Prediction Markets for Paper Evaluations

Title:

Analysis of virus genomes from glacial environments reveals novel virus groups with unusual host interactions

Authors:

Bellas, CM, Anesio, AMB & Barker, GLA

Year:

2015

Journal:

Frontiers in Microbiology

Weblink:

https://dx.doi.org/10.3389/fmicb.2015.00656

Abstract:

Microbial communities in glacial ecosystems are diverse, active, and subjected to strong viral pressures and infection rates. In this study we analyse putative virus genomes assembled from three dsDNA viromes from cryoconite hole ecosystems of Svalbard and the Greenland Ice Sheet to assess the potential hosts and functional role viruses play in these habitats. We assembled 208 million reads from the virus-size fraction and developed a procedure to select genuine virus scaffolds from cellular contamination. Our curated virus library contained 546 scaffolds up to 230 Kb in length, 54 of which were circular virus consensus genomes. Analysis of virus marker genes revealed a wide range of viruses had been assembled, including bacteriophages, cyanophages, nucleocytoplasmic large DNA viruses and a virophage, with putative hosts identified as Cyanobacteria, Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, Firmicutes, eukaryotic algae and amoebae. Whole genome comparisons revealed the majority of circular genome scaffolds (CGS) formed 12 novel groups, two of which contained multiple phage members with plasmid-like properties, including a group of phage-plasmids possessing plasmid-like partition genes and toxin-antitoxin addiction modules to ensure their replication and a satellite phage-plasmid group. Surprisingly we also assembled a phage that not only encoded plasmid partition genes, but a clustered regularly interspaced short palindromic repeat (CRISPR)/Cas adaptive bacterial immune system. One of the spacers was an exact match for another phage in our virome, indicating that in a novel use of the system, the lysogen was potentially capable of conferring immunity on its bacterial host against other phage. Together these results suggest that highly novel and diverse groups of viruses are present in glacial environments, some of which utilize very unusual life strategies and genes to control their replication and maintain a long-term relationship with their hosts.

Citations:

27

Citations per year:

6.7

Title:

Evolution on the move: specialization on widespread resources associated with rapid range expansion in response to climate change

Authors:

Bridle, JR, Buckley, J, Bodsworth, EJ & Thomas, CD

Year:

2014

Journal:

Proceedings of The Royal Society B

Weblink:

https://dx.doi.org/10.1098/rspb.2013.1800

Abstract:

Generalist species and phenotypes are expected to perform best under rapid environmental change. In contrast to this view that generalists will inherit the Earth, we find that increased use of a single host plant is associated with the recent climate-driven range expansion of the UK brown argus butterfly. Field assays of female host plant preference across the UK reveal a diversity of adaptations to host plants in long-established parts of the range, whereas butterflies in recently colonized areas are more specialized, consistently preferring to lay eggs on one host plant species that is geographically widespread throughout the region of expansion, despite being locally rare. By common-garden rearing of females’ offspring, we also show an increase in dispersal propensity associated with the colonization of new sites. Range expansion is therefore associated with an increase in the spatial scale of adaptation as dispersive specialists selectively spread into new regions. Major restructuring of patterns of local adaptation is likely to occur across many taxa with climate change, as lineages suited to regional colonization rather than local success emerge and expand.

Citations:

18

Citations per year:

3.3

Title:

A native promoter and inclusion of an intron is necessary for efficient expression of GFP or mRFP in Armillaria mellea

Authors:

Ford, KL, Baumgartner, K, Henricot, B, Bailey, AM & Foster, GD

Year:

2016

Journal:

Scientific Reports

Weblink:

https://dx.doi.org/10.1038/srep29226

Abstract:

