480 Works

Data from: DNA from soil mirrors plant taxonomic and growth form diversity

Nigel G. Yoccoz, Kari-Anne Brathen, Ludovic Gielly, James Haile, Mary E. Edwards, Tomasz Goslar, H. Von Stedingk, Anne K. Brysting, Eric Coissac, Francois Pompanon, J. H. Sønstebø, Christian Miquel, Alice Valentini, Francesco De Bello, Jérôme Chave, Wilfried Thuiller, Patrick Wincker, Corinne Cruaud, Frederick Gavory, Morten Rasmussen, M. Thomas P. Gilbert, Ludovic Orlando, Christian Brochmann, Eske Willerslev & Pierre Taberlet
Ecosystems across the globe are threatened by climate change and human activities. New rapid survey approaches for monitoring biodiversity would greatly advance assessment and understanding of these threats. Taking advantage of next-generation DNA sequencing, we tested an approach we call metabarcoding: high-throughput and simultaneous taxa identification based on a very short (usually less than 100 base pairs) but informative DNA fragment. Short DNA fragments allow the use of degraded DNA from environmental samples. All analyses...

Data from: Locomotory abilities and habitat of the Cretaceous bird Gansus yumenensis inferred from limb length proportions

Robert L. Nudds, Jessie Atterholt, Xia Wang, H. L. You, Gareth J. Dyke & H.-L. You
The relative length proportions of the three bony elements of the pelvic (femur, tibiotarsus and tarsometatarsus) and pectoral (humerus, ulna and manus) limbs of the early Cretaceous bird Gansus yumenensis, a well-represented basal ornithuromorph from China are investigated and compared to those of extant taxa. Ternary plots show that the pectoral limb length proportions of Gansus are most similar to Apodiformes (swifts and hummingbirds), which plot away from all other extant birds. In contrast, the...

Data from: Year-round sexual harassment as a behavioral mediator of vertebrate population dynamics

Victoria Wearmouth, Emily Southall, David Morritt, Richard C. Thompson, Innes C. Cuthill, Julian Partridge, David W. Sims & Julian C. Partridge
Within-species sexual segregation is a widespread phenomenon among vertebrates but its causes remain a topic of much debate. Female avoidance of male coercive mating attempts has the potential to influence the social structure of animal populations, yet it has been largely overlooked as a driver of sexual separation. Indeed, its potential role in long-term structuring of natural populations has not been studied. Here we use a comparative approach to examine the suitability of multiple hypotheses...

RCUK Policy on Open Access: compliance monitoring data.

Kate Walker & Wendy White
This details the open access papers, journal articles and conference papers, with a least one author at the University of Southampton that are compliant with the RCUK Policy on Open Access. The data should be looked at in conjunction with the University of Southampton RCUK Policy on Open Access: compliance monitoring report.

Data from: The role of ontogeny in physiological tolerance: decreasing hydrostatic pressure tolerance with development in the northern stone crab Lithodes maja

Catriona Munro, James P. Morris, Alastair Brown, Chris Hauton & Sven Thatje
Extant deep-sea invertebrate fauna represent both ancient and recent invasions from shallow-water habitats. Hydrostatic pressure may present a significant physiological challenge to organisms seeking to colonize deeper waters or migrate ontogenetically. Pressure may be a key factor contributing to bottlenecks in the radiation of taxa and potentially drive speciation. Here, we assess shifts in the tolerance of hydrostatic pressure through early ontogeny of the northern stone crab Lithodes maja, which occupies a depth range of...

Data from: Early Pennsylvanian (Langsettian) fish assemblages from the Joggins Formation, Canada, and their implications for palaeoecology and palaeogeography

David K. Carpenter, Howard J. Falcon-Lang, Michael J. Benton & Melissa Grey
A review of all available specimens of fossil fishes from the classic Pennsylvanian Joggins locality of Nova Scotia, Canada, reveals the existence of a diverse community of chondrichthyans (xenacanthids, ctenacanthids and the enigmatic Ageleodus), acanthodians (gyracanthids), sarcopterygians (rhizodontids, megalichthyids, rhizodopsids and dipnoans) and actinopterygians (haplolepids). Reassessment of supposed endemic species (Ctenoptychius cristatus, Sagenodus plicatus, Gyracanthus duplicatus) indicates they are invalid, and overall, the assemblage comprises cosmopolitan taxa that were widespread around the coasts of tropical...

