324 Works

Data from: Imprints from genetic drift and mutation imply relative divergence times across marine transition zones in a pan-European small pelagic fish (Sprattus sprattus)

Morten T. Limborg, Reinhold Hanel, Paul V. Debes, Anna-Karin Ring, Costas S. Tsigenopoulos, Dorte Bekkevold & Carl Andre
Geographic distributions of most temperate marine fishes are affected by post-glacial recolonisation events which have left complex genetic imprints on populations of marine species. This study investigated population structure and demographic history of European sprat (Sprattus sprattus L.) by combining inference from both mtDNA and microsatellite genetic markers throughout the species distribution. We compared effects from genetic drift and mutation for both genetic markers in shaping genetic differentiation across four transition zones. Microsatellite markers revealed...

Data from: Genetic and phenotypic differentiation among Galaxias maculatus populations in a Patagonian postglacial lake system

Cecilia Carrea, Juan P. Barriga, Victor E. Cussac & Daniel E. Ruzzante
Understanding the influence of landscape features on population differentiation is fundamental to evolutionary biology studies. We examined spatial patterns of genetic and phenotypic variability among Galaxias maculatus populations in a complex of four postglacial lakes in northwestern Patagonia differing in size and connectivity among them. A hierarchical Bayesian analysis grouped the individuals collected from 11 localities into 3 genetic clusters, first defining the populations of the two large lakes and separating the two small lakes...

Data from: Ten days of darkness causes temporary blindness during an early critical period in higher mammals

Donald E. Mitchell, Nathan A. Crowder, Kaitlyn Holman, Matthew Smithen & Kevin R. Duffy
Extended periods of darkness have long been used to study how the mammalian visual system develops in the absence of any instruction from vision. Because of the relative ease of implementation of darkness as a means to eliminate visually driven neural activity, it has usually been imposed earlier in life and for much longer periods than was the case for other manipulations of the early visual input used for study of their influences on visual...

Data from: Migratory constraints on yolk precursors limit yolk androgen deposition and underlie a brood reduction strategy in rockhopper penguins

Glenn T. Crossin, Maud Poisbleau, Laurent Demongin, Olivier Chastel, Tony D. Williams, Marcel Eens & Petra Quillfeldt
Hormonally mediated maternal effects link maternal phenotype and environmental conditions to offspring phenotype. The production of lipid-rich maternal yolk precursors may provide a mechanism by which lipophilic steroid hormones can be transported to developing yolks, thus predicting a positive correlation between yolk precursors in mothers and androgen levels in eggs. Using rockhopper penguins (Eudyptes chrysocome), which produce a two-egg clutch characterized by extreme egg-size dimorphism, reversed hatching asynchrony and brood-reduction, we examined correlations between circulating...

Data from: A unified anatomy ontology of the vertebrate skeletal system

Wasila M. Dahdul, James P. Balhoff, David C. Blackburn, Alexander D. Diehl, Melissa A. Haendel, Brian K. Hall, Hilmar Lapp, John G. Lundberg, Christopher J. Mungall, Martin Ringwald, Erik Segerdell, Ceri E. Van Slyke, Matthew K. Vickaryous, Monte Westerfield & Paula M. Mabee
The skeleton is of fundamental importance in research in comparative vertebrate morphology, paleontology, biomechanics, developmental biology, and systematics. Motivated by research questions that require computational access to and comparative reasoning across the diverse skeletal phenotypes of vertebrates, we developed a module of anatomical concepts for the skeletal system, the Vertebrate Skeletal Anatomy Ontology (VSAO), to accommodate and unify the existing skeletal terminologies for the species-specific (mouse, the frog Xenopus, zebrafish) and multispecies (teleost, amphibian) vertebrate...

Data from: A large-scale field study examining effects of exposure to clothianidin seed-treated canola on honey bee colony health, development, and overwintering success

G. Christopher Cutler, Cynthia D. Scott-Dupree, Maryam Sultan, Andrew D. McFarlane & Larry Brewer
In summer 2012, we initiated a large-scale field experiment in southern Ontario, Canada, to determine whether exposure to clothianidin seed-treated canola (oil seed rape) has any adverse impacts on honey bees. Colonies were placed in clothianidin seed-treated or control canola fields during bloom, and thereafter were moved to an apiary with no surrounding crops grown from seeds treated with neonicotinoids. Colony weight gain, honey production, pest incidence, bee mortality, number of adults, and amount of...