Armillaria mellea is a significant pathogen that causes Armillaria root disease on numerous hosts in forests, gardens and agricultural environments worldwide. Using a yeast-adapted pCAMBIA0380 Agrobacterium vector, we have constructed a series of vectors for transformation of A. mellea, assembled using yeast-based recombination methods. These have been designed to allow easy exchange of promoters and inclusion of introns. The vectors were first tested by transformation into basidiomycete Clitopilus passeckerianus to ascertain vector functionality then used to transform A. mellea. We show that heterologous promoters from the basidiomycetes Agaricus bisporus and Phanerochaete chrysosporium that were used successfully to control the hygromycin resistance cassette were not able to support expression of mRFP or GFP in A. mellea. The endogenous A. mellea gpd promoter delivered efficient expression, and we show that inclusion of an intron was also required for transgene expression. GFP and mRFP expression was stable in mycelia and fluorescence was visible in transgenic fruiting bodies and GFP was detectable in planta. Use of these vectors has been successful in giving expression of the fluorescent proteins GFP and mRFP in A. mellea, providing an additional molecular tool for this pathogen..

Citations:

7

Citations per year:

2.3

Title:

UV-B detected by the UVR8 photoreceptor antagonizes auxin signaling and plant shade avoidance

Authors:

Hayes, S, Velanis, CN, Jenkins, GI & Franklin, KA

Year:

2014

Journal:

PNAS

Weblink:

https://dx.doi.org/10.1073/pnas.1403052111

Abstract:

Plants detect different facets of their radiation environment via specific photoreceptors to modulate growth and development. UV-B is perceived by the photoreceptor UV RESISTANCE LOCUS 8 (UVR8). The molecular mechanisms linking UVR8 activation to plant growth are not fully understood, however. When grown in close proximity to neighboring vegetation, shade-intolerant plants initiate dramatic stem elongation to overtop competitors. Here we show that UV-B, detected by UVR8, provides an unambiguous sunlight signal that inhibits shade avoidance responses in Arabidopsis thaliana by antagonizing the phytohormones auxin and gibberellin. UV-B triggers degradation of the transcription factors PHYTOCHROME INTERACTING FACTOR 4 and PHYTOCHROME INTERACTING FACTOR 5 and stabilizes growth-repressing DELLA proteins, inhibiting auxin biosynthesis via a dual mechanism. Our findings show that UVR8 signaling is closely integrated with other photoreceptor pathways to regulate auxin signaling and plant growth in sunlight.
In many plant species, the detection of neighboring vegetation provokes a suite of elongation responses, collectively termed the “shade avoidance syndrome.” Encroaching neighbors absorb red (R) light and reflect far-red (FR) light, lowering the ratio of R:FR sensed by phytochrome photoreceptors (1). This leads to the stabilization and activation of a subset of bHLH transcription factors, PHYTOCHROME INTERACTING FACTORS (PIFs), which drive auxin biosynthesis and elongation growth (2, 3). If the low R:FR signal persists, then flowering is accelerated to promote seed set (1).
UV-B, detected by the UVR8 photoreceptor, regulates plant morphogenesis (4, 5). UV-B is strongly absorbed by vegetation (6) and could signal to plants that they are in sunlight to counter shade avoidance responses. The potential role of UVR8 in regulating shade avoidance has not been explored, however.
To investigate the effects of UV-B in shade avoidance, we analyzed plant responses to simultaneous treatments of low R:FR and narrow-band UV-B. We show that low-dose UV-B perceived by UVR8 strongly inhibits hypocotyl and petiole elongation, even in the presence of a strong low R:FR signal. This occurs via a dual mechanism that simultaneously degrades and inactivates PIF4 and PIF5, thereby inhibiting auxin biosynthesis and cell elongation.