Data from: Rapid scavenging of jellyfish carcasses reveals the importance of gelatinous material to deep-sea food webs

Andrew K. Sweetman, Craig R. Smith, Trine Dale & Daniel O. B. Jones
Jellyfish blooms are common in many oceans, and anthropogenic changes appear to have increased their magnitude in some regions. Although mass falls of jellyfish carcasses have been observed recently at the deep seafloor, the dense necrophage aggregations and rapid consumption rates typical for vertebrate carrion have not been documented. This has led to a paradigm of limited energy transfer to higher trophic levels at jelly falls relative to vertebrate organic falls. We show from baited...

Data from: Fish and tetrapod communities across a marine to brackish salinity gradient in the Pennsylvanian (early Moscovian) Minto Formation of New Brunswick, Canada, and their palaeoecological and palaeogeographical implications

Aodhán Ó Gogáin, Howard J. Falcon-Lang, David K. Carpenter, Randall F. Miller, Michael J. Benton, Peir K. Pufahl, Marcello Ruta, Thomas G. Davies, Steven J. Hinds & Matthew R. Stimson
Euryhaline adaptations in Pennsylvanian vertebrates allowed them to inhabit the marine to freshwater spectrum. This is illustrated by new assemblages of fish and tetrapods from the early Moscovian Minto Formation of New Brunswick, Canada. Fish include chondrichthyans (xenacanthids and the enigmatic Ageleodus), acanthodians (gyracanthids and acanthodiforms), sarcopterygians (rhizodontids, megalichthyids and dipnoans), and actinopterygians (eurynotiforms). Tetrapods include small- to medium-sized, and largely aquatic, stem tetrapods (colosteids) and anthracosaurs (embolomeres). A key finding is that the parautochthonous...

Coastal Biodiversity and Ecosystem Service Sustainability (CBESS) sediment particle size in mudflat and saltmarsh habitats

C.L. Wood, S.J. Hawkins, J.A. Godbold & M. Solan
The dataset details particle size of sediments across 6 intertidal sites in the winter and summer of 2013. The data provide a quantitative measure of the sediment particle size fractions present within surface sediments (up to a depth of 2 cm). Three sites were located in Essex, South East England and the other 3 in Morecambe Bay, North West England. Each site consisted of a saltmarsh habitat and adjacent mudflat habitat. 22 sampling quadrats were...

Coastal Biodiversity and Ecosystem Service Sustainability (CBESS) macrofaunal community metrics - total abundance (TA), total biomass (TB), species richness (SR), evenness (J) and community bioturbation potential (BPc) in mudflat and saltmarsh habitats

C.L. Wood, S.J. Hawkins, J.A. Godbold & M. Solan
The dataset details total abundance (TA), total biomass (TB), species richness (SR) and evenness (J) [all based on abundance and biomass] and community bioturbation potential (BPc) across six intertidal sites in the winter and summer of 2013. The data provide metrics relating to the macrofaunal communities present within the top 10cm of sediment. Three sites were located in Essex, South East England and the other three in Morecambe Bay, North West England. Each site consisted...

Data from: Commercial chicken breeds exhibit highly divergent patterns of linkage disequilibrium

Reuben Pengelly, Almas A Gheyas, Richard Kuo, Enrico Mossotto, Eleanor G Seaby, David W Burt, Sarah Ennis & Andrew Collins
The analysis of linkage disequilibrium (LD) underpins the development of effective genotyping technologies, trait mapping and understanding of biological mechanisms such as those driving recombination and the impact of selection. We apply the Malécot-Morton model of LD to create additive LD maps which describe the high-resolution LD landscape of commercial chickens. We investigated LD in chickens (Gallus gallus) at the highest resolution to date for broiler, white egg and brown egg layer commercial lines. There...

Data from: The genomic bases of morphological divergence and reproductive isolation driven by ecological speciation in Senecio (Asteraceae)

Mark A Chapman, Simon J Hiscock & Dmitry A Filatov
Ecological speciation, driven by adaptation to contrasting environments, provides an attractive opportunity to study the formation of distinct species, and the role of selection and genomic divergence in this process. Here, we focus on a particularly clear-cut case of ecological speciation to reveal the genomic bases of reproductive isolation and morphological differences between closely related Senecio species, whose recent divergence within the last ~200,000 years was likely driven by the uplift of Mt. Etna (Sicily)....