Data from: Supertrees based on the subtree prune-and-regraft distance

Chris Whidden, Norbert Zeh, Robert G. Beiko & Christopher Whidden
Supertree methods reconcile a set of phylogenetic trees into a single structure that is often interpreted as a branching history of species. A key challenge is combining conflicting evolutionary histories that are due to artifacts of phylogenetic reconstruction and phenomena such as lateral gene transfer (LGT). Although they often work well in practice, existing supertree approaches use optimality criteria that do not reflect underlying processes, have known biases and may be unduly influenced by LGT....

Data from: Genomics assisted ancestry deconvolution in grape

Jason K. Sawler, Bruce Reisch, Mallikarjuna K. Aradhya, Bernard Prins, Gan-Yuan Zhong, Heidi Schwaninger, Charles Simon, Edward Buckler, Sean Myles & Jason Sawler
The genus Vitis (the grapevine) is a group of highly diverse, diploid woody perennial vines consisting of approximately 60 species from across the northern hemisphere. It is the world’s most valuable horticultural crop with ~8 million hectares planted, most of which is processed into wine. To gain insights into the use of wild Vitis species during the past century of interspecific grape breeding and to provide a foundation for marker-assisted breeding programmes, we present a...

Data from: Subfunctionalization of peroxisome proliferator response elements accounts for retention of duplicated fabp1 genes in zebrafish

Robert B Laprairie, Eileen M Denovan-Wright & Jonathan M Wright
Background: In the duplication-degeneration-complementation (DDC) model, a duplicated gene has three possible fates: it may lose functionality through the accumulation of mutations (non-functionalization), acquire a new function (neo-functionalization), or each duplicate gene may retain a subset of functions of the ancestral gene (sub-functionalization). The role that promoter evolution plays in retention of duplicated genes in eukaryotic genomes is not well understood. Fatty acid-binding proteins (Fabp) belong to a multigene family that are highly conserved in...

Data from: Adaptive phenotypic response to climate enabled by epigenetics in a K-strategy species, the fish Leucoraja ocellata (Rajidae)

Jackie Lighten, Danny Incarnato, Ben J. Ward, Cock Van Oosterhout, Ian Bradbury, Mark Hanson & Paul Bentzen
The relative importance of genetic versus epigenetic changes in adaptive evolution is a hotly debated topic, with studies showing that some species appear to be able to adapt rapidly without significant genetic change. Epigenetic mechanisms may be particularly important for the evolutionary potential of species with long maturation times and low reproductive potential (‘K-strategists’), particularly when faced with rapidly changing environmental conditions. Here we study the transcriptome of two populations of the winter skate (Leucoraja...

Data from: Spatial patterns and predictors of trophic control in marine ecosystems

Daniel G. Boyce, Kenneth T. Frank, Boris Worm & William C. Leggett
A key question in ecology is under which conditions ecosystem structure tends to be controlled by resource availability vs. consumer pressure. Several hypotheses derived from theory, experiments and observational field studies have been advanced, yet a unified explanation remains elusive. Here, we identify common predictors of trophic control in a synthetic analysis of 52 observational field studies conducted within marine ecosystems across the Northern Hemisphere and published between 1951 and 2014. Spatial regression analysis of...

Data from: Organelles that illuminate the origins of Trichomonas hydrogenosomes and Giardia mitosomes

Michelle M. Leger, Martin Kolisko, Ryoma Kamikawa, Courtney W. Stairs, Keitaro Kume, Ivan Čepička, Jeffrey D. Silberman, Jan O. Andersson, Feifei Xu, Akinori Yabuki, Laura Eme, Qianqian Zhang, Kiyotaka Takishita, Yuji Inagaki, Alastair G. B. Simpson, Tetsuo Hashimoto & Andrew J. Roger
Many anaerobic microbial parasites possess highly modified mitochondria known as mitochondrion-related organelles (MROs). The best-studied of these are the hydrogenosomes of Trichomonas vaginalis and Spironucleus salmonicida, which produce ATP anaerobically through substrate-level phosphorylation with concomitant hydrogen production; and the mitosomes of Giardia intestinalis, which are functionally reduced and lack any role in ATP production. However, to understand the metabolic specializations that these MROs underwent in adaptation to parasitism, data from their free-living relatives are needed....

Data from: Recurrent myocardial infarction: mechanisms of free-floating adaptation and autonomic derangement in networked cardiac neural control

Guy Kember, Jeffrey Ardell, Kalyanam Shivkumar & J. Andrew Armour
The cardiac nervous system continuously controls cardiac function whether or not pathology is present. While myocardial infarction typically has a major and catastrophic impact, population studies have shown that longer-term risk for recurrent myocardial infarction and the related potential for sudden cardiac death depends mainly upon standard atherosclerotic variables and autonomic nervous system maladaptations. Investigative neurocardiology has demonstrated that autonomic control of cardiac function includes local circuit neurons for networked control within the peripheral nervous...

