21 Works

Data from: The evolutionary history of dogs in the Americas

Máire Ní Leathlobhair, Angela R. Perri, Evan K. Irving-Pease, Kelsey E. Witt, Anna Linderholm, James Haile, Ophelie Lebrasseur, Carly Ameen, Jeffrey Blick, Adam R. Boyko, Selina Brace, Yahaira Nunes Cortes, Susan J. Crockford, Alison Devault, Evangelos A. Dimopoulos, Morley Eldridge, Jacob Enk, Shyam Gopalakrishnan, Kevin Gori, Vaughan Grimes, Eric Guiry, Anders J. Hansen, Ardern Hulme-Beaman, John Johnson, Andrew Kitchen … & Laurent A. F. Frantz
Dogs were present in the Americas prior to the arrival of European colonists, but the origin and fate of these pre-contact dogs are largely unknown. We sequenced 71 mitochondrial and seven nuclear genomes from ancient North American and Siberian dogs spanning ~9,000 years. Our analysis indicates that American dogs were not domesticated from North American wolves. Instead, American dogs form a monophyletic lineage that likely originated in Siberia and dispersed into the Americas alongside people....

Data from: Fine-scale genetic structure and helping decisions in a cooperatively breeding bird

Amy E. Leedale, Stuart P. Sharp, Michelle Simeoni, Elva J.H. Robinson, Ben J. Hatchwell & Elva J. H. Robinson
In animal societies, characteristic demographic and dispersal patterns may lead to genetic structuring of populations, generating the potential for kin selection to operate. However, even in genetically structured populations, social interactions may still require kin discrimination for cooperative behaviour to be directed towards relatives. Here, we use molecular genetics and long-term field data to investigate genetic structure in an adult population of long-tailed tits Aegithalos caudatus, a cooperative breeder in which helping occurs within extended...

Data from: Plasmid stability is enhanced by higher-frequency pulses of positive selection

Cagla H. Stevenson, James P. J. Hall, Michael A. Brockhurst, Ellie Harrison & Cagla Stevenson
Plasmids accelerate bacterial adaptation by sharing ecologically important traits between lineages. However, explaining plasmid stability in bacterial populations is challenging due to their associated costs. Previous theoretical and experimental studies suggest that pulsed positive selection may explain plasmid stability by favouring gene mobility and promoting compensatory evolution to ameliorate plasmid cost. Here we test how the frequency of pulsed positive selection affected the dynamics of a mercury resistance plasmid, pQBR103, in experimental populations of Pseudomonas...

Data from: Forgotten Mediterranean calving grounds of gray and North Atlantic right whales: evidence from Roman archaeological records

Ana S.L. Rodrigues, Anne Charpentier, Darío Bernal-Casasola, Armelle Gardeisen, Carlos Nores, José Antonio Pis Millán, Krista McGrath, Camilla F. Speller & Ana S. L. Rodrigues
Right whales (Eubalaena glacialis) were extirpated from the eastern North Atlantic by commercial whaling. Gray whales (Eschrichtius robustus) disappeared from the entire North Atlantic in still-mysterious circumstances. Here we test the hypotheses that both of these species previously occurred in the Mediterranean Sea, an area not currently considered part of their historical range. We used ancient DNA barcoding and collagen fingerprinting methods to taxonomically identify a rare set of 10 presumed whale bones from Roman...

Data from: How many faces do people know?

Rob Jenkins, Andrew J. Dowsett & A. Mike Burton
Over our species history, humans have typically lived in small groups of under a hundred individuals. However, our face recognition abilities appear to equip us to recognize very many individuals, perhaps thousands. Modern society provides access to huge numbers of faces, but no one has established how many faces people actually know. Here we describe a method for estimating this number. By combining separate measures of recall and recognition, we show that people know about...

