactose to control the Escherichia coli lac operon. Most studies of lac operon regulation have focused on a few closely related strains. To determine the range...

Data from: Koe: Web-based software to classify acoustic units and analyse sequence structure in animal vocalisations

Yukio Fukuzawa, Wesley H. Webb, Michelle M. Roper, Stephen Marsland, Dianne H. Brunton, Andrew Gilman & Matthew D. M. Pawley
1. Classifying acoustic units is often a key step in studying repertoires and sequence structure in animal communication. Manual classification by eye and ear remains the primary method, but new tools and techniques are urgently needed to expedite the process for large, diverse datasets. 2. Here we introduce Koe, an application for classifying and analysing animal vocalisations. Koe offers bulk-labelling of units via interactive ordination plots and unit tables, as well as visualisation and playback,...

Wavelet filters for automated recognition of birdsong in long-time field recordings

Nirosha Priyadarshani, Stephen Marsland, Julius Juodakis, Isabel Castro & Virginia Listanti
1. Ecoacoustics has the potential to provide a large amount of information about the abundance of many animal species at a relatively low cost. Acoustic recording units are widely used in field data collection, but the facilities to reliably process the data recorded -- recognising calls that are relatively infrequent, and often significantly degraded by noise and distance to the microphone -- are not well developed yet. 2. We propose a call detection method for...

Male-biased sexual selection, but not sexual dichromatism, predicts speciation in birds

Justin Cally, Devi Stuart-Fox, Luke Holman, James Dale & Iliana Medina
Sexual selection is thought to shape phylogenetic diversity by affecting speciation or extinction rates. However, the net effect of sexual selection on diversification is hard to predict, because many of the hypothesised effects on speciation or extinction have opposing signs and uncertain magnitudes. Theoretical work also suggests that the net effect of sexual selection on diversification should depend strongly on ecological factors, though this prediction has seldom been tested. Here, we test whether variation in...

Data from: Mammalian evolution: timing and implications from using the LogDeterminant transform for proteins of differing amino acid composition

Peter J. Waddell, Michael D. Hendy, David Penny & Masami Hasegawa
We explore the tree of mammalian mtDNA sequences, using particularly the LogDet transform on amino acid sequences, the distance Hadamard transform, and the Closest Tree selection criterion. The amino acid composition of different species show significant differences, even within mammals. After compensating for these differences, nearest-neighbor bootstrap results suggest that the tree is locally stable, though a few groups show slightly greater rearrangements when a large proportion of the constant sites are removed. Many parts...

Data from: An upper bound for accuracy of prediction using GBLUP

Emre Karaman, Hao Cheng, Mehmet Z. Firat, Dorian J. Garrick & Rohan L. Fernando
This study aims at characterizing the asymptotic behavior of genomic prediction R2 as the size of the reference population increases for common or rare QTL alleles through simulations. Haplotypes derived from whole-genome sequence of 85 Caucasian individuals from the 1,000 Genomes Project were used to simulate random mating in a population of 10,000 individuals for at least 100 generations to create the LD structure in humans for a large number of individuals. To reduce computational...

Data from: Influences of past climatic changes on historical population structure and demography of a cosmopolitan marine predator, the common dolphin (genus Delphinus)

Ana Amaral, Luciano Beheregaray, Kerstin Bilgmann, Luís Freitas, Kelly Robertson, Marina Sequeira, Karen Stockin, M. M. Coelho & Luciana Möller
Climatic oscillations during the Pleistocene have greatly influenced the distribution and connectivity of many organisms, leading to extinctions but also generating biodiversity. While the effects of such changes have been extensively studied in the terrestrial environment, studies focusing on the marine realm are still scarce. Here we used sequence data from one mitochondrial and five nuclear loci to assess the potential influence of Pleistocene climatic changes on the phylogeography and demographic history of a cosmopolitan...

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  • Massey University
  • Museum of New Zealand Te Papa Tongarewa
  • University of Queensland
  • McMaster University
  • Montana State University
  • Victoria University of Wellington
  • Livestock Improvement Corporation
  • Northwest University
  • Wildlife Conservation Society Canada
  • Monash University