Citations:

60

Citations per year:

12.3

Title:

Functional analysis of Agaricus bisporus serine proteinase 1 reveals roles in utilization of humic rich substrates and adaptation to the leaf‐litter ecological niche

Authors:

Heneghan, MN, Burns, C, Costa, AMSB, Burton, KS, Challen, MP, Bailey, AM & Foster, GD

Year:

2016

Journal:

Environmental Microbiology

Weblink:

https://dx.doi.org/10.1111/1462-2920.13350

Abstract:

Agaricus bisporus is a secondary decomposer fungus and an excellent model for the adaptation, persistence and growth of fungi in humic‐rich environments such as soils of temperate woodland and pastures. The A. bisporus serine proteinase SPR1 is induced by humic acids and is highly expressed during growth on compost. Three Spr1 gene silencing cassettes were constructed around sense, antisense and non‐translatable‐stop strategies (pGRsensehph, pGRantihph and pGRstophph). Transformation of A. bisporus with these cassettes generated cultures showing a reduction in extracellular proteinase activity as demonstrated by the reduction, or abolition, of a clearing zone on plate‐based bioassays. These lines were then assessed by detailed enzyme assay, RT‐qPCR and fruiting. Serine proteinase activity in liquid cultures was reduced in 83% of transformants. RT‐qPCR showed reduced Spr1 mRNA levels in all transformants analysed, and these correlated with reduced enzyme activity. When fruiting was induced, highly‐silenced transformant AS5 failed to colonize the compost, whilst for those that did colonize the compost, 60% gave a reduction in mushroom yield. Transcriptional, biochemical and developmental observations, demonstrate that SPR1 has an important role in nutrient acquisition in compost and that SPR1 is a key enzyme in the adaptation of Agaricus to the humic‐rich ecological niche formed during biomass degradation.

Citations:

1

Citations per year:

0.4

Title:

Anthropogenic noise increases fish mortality by predation

Authors:

Simpson, SD, Radford, AN, Nedelec, SL, Ferrari, MCO, Chivers, DP, McCormick, MI & Meekan, MG

Year:

2016

Journal:

Nature Communications

Weblink:

https://dx.doi.org/10.1038/ncomms10544

Abstract:

Noise-generating human activities affect hearing, communication and movement in terrestrial and aquatic animals, but direct evidence for impacts on survival is rare. We examined effects of motorboat noise on post-settlement survival and physiology of a prey fish species and its performance when exposed to predators. Both playback of motorboat noise and direct disturbance by motorboats elevated metabolic rate in Ambon damselfish (Pomacentrus amboinensis), which when stressed by motorboat noise responded less often and less rapidly to simulated predatory strikes. Prey were captured more readily by their natural predator (dusky dottyback, Pseudochromis fuscus) during exposure to motorboat noise compared with ambient conditions, and more than twice as many prey were consumed by the predator in field experiments when motorboats were passing. Our study suggests that a common source of noise in the marine environment has the potential to impact fish demography, highlighting the need to include anthropogenic noise in management plans.

Citations:

70

Citations per year:

20.5

Title:

Cyp27c1 Red-Shifts the Spectral Sensitivity of Photoreceptors by Converting Vitamin A1 into A2

Authors:

Enright, JM, Toomey, MB, Sato, SY, Temple, SE, Allen, JR, Fujiwara, R, Kramlinger, VM, Nagy, LD, Johnson, KM, Xiao, Y, How, MJ, Johnson, SL, Roberts, NW, Kefalov, VJ, Guengerich, P & Corbo, JC

Year:

2015

Journal:

Current Biology

Weblink:

https://dx.doi.org/10.1016/j.cub.2015.10.018

Abstract:

Some vertebrate species have evolved means of extending their visual sensitivity beyond the range of human vision. One mechanism of enhancing sensitivity to long-wavelength light is to replace the 11-cis retinal chromophore in photopigments with 11-cis 3,4-didehydroretinal. Despite over a century of research on this topic, the enzymatic basis of this perceptual switch remains unknown. Here, we show that a cytochrome P450 family member, Cyp27c1, mediates this switch by converting vitamin A1 (the precursor of 11-cis retinal) into vitamin A2 (the precursor of 11-cis 3,4-didehydroretinal). Knockout of cyp27c1 in zebrafish abrogates production of vitamin A2, eliminating the animal’s ability to red-shift its photoreceptor spectral sensitivity and reducing its ability to see and respond to near-infrared light. Thus, the expression of a single enzyme mediates dynamic spectral tuning of the entire visual system by controlling the balance of vitamin A1and A2 in the eye.