Data from: Social interactions predict genetic diversification: an experimental manipulation in shorebirds

Charles Cunningham, Jorge E. Parra, Lucy Coals, Marcela Beltrán, Sama Zefania & Tamás Székely
Mating strategy and social behaviour influence gene flow and thus affect levels of genetic differentiation and potentially speciation. Previous genetic analyses of closely related plovers Charadrius spp. found strikingly different population genetic structure in Madagascar: Kittlitz’s plovers are spatially homogenous whereas white-fronted plovers have well segregated and geographically distinct populations. Here we test the hypotheses that Kittlitz’s plovers are spatially interconnected and have extensive social interactions that facilitate gene flow, whereas white-fronted plovers are spatially...

Data from: Contrasting geographic structure in evolutionarily divergent Lake Tanganyika catfishes

Claire R. Peart, Kanchon K. Dasmahapatra & Julia J. Day
Geographic isolation is suggested to be among the most important processes in the generation of cichlid fish diversity in East Africa’s Great lakes, both through isolation by distance and fluctuating connectivity caused by changing lake levels. However, even broad scale phylogeographic patterns are currently unknown in many non-cichlid littoral taxa from these systems. To begin to address this we generated restriction-site associated DNA sequence (RADseq) data to investigate phylogeographic structure throughout Lake Tanganyika in two...

Arbuscular mycorrhizal fungi diversity data from a grassland microcosm experiment [NERC Soil Biodiversity Programme]

D. Johnson, P.J. Vandenkoornhuyse, J.R. Leake, L. Gilbert, , J.P Grime, J.P.W. Young & D.J. Read
These arbuscular mycorrhizal (AM) fungi diversity data were collected in 2000 as part of an investigation in an unfertilized limestone grassland soil supporting different synthesized vascular plant assemblages that had developed for three years. The experimental treatments comprised: bare soil; monocultures of the non mycotrophic sedge Carex flacca; monocultures of the mycotrophic grass Festuca ovina; and a species-rich mixture of four forbs, four grasses and four sedges. The experiment was undertaken in microcosms, set up...

Data from: Human cytomegalovirus epidemiology and relationship to tuberculosis and cardiovascular disease risk factors in a rural Ugandan cohort

Lisa Stockdale, Stephen Nash, Angela Nalwoga, Hannah Painter, Gershim Asiki, Helen Fletcher & Robert Newton
Human cytomegalovirus (HCMV) infection has been associated with increased mortality, specifically cardiovascular disease (CVD), in high-income countries (HICs). There is a paucity of data in low- and middle-income countries (LMICs) where HCMV seropositivity is higher. Serum samples from 2,174 Ugandan individuals were investigated for HCMV antibodies and data linked to demographic information, co-infections and a variety of CVD measurements. HCMV seropositivity was 83% by one year of age, increasing to 95% by five years. Female...

Data from: Social immunity in honeybees—Density dependence, diet, and body mass trade‐offs

Ben Jones, Emily Shipley & Kathryn E. Arnold
Group living is favourable to pathogen spread due to the increased risk of disease transmission between individuals. Similar to individual immune defences, social immunity, i.e. anti-parasite defences mounted for the benefit of individuals other than the actor, are predicted to be altered in social groups. The eusocial honey bee (Apis mellifera) secretes glucose oxidase (GOX), an antiseptic enzyme, throughout its colony, thereby providing immune protection to other individuals in the hive. We conducted a laboratory...

Data from: Rapid evolution of generalised resistance mechanisms can constrain the efficacy of phage-antibiotic treatments

Claire E. Moulton-Brown & Ville-Petri Friman
Antimicrobial resistance has been estimated to be responsible for over 700,000 deaths per year, therefore new antimicrobial therapies are urgently needed. One way to increase the efficiency of antibiotics is to use them in combination with bacteria-specific parasitic viruses, phages, which have been shown to exert additive or synergistic effects in controlling bacteria. However, it is still unclear to what extent these combinatory effects are limited by rapid evolution of resistance, especially when the pathogen...