Data from: Genotyping-by-sequencing of genome-wide microsatellite loci reveals fine-scale harvest composition in a coastal Atlantic salmon fishery

Ian R. Bradbury, Brendan F. Wringe, Beth Watson, Ian Paterson, John Horne, Robert Beiko, Sarah J. Lehnert, Marie Clément, Eric C. Anderson, Nicholas W. Jeffery, Steven Duffy, Emma Sylvester, Martha Robertson & Paul Bentzen
Individual assignment and genetic mixture analysis are commonly utilized in contemporary wildlife and fisheries management. Although microsatellite loci provide unparalleled numbers of alleles per locus, their use in assignment applications is increasingly limited. However, next-generation sequencing, in conjunction with novel bioinformatic tools allows large numbers of microsatellite loci to be simultaneously genotyped, presenting new opportunities for individual assignment and genetic mixture analysis. Here we scanned the published Atlantic salmon genome to identify 706 microsatellite loci,...

Data from: Kinship influences sperm whale social organization within, but generally not among, social units

Christine M. Konrad, Shane Gero, Timothy Frasier & Hal Whitehead
Sperm whales have a multi-level social structure based upon long-term, cooperative social units. What role kinship plays in structuring this society is poorly understood. We combined extensive association data (518 days, during 2005-2016) and genetic data (18 microsatellites and 346bp mtDNA control region sequences) for 65 individuals from 12 social units from the Eastern Caribbean to examine patterns of kinship and social behaviour. Social units were clearly matrilineally-based, evidenced by greater relatedness within social units...

Data from: Spatio-temporal dynamics of density-dependent dispersal during a population colonisation

Sebastiano De Bona, Matthieu Bruneaux, Alex E.G. Lee, David N. Reznick, Paul Bentzen & Andrés López-Sepulcre
Predicting population colonisations requires understanding how spatio-temporal changes in density affect dispersal. Density can inform on fitness prospects, acting as a cue for either habitat quality, or competition over resources. However, when escaping competition, high local density should only increase emigration if lower-density patches are available elsewhere. Few empirical studies on dispersal have considered the effects of density at the local and landscape scale simultaneously. To explore this, we analyze 5 years of individual-based data...

Data from: Kin selection and allocare in sperm whales

Christine M. Konrad, Timothy R. Frasier, Hal Whitehead & Shane Gero
Cooperative care and defense of young are hypothesized to be foundational to the societies of several species, including the sperm whale (Physeter macrocephalus). However, the extent of allocare among sperm whales and the mechanisms driving it have not been well-characterized. Sperm whale social units are matrilineally-based, making kin selection a likely key driver of allocare, but the relationship between kinship and calf care is essentially unknown. We investigate calf care in the context of kinship,...

Data from: The relative importance of modeling site pattern heterogeneity versus partition-wise heterotachy in phylogenomic inference

Huaichun Wang, Edward Susko & Andrew J. Roger
Large taxa-rich genome-scale data sets are often necessary for resolving ancient phylogenetic relationships. But accurate phylogenetic inference requires that they are analyzed with realistic models that account for the heterogeneity in substitution patterns amongst the sites, genes and lineages. Two kinds of adjustments are frequently used: models that account for heterogeneity in amino acid frequencies at sites in proteins, and partitioned models that accommodate the heterogeneity in rates (branch lengths) among different proteins in different...

Data from: A single Tim translocase in the mitosomes of Giardia intestinalis illustrates convergence of protein import machines in anaerobic eukaryotes

Eva Pyrihova, Alžběta Motyčková, Luboš Voleman, Natalia Wandyszewska, Radovan Fišer, Gabriela Seydlová, Andrew J. Roger, Martin Kolisko, Pavel Dolezal & Andrew Roger
Mitochondria have evolved diverse forms across eukaryotic diversity in adaptation to anaerobiosis. Mitosomes are the simplest and the least well-studied type of anaerobic mitochondria. Transport of proteins via TIM complexes, composed of three proteins of the Tim17 protein family (Tim17/22/23), is one of the key unifying aspects of mitochondrial and mitochondria-derived organelles. However, multiple experimental and bioinformatic attempts have so far failed to identify the nature of TIM in mitosomes of the anaerobic metamonad protist,...