Citations:

40

Citations per year:

11.2

Title:

Delayed Response and Biosonar Perception Explain Movement Coordination in Trawling Bats

Authors:

Giuggioli, L, McKetterick, TJ & Holderied, M

Year:

2015

Journal:

PLOS Computational Biology

Weblink:

https://dx.doi.org/10.1371/journal.pcbi.1004089

Abstract:

Animal coordinated movement interactions are commonly explained by assuming unspecified social forces of attraction, repulsion and alignment with parameters drawn from observed movement data. Here we propose and test a biologically realistic and quantifiable biosonar movement interaction mechanism for echolocating bats based on spatial perceptual bias, i.e. actual sound field, a reaction delay, and observed motor constraints in speed and acceleration. We found that foraging pairs of bats flying over a water surface swapped leader-follower roles and performed chases or coordinated manoeuvres by copying the heading a nearby individual has had up to 500 ms earlier. Our proposed mechanism based on the interplay between sensory-motor constraints and delayed alignment was able to recreate the observed spatial actor-reactor patterns. Remarkably, when we varied model parameters (response delay, hearing threshold and echolocation directionality) beyond those observed in nature, the spatio-temporal interaction patterns created by the model only recreated the observed interactions, i.e. chases, and best matched the observed spatial patterns for just those response delays, hearing thresholds and echolocation directionalities found to be used by bats. This supports the validity of our sensory ecology approach of movement coordination, where interacting bats localise each other by active echolocation rather than eavesdropping.

Citations:

16

Citations per year:

3.7

Title:

Elevated CO2-Induced Responses in Stomata Require ABA and ABA Signaling

Authors:

Chater, C, Peng, K, Movahedi, M, Dunn, JA, Walker, HJ, Liang, YK, McLachlan, DH, Casson, S, Isner, JC, Wilson, I, Neill, SJ, Hedrich, R, Gray, JE & Hetherington, AM

Year:

2015

Journal:

Current Biology

Weblink:

https://dx.doi.org/10.1016/j.cub.2015.09.013

Abstract:

An integral part of global environment change is an increase in the atmospheric concentration of CO2 ([CO2]) [1]. Increased [CO2] reduces leaf stomatal apertures and density of stomata that plays out as reductions in evapotranspiration [2, 3, 4]. Surprisingly, given the importance of transpiration to the control of terrestrial water fluxes [5] and plant nutrient acquisition [6], we know comparatively little about the molecular components involved in the intracellular signaling pathways by which [CO2] controls stomatal development and function [7]. Here, we report that elevated [CO2]-induced closure and reductions in stomatal density require the generation of reactive oxygen species (ROS), thereby adding a new common element to these signaling pathways. We also show that the PYR/RCAR family of ABA receptors [8, 9] and ABA itself are required in both responses. Using genetic approaches, we show that ABA in guard cells or their precursors is sufficient to mediate the [CO2]-induced stomatal density response. Taken together, our results suggest that stomatal responses to increased [CO2] operate through the intermediacy of ABA. In the case of [CO2]-induced reductions in stomatal aperture, this occurs by accessing the guard cell ABA signaling pathway. In both [CO2]-mediated responses, our data are consistent with a mechanism in which ABA increases the sensitivity of the system to [CO2] but could also be explained by requirement for a CO2-induced increase in ABA biosynthesis specifically in the guard cell lineage. Furthermore, the dependency of stomatal [CO2] signaling on ABA suggests that the ABA pathway is, in evolutionary terms, likely to be ancestral.