Data from: A practical introduction to microbial molecular ecology through the use of isolation chips

Anna M. Alessi, Kelly R. Redeker, James P.J. Chong & James P. J. Chong
In the context of anti-microbial resistance as one of the most serious issues faced globally by health providers, we explored a practical introduction to molecular microbial ecology. We designed field work and practical experiments for third year members of a four year undergraduate Masters Programme in which the students employed traditional and novel isolation techniques to identify antimicrobial activities from soil dwelling microorganisms. Students gained experience in isolating DNA from complex microbial communities, amplifying 16S...

Data from: Natural history and survival in stage 1 Val30Met transthyretin familial amyloid polyneuropathy

Teresa Coelho, Mónica Inês, Isabel Conceiçao, Marta Soares, Mamede De Carvalho & João Costa
Objectives: To assess natural history and treatment effect on survival among transthyretin-associated familial amyloid polyneuropathy (TTR-FAP) Val30Met patients. Methods: Multi-institutional, hospital-based study of TTR-FAP Val30Met patients prospectively followed-up until December 2016, grouped into untreated (n = 1,771), liver transplant (LTx) (n = 957) or tafamidis-treated (n = 432) cohorts. Standardized mortality ratios (SMR), Kaplan-Meier and Cox methods were used to estimate excess mortality, survival probabilities and adjusted hazard ratios (HR) for all-cause mortality, respectively. Results:...

Arbuscular mycorrhizal fungi diversity data from Sourhope field experiment site, Scotland, 2001 [NERC Soil Biodiversity Programme]

P. Vandenkoornhuyse, K.P. Ridgway, I.J. Watson, A.H. Fitter & J.P.W. Young
These data comprise arbuscular mycorrhizal (AM) fungi diversity data from Sourhope field experiment site. AM fungi are biotrophic symbionts colonizing the majority of land plants, and are of major importance in plant nutrient supply. Using the terminal restriction fragment length polymorphism (T-RFLP) strategy, the diversity of AM fungi was assessed in 89 roots of three grass species (Agrostis capillaris, Festuca rubra, Poa pratensis) that co-occurred in the same plots of the Sourhope field experiment. The...

Data from: Multiple adaptive and non-adaptive processes determine responsiveness to heterospecific alarm calls in African savannah herbivores

Kristine Meise, Daniel W. Franks & Jakob Bro-Jorgensen
Heterospecific alarm calls may provide crucial survival benefits shaping animal behaviour. Multispecies studies can disentangle the relative importance of the various processes determining these benefits, but previous studies have included too few species for alternative hypotheses to be tested quantitatively in a comprehensive analysis. In a community-wide study of African savannah herbivores, we here, for the first time to our knowledge, partition alarm responses according to distinct aspects of the signaller–receiver relationship and thereby uncover...

Data from: Contrasting patterns of local richness of seedlings, saplings and trees may have implications for regeneration in rainforest remnants

Gail Stride, Chris D. Thomas, Suzan Benedick, Jenny A. Hodgson, Ahmad Jelling, Michael J.M. Senior & Jane K. Hill
Remnants of lowland rainforest remain following deforestation, but the longer-term effects of fragmentation remain poorly understood, partly due to the long generation times of trees. We study rainforest trees in three size classes: seedlings (<1 cm dbh), saplings (1-5 cm dbh) and trees (>5 cm), that broadly reflect pre- and post-fragmentation communities, and we examine the impacts of fragmentation on forest regeneration in Sabah, Malaysian Borneo. We found that seedling richness (measured as the number...

Data from: Facilitation promotes invasions in plant-associated microbial communities

Mei Li, Zhong Wei, Jianing Wang, Alexandre Jousset, Ville-Petri Friman, Yangchun Xu, Qirong Shen & Thomas Pommier
While several studies have established a positive correlation between community diversity and invasion resistance, it is less clear how species interactions within resident communities shape this process. Here, we experimentally tested how antagonistic and facilitative pairwise interactions within resident model microbial communities predict invasion by the plant–pathogenic bacterium Ralstonia solanacearum. We found that facilitative resident community interactions promoted and antagonistic interactions suppressed invasions both in the lab and in the tomato plant rhizosphere. Crucially, pairwise...