Data from: Fine-scale population differences in Atlantic cod reproductive success: a potential mechanism for ecological speciation in a marine fish

Nancy E. Roney, Rebekah A. Oomen, Halvor Knutsen, Esben M. Olsen & Jeffrey A. Hutchings
Successful resource-management and conservation outcomes ideally depend on matching the spatial scales of population demography, local adaptation, and threat mitigation. For marine fish with high dispersal capabilities, this remains a fundamental challenge. Based on daily parentage assignments of more than 4000 offspring, we document fine-scaled temporal differences in individual reproductive success for two spatially adjacent (<10km) populations of a broadcast-spawning marine fish. Distinguished by differences in genetics and life history, Atlantic cod (Gadus morhua) from...

Data from: Range-wide genomic data synthesis reveals transatlantic vicariance and secondary contact in Atlantic cod

Robert Fairweather, Ian R. Bradbury, Sarah J. Heylar, Mark De Bruyn, Nina O. Therkildsen, Paul Bentzen, Jakob Hemmer-Hansen & Gary R. Carvalho
Recent advances in genetic and genomic analysis have greatly improved our understanding of spatial population structure in marine species. However, studies addressing phylogeographic patterns at oceanic spatial scales remain rare. In Atlantic cod (Gadus morhua), existing range‐wide examinations suggest significant transatlantic divergence, although the fine‐scale contemporary distribution of populations and potential for secondary contact are largely unresolved. Here, we explore transatlantic phylogeography in Atlantic cod using a data‐synthesis approach, integrating multiple genome‐wide single‐nucleotide polymorphism (SNP)...

Data from: Raising the bar: recovery ambition for species at risk in canada and the US

Kylee A. Pawluk, Caroline H. Fox, Christina N. Service, Eva H. Stredulinsky & Heather Bryan
Routinely crossing international borders and/or persisting in populations across multiple countries, species are commonly subject to a patchwork of endangered species legislation. Canada and the United States share numerous endangered species; their respective acts, the Species at Risk Act (SARA) and the Endangered Species Act (ESA), require documents that outline requirements for species recovery. Although there are many priorities for improving endangered species legislation effectiveness, species recovery goals are a crucial component. We compared recovery...

Multiple decades of stocking has resulted in limited hatchery introgression in wild brook trout (Salvelinus fontinalis) populations of Nova Scotia

Sarah Lehnert, Shauna Baillie, John MacMillan, Ian Paterson, Colin Buhariwalla, Ian Bradbury & Paul Bentzen
Many populations of freshwater fishes are threatened with losses, and increasingly, the release of hatchery individuals is one strategy being implemented to support wild populations. However, stocking of hatchery individuals may pose long-term threats to wild populations, particularly if genetic interactions occur between wild and hatchery individuals. One highly prized sport fish that has been heavily stocked throughout its range is the brook trout (Salvelinus fontinalis). In Nova Scotia, Canada, hatchery brook trout have been...

Data from: Hemimastigophora is a novel supra-kingdom-level lineage of Eukaryotes

Gordon Lax, Yana Eglit, Laura Eme, Erin M. Bertrand, Andrew J. Roger & Alastair G.B. Simpson
Almost all eukaryote life forms have now been placed within one of five to eight supra-kingdom-level groups using molecular phylogenetics1,2,3,4. The ‘phylum’ Hemimastigophora is probably the most distinctive morphologically defined lineage that still awaits such a phylogenetic assignment. First observed in the nineteenth century, hemimastigotes are free-living predatory protists with two rows of flagella and a unique cell architecture5,6,7; to our knowledge, no molecular sequence data or cultures are currently available for this group. Here...

Past and future decline of tropical pelagic biodiversity

Moriaki Yasuhara, Chih-Lin Wei, Michal Kucera, Mark Costello, Derek Tittensor, Wolfgang Kiessling, Timothy Bonebrake, Clay Tabor, Ran Feng, Andrés Baselga, Kerstin Kretschmer, Buntarou Kusumoto & Yasuhiro Kubota
A major research question concerning global pelagic biodiversity remains unanswered: when did the apparent tropical biodiversity depression (i.e., bimodality of latitudinal diversity gradient [LDG]) begin? The bimodal LDG may be a consequence of recent ocean warming or of deep-time evolutionary speciation and extinction processes. Using rich time-slice datasets of planktonic foraminifers, we show here that a unimodal (or only weakly bimodal) diversity gradient, with a plateau in the tropics, occurred during the last ice age...

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