Citations:

60

Citations per year:

16.2

Title:

Complex trait architecture: the pleiotropic model revisited

Authors:

North, TL & Beaumont, MA

Year:

2015

Journal:

Scientific Reports

Weblink:

https://dx.doi.org/10.1038/srep09351

Abstract:

There is currently much debate about how much the genetic heritability of complex traits is due to very rare alleles. This issue is important because it determines sampling strategies for genetic association studies. Several recent theoretical papers based on a pleiotropic model for trait evolution suggest that it is possible that a large proportion of the genetic variance could be explained by rare alleles. This model assumes that mutations with a large effect on fitness also tend to have large positive or negative effects on phenotypic traits. We show that conclusions based on standard diffusion results are generally applicable to simulations of whole genomes with overlapping generations in a finite population, although the variance contribution of rare alleles is somewhat smaller than theoretical predictions. We show that under many scenarios the pleiotropic model predicts trait distributions that are unrealistically leptokurtic. We argue that this imposes a limit on the relationship between fitness and trait effects.

Citations:

5

Citations per year:

1.2

Title:

UV-B antagonises shade avoidance and increases levels of the flavonoid quercetin in coriander (Coriandrum sativum)

Authors:

Fraser, DP, Sharma, A, Fletcher, T, Budge, S, Moncrieff, C, Dodd, AN & Franklin, KA

Year:

2017

Journal:

Scientific Reports

Weblink:

https://dx.doi.org/10.1038/s41598-017-18073-8

Abstract:

Despite controlling a diverse array of regulatory processes in plants, UV-B wavelengths (280–315 nm) are attenuated by common greenhouse materials such as glass and polycarbonate and are therefore depleted in many commercial growing environments. In this study, we analysed the architecture, pigment accumulation and antioxidant capacity of coriander (Coriandrum sativum, also known as cilantro) plants grown with and without supplementary UV-B (1.5 µmol m−2 s−1). We demonstrate that UV-B limits stem elongation responses to neighbour proximity perception (shade avoidance), promoting a more compact plant architecture. In addition, UV-B increased leaf quercetin content and total antioxidant capacity. Arabidopsis thaliana mutants deficient in flavonoid biosynthesis were not impaired in shade avoidance inhibition, suggesting that UV-B-induced flavonoid synthesis is not a component of this response. Our results indicate that UV-B supplementation may provide a method to manipulate the architecture, flavour and nutritional content of potted herbs whilst reducing the deleterious impacts of dense planting on product quality.

Citations:

3

Citations per year:

1.9

Title:

Characterization of polyploid wheat genomic diversity using a high‐density 90 000 single nucleotide polymorphism array

Authors:

Wang, S, Wong, D, Forrest, K, Allen, A, Chao, S, Huang, BE, Maccaferri, M, Salvi, S, Milner, SG, Cattivelli, L, Mastrangelo, AM, Whan, A, Stephen, S, Barker, G, Wieseke, R, Plieske, J, International Wheat Genome Sequencing Consortium, Lillemo, M, Mather, D, Appels, R, Dolferus, R, Brown‐Guedira. G, Korol, A, Akhunova, AR, Feuillet, C, Salse, J, Morgante, M, Pozniak, C, Luo, MC, Dvorak, J, Morell, M, Dubcovsky, J, Ganal, M, Tuberosa, R, Lawley, C, Mikoulitch, I, Cavanagh, C, Edwards, KJ, Hayden, M, Akhunov, E

Year:

2014

Journal:

Plant Biotechnology Journal

Weblink:

https://dx.doi.org/10.1111/pbi.12183

Abstract:

High‐density single nucleotide polymorphism (SNP) genotyping arrays are a powerful tool for studying genomic patterns of diversity, inferring ancestral relationships between individuals in populations and studying marker–trait associations in mapping experiments. We developed a genotyping array including about 90 000 gene‐associated SNPs and used it to characterize genetic variation in allohexaploid and allotetraploid wheat populations. The array includes a significant fraction of common genome‐wide distributed SNPs that are represented in populations of diverse geographical origin. We used density‐based spatial clustering algorithms to enable high‐throughput genotype calling in complex data sets obtained for polyploid wheat. We show that these model‐free clustering algorithms provide accurate genotype calling in the presence of multiple clusters including clusters with low signal intensity resulting from significant sequence divergence at the target SNP site or gene deletions. Assays that detect low‐intensity clusters can provide insight into the distribution of presence–absence variation (PAV) in wheat populations. A total of 46 977 SNPs from the wheat 90K array were genetically mapped using a combination of eight mapping populations. The developed array and cluster identification algorithms provide an opportunity to infer detailed haplotype structure in polyploid wheat and will serve as an invaluable resource for diversity studies and investigating the genetic basis of trait variation in wheat.