Data from: Carbon resource richness shapes bacterial competitive interactions by alleviating growth-antibiosis trade-off

Chunlan Yang, Yue Dong, Ville-Petri Friman, Alexandre Jousset, Zhong Wei, Yangchun Xu & Qirong Shen
Antibiosis and resource competition are major drivers shaping the assembly, diversity and functioning of microbial communities. While it is recognised that competition is sensitive to environmental conditions, it is unclear to what extent this mediated by the availability of different carbon resources. Here we used a model laboratory system to directly test this by exploring how carbon resource richness and identity shape resource competition and antibiosis between plant probiotic Bacillus amyloliquefaciens and phytopathogenic Ralstonia solanacearum...

Data from: NMDA receptor antagonists and pain relief: a meta-analysis of experimental trials

Trevor Thompson, Fiona Whiter, Katy Gallop, Nicola Veronese, Marco Solmi, Paul Newton & Brendon Stubbs
OBJECTIVES: We conducted a meta-analysis of controlled trials that used experimental models of acute pain and hyperalgesia to examine the analgesic effects of N-methyl-D-aspartate receptor (NMDAR) antagonists. METHODS: Six major databases were systematically searched (to 03/2018) for studies using human evoked pain models to compare NMDAR antagonists with no-intervention controls. Pain outcome data were analyzed with random-effects meta-analysis. RESULTS: Searches identified 70 eligible trials (N=1069). Meta-analysis found that low-dose ketamine (<1 mg/kg) produced a decrease...

Data from: Sexually dimorphic gene expression and transcriptome evolution provides mixed evidence for a fast‐Z effect in Heliconius

Ana Pinharanda, Marjolaine Rousselle, Simon H. Martin, Joseph J. Hanly, John W. Davey, Sujai Kumar, Nicolas Galtier & Chris D. Jiggins
Sex chromosomes have different evolutionary properties compared to autosomes due to their hemizygous nature. In particular, recessive mutations are more readily exposed to selection, which can lead to faster rates of molecular evolution. Here, we report patterns of gene expression and molecular evolution for a group of butterflies. First, we improve the completeness of the Heliconius melpomene reference annotation, a neotropical butterfly with a ZW sex determination system. Then, we analyse RNA from male and...

Data from: Multi-proxy evidence highlights a complex evolutionary legacy of maize in South America

Logan Kistler, S. Yoshi Maezumi, Jonas Gregorio De Souza, Natalia A. S. Przelomska, Flaviane Malaquias Costa, Oliver Smith, Hope Loiselle, Jazmín Ramos-Madrigal, Nathan Wales, Eduardo Rivail Ribeiro, Ryan R. Morrison, Claudia Grimaldo, Andre P. Prous, Bernardo Arriaza, M. Thomas P. Gilbert, Fabio De Oliveira Freitas & Robin G. Allaby
Domesticated maize evolved from wild teosinte under human influences in Mexico beginning around 9,000 BP, traversed Central America by ~7,500 BP, and spread into South America by ~6,500 BP. Landrace and archaeological maize genomes from South America suggest that the ancestral population to South American maize was brought out of the domestication center in Mexico and became isolated from the wild teosinte gene pool before traits of domesticated maize were fixed. Deeply structured lineages then...

Registration Year

  • 2018

Resource Types

  • Dataset


  • University of York
  • University of Liverpool
  • University of Sheffield
  • UK Centre for Ecology & Hydrology
  • University of Cambridge
  • Utrecht University
  • University of Oxford
  • Nanjing Agricultural University
  • University of Padua
  • University of Bath