Data from: A toolkit for optimizing fish passage barrier mitigation actions

Steven King, Jesse R. O'Hanley, Lynda R. Newbold, Paul S. Kemp & Matthew W. Diebel
The presence of dams, stream–road crossings and other infrastructure often compromises the connectivity of rivers, leading to reduced fish abundance and diversity. The assessment and mitigation of river barriers is critical to the success of restoration efforts aimed at restoring river integrity. In this study, we present a combined modelling approach involving statistical regression methods and mixed integer linear programming to maximize resident fish species richness within a catchment through targeted barrier mitigation. Compared to...

Data from: TAPBPR alters MHC class I peptide presentation by functioning as a peptide exchange catalyst

Clemens Hermann, Andy Van Hateren, Nico Trautwein, Andreas Neerincx, Patrick J. Duriez, Stefan Stevanović, John Trowsdale, Janet E. Deane, Tim Elliott & Louise H. Boyle
Our understanding of the antigen presentation pathway has recently been enhanced with the identification that the tapasin-related protein TAPBPR is a second MHC I-specific chaperone. We sought to determine whether, like tapasin, TAPBPR can also influence MHC I peptide selection by functioning as a peptide exchange catalyst. We show that TAPBPR can catalyse the dissociation of peptides from peptide-MHC I complexes, enhance the loading of peptide-receptive MHC I molecules, and discriminate between peptides based on...

Groundwater microbiology and chemistry of shallow wells, boreholes and springs in Kisumu, Kenya in 2014

S. Pedley, J. Okotto-Okotto, L. Okotto, H. Price & J. Wright
This dataset contains free residual chlorine, turbidity, nitrate, chloride, sulphate, fluoride, phosphate and thermatolerant coliform concentrations in groundwater from a variety of sources within two neighbourhoods of Kisumu, Kenya. A total of 73 groundwater sources were tested between February and March 2014. The data were collected as part of the Groundwater2030 project, which aims to reduce the health problems that result from consumption of contaminated groundwater in urban areas of Africa. The project was co-ordinated...

Data from: Response of seaward migrating European eel (Anguilla anguilla) to manipulated flow fields

Adam T. Piper, Costantino Manes, Fabio Siniscalchi, Andrea Marion, Rosalind M. Wright & Paul S. Kemp
Anthropogenic structures (e.g. weirs and dams) fragment river networks and restrict the movement of migratory fish. Poor understanding of behavioural response to hydrodynamic cues at structures currently limits the development of effective barrier mitigation measures. This study aimed to assess the effect of flow constriction and associated flow patterns on eel behaviour during downstream migration. In a field experiment, we tracked the movements of 40 tagged adult European eels (Anguilla anguilla) through the forebay of...

Socio-economic survey of domestic groundwater handling and use for source customers in Kisumu, Kenya in 2014

L.G. Okotto, J. Okotto-Okotto, H. Price, S. Pedley & J. Wright
This dataset contains the anonymised results of a survey of customers who buy groundwater for consumption in Kisumu, Kenya. Data includes information on the amount of water bought and ways in which this water was used and handled, as well as their use of water from other sources. Data about assets and services, including access to food, are also included. The surveys were carried out during February and March 2014 and include data from 137...

Data from: Sexual isolation promotes divergence between parapatric lake and stream stickleback

Daniel Berner, Matthias Ammann, Eleanor Spencer, Attila Rueegg, Daniel Luescher & Dario Moser
Speciation can be initiated by adaptive divergence between populations in ecologically different habitats, but how sexually based reproductive barriers contribute to this process is less well understood. We here test for sexual isolation between ecotypes of threespine stickleback fish residing in adjacent lake and stream habitats in the Lake Constance basin, Central Europe. Mating trials in outdoor mesocosms allowing for natural reproductive behavior reveal that mating occurs preferentially between partners of the same than of...

peanutButter: An R package to produce rapid-response gridded population estimates from building footprints, version 0.1.0

Douglas Leasure, Claire Dooley, Maksym Bondarenko, Andrew Tatem & WorldPop
peanutButter is an R package that allows you to produce gridded population estimates from building footprints using the "peanut butter" method of spreading people evenly among buildings based on a set of simple parameters. This package allows you to: 1) produce gridded population estimates using a bottom-up approach that applies your estimates of average people per building for urban and rural areas to each building in the corresponding settlement type, 2) produce gridded population estimates...