Citations:

574

Citations per year:

104.2

Title:

Stacks off tracks: a role for the golgin AtCASP in plant endoplasmic reticulum-Golgi apparatus tethering

Authors:

Osterrieder, A, Sparkes, IA, Botchway, SW, Ward, A, Ketelaar, T, De Ruijter, N & Hawes, C

Year:

2017

Journal:

Journal of Experimental Botany

Weblink:

https://dx.doi.org/10.1093/jxb/erx167

Abstract:

The plant Golgi apparatus modifies and sorts incoming proteins from the endoplasmic reticulum (ER) and synthesizes cell wall matrix material. Plant cells possess numerous motile Golgi bodies, which are connected to the ER by yet to be identified tethering factors. Previous studies indicated a role for cis-Golgi plant golgins, which are long coiled-coil domain proteins anchored to Golgi membranes, in Golgi biogenesis. Here we show a tethering role for the golgin AtCASP at the ER-Golgi interface. Using live-cell imaging, Golgi body dynamics were compared in Arabidopsis thaliana leaf epidermal cells expressing fluorescently tagged AtCASP, a truncated AtCASP-ΔCC lacking the coiled-coil domains, and the Golgi marker STtmd. Golgi body speed and displacement were significantly reduced in AtCASP-ΔCC lines. Using a dual-colour optical trapping system and a TIRF-tweezer system, individual Golgi bodies were captured in planta. Golgi bodies in AtCASP-ΔCC lines were easier to trap and the ER-Golgi connection was more easily disrupted. Occasionally, the ER tubule followed a trapped Golgi body with a gap, indicating the presence of other tethering factors. Our work confirms that the intimate ER-Golgi association can be disrupted or weakened by expression of truncated AtCASP-ΔCC and suggests that this connection is most likely maintained by a golgin-mediated tethering complex.

Citations:

6

Citations per year:

2.9

Title:

Scale‐dependent effects of landscape variables on gene flow and population structure in bats

Authors:

Razgour, O, Rebelo, H, Puechmaille, SJ, Juste, J, Ibáñez, C, Kiefer, A, Burke, T, Dawson, DA & Jones, G

Year:

2014

Journal:

Diversity and Distributions

Weblink:

https://dx.doi.org/10.1111/ddi.12200

Abstract:

Aim. A common pattern in biogeography is the scale‐dependent effect of environmental variables on the spatial distribution of species. We tested the role of climatic and land cover variables in structuring the distribution of genetic variation in the grey long‐eared bat, Plecotus austriacus, across spatial scales. Although landscape genetics has been widely used to describe spatial patterns of gene flow in a variety of taxa, volant animals have generally been neglected because of their perceived high dispersal potential.
Location. England and Europe.
Methods. We used a multiscale integrated approach, combining population genetics with species distribution modelling and geographical information under a causal modelling framework, to identify landscape barriers to gene flow and their effect on population structure and conservation status. Genotyping involved 23 polymorphic microsatellites and 259 samples from across the species' range.
Results. We identified distinct population structure shaped by geographical barriers and evidence of population fragmentation at the northern edge of the range. Habitat suitability (as captured by species distribution models, SDMs) was the most important landscape variable affecting genetic connectivity at the broad spatial scale, while at the fine scale, lowland unimproved grasslands, the main foraging habitat of P. austriacus, played a pivotal role in promoting genetic connectivity.
Main conclusions. The importance of lowland unimproved grasslands in determining the biogeography and genetic connectivity in P. austriacus highlights the importance of their conservation as part of a wider landscape management for fragmented edge populations. This study illustrates the value of using SDMs in landscape genetics and highlights the need for multiscale approaches when studying genetic connectivity in volant animals or taxa with similar dispersal abilities."