Secondary contacts and genetic admixture shape colonisation by an amphiatlantic epibenthic invertebrate

Jamie Hudson, Kerstin Johannesson, Christopher McQuaid & Marc Rius
Research on the genetics of invasive species often focuses on patterns of genetic diversity and population structure within the introduced range. However, a growing body of literature is demonstrating the need to study the native range, and how native genotypes affect both ecological and evolutionary mechanisms within the introduced range. Here we used genotyping-by-sequencing to study both native and introduced ranges [based on 1,653 single nucleotide polymorphisms (SNPs)] of the amphiatlantic marine invertebrate Ciona intestinalis....

Global 100m Mastergrids

WorldPop
National and subnational boundaries used in the framework of the Global Project - Funded by The Bill and Melinda Gates Foundation (OPP1134076)

Data from: Metabolic costs imposed by hydrostatic pressure constrain bathymetric range in the lithodid crab Lithodes maja

Alastair Brown, Sven Thatje, James P. Morris, Andrew Oliphant, Elizabeth A. Morgan, Chris Hauton, Daniel O. B. Jones & David W. Pond
Changing climate is shifting the distributions of marine species, yet the potential for shifts in depth distributions is virtually unexplored. Hydrostatic pressure is proposed to contribute to a physiological bottleneck constraining depth range extension in shallow-water taxa. However, bathymetric limitation by hydrostatic pressure remains undemonstrated, and the mechanism limiting hyperbaric tolerance remains hypothetical. Here, we assess the effects of hydrostatic pressure in the lithodid crab Lithodes maja (bathymetric range 4-790 m depth, approximately equivalent to...

Data from: The challenges of detecting subtle population structure and its importance for the conservation of emperor penguins

Jane L. Younger, Gemma V. Clucas, Damian Kao, Alex D. Rogers, Karim Gharbi, Tom Hart & Karen J. Miller
Understanding the boundaries of breeding populations is of great importance for conservation efforts and estimates of extinction risk for threatened species. However, determining these boundaries can be difficult when population structure is subtle. Emperor penguins are highly reliant on sea ice, and some populations may be in jeopardy as climate change alters sea-ice extent and quality. An understanding of emperor penguin population structure is therefore urgently needed. Two previous studies have differed in their conclusions,...

Data from: TAPBPR bridges UDP-glucose:glycoprotein glucosyltransferase 1 onto MHC class I to provide quality control in the antigen presentation pathway

Andreas Neerincx, Clemens Hermann, Robin Antrobus, Andy Van Hateren, Cao Huan, Nico Trautwein, Stefan Stevanović, Tim Elliott, Janet E. Deane, Louise H. Boyle & Huan Cao
Recently we revealed that TAPBPR is a peptide exchange catalyst important for optimal peptide selection by MHC class I molecules. Here we asked if any other co-factors associate with TAPBPR which would explain its effect on peptide selection. We identify an interaction between TAPBPR and UDP-glucose:glycoprotein glucosyltransferase 1 (UGT1), a folding sensor in the calnexin/calreticulin quality control cycle known to regenerate the Glc1Man9GlcNAc2 moiety on glycoproteins. Our results suggest the formation of a multimeric complex,...

Data from: An integrated framework to identify wildlife populations under threat from climate change

Orly Razgour, John B. Taggart, Stéphanie Manel, Javier Juste, Carlos Ibáñez, Hugo Rebelo, Antton Alberdi, Gareth Jones & Kirsty Park
Climate change is a major threat to global biodiversity that will produce a range of new selection pressures. Understanding species responses to climate change requires an interdisciplinary perspective, combining ecological, molecular and environmental approaches. We propose an applied integrated framework to identify populations under threat from climate change based on their extent of exposure, inherent sensitivity due to adaptive and neutral genetic variation and range shift potential. We consider intraspecific vulnerability and population-level responses, an...

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