Citations:

18

Citations per year:

3.3

Title:

Functional group diversity increases with modularity in complex food webs

Authors:

Montoya, D, Yallop, ML & Memmott, J

Year:

2015

Journal:

Nature Communications

Weblink:

https://dx.doi.org/10.1038/ncomms8379

Abstract:

Biodiversity increases the ability of ecosystems to provide multiple functions. Most studies report a positive relationship between species richness and the number of ecosystem functions. However, it is not known whether the number of functional groups is related to the structure of the underlying species interaction network. Here we present food web data from 115 salt marsh islands and show that network structure is associated with the number of functional groups present. Functional group diversity is heterogeneously distributed across spatial scales, with some islands hosting more functional groups than others. Functional groups form modules within the community so that food webs with more modular architectures have more functional group diversity. Further, in communities with different interaction types, modularity can be seen as the multifunctional equivalent of trophic complementarity. Collectively, these findings reveal spatial heterogeneity in the number of functional groups that emerges from patterns in the structure of the food web.

Citations:

23

Citations per year:

5.7

Title:

Background complexity and the detectability of camouflaged targets by birds and humans

Authors:

Xiao, F & Cuthill, IC

Year:

2016

Journal:

Proceedings of The Royal Society B

Weblink:

https://dx.doi.org/10.1098/rspb.2016.1527

Abstract:

Remaining undetected is often key to survival, and camouflage is a widespread solution. However, extrinsic to the animal itself, the complexity of the background may be important. This has been shown in laboratory experiments using artificially patterned prey and backgrounds, but the mechanism remains obscure (not least because ‘complexity’ is a multifaceted concept). In this study, we determined the best predictors of detection by wild birds and human participants searching for the same cryptic targets on trees in the field. We compared detection success to metrics of background complexity and ‘visual clutter’ adapted from the human visual salience literature. For both birds and humans, the factor that explained most of the variation in detectability was the textural complexity of the tree bark as measured by a metric of feature congestion (specifically, many nearby edges in the background). For birds, this swamped any effects of colour match to the local surroundings, although for humans, local luminance disparities between the target and tree became important. For both taxa, a more abstract measure of complexity, entropy, was a poorer predictor. Our results point to the common features of background complexity that affect visual search in birds and humans, and how to quantify them.

Citations:

27

Citations per year:

9.6

Title:

The anti-predator role of within-nest emergence synchrony in sea turtle hatchlings

Authors:

Santos, RG, Pinheiro, HT, Martins, AS, Riul, P, Bruno, SC, Janzen, FJ & Ioannou, CC

Year:

2016

Journal:

Proceedings of The Royal Society B

Weblink:

https://dx.doi.org/10.1098/rspb.2016.0697

Abstract:

Group formation is a common behaviour among prey species. In egg-laying animals, despite the various factors that promote intra-clutch variation leading to asynchronous hatching and emergence from nests, synchronous hatching and emergence occurs in many taxa. This synchrony may be adaptive by reducing predation risk, but few data are available in any natural system, even for iconic examples of the anti-predator function of group formation. Here, we show for the first time that increased group size (number of hatchlings emerging together from a nest) reduces green turtle (Chelonia mydas) hatchling predation. This effect was only observed earlier in the night when predation pressure was greatest, indicated by the greatest predator abundance and a small proportion of predators preoccupied with consuming captured prey. Further analysis revealed that the effect of time of day was due to the number of hatchlings already killed in an evening; this, along with the apparent lack of other anti-predatory mechanisms for grouping, suggests that synchronous emergence from a nest appears to swamp predators, resulting in an attack abatement effect. Using a system with relatively pristine conditions for turtle hatchlings and their predators provides a more realistic environmental context within which intra-nest synchronous emergence has evolved.

Citations:

19

Citations per year:

6.4

Title:

Anthropogenic noise compromises antipredator behaviour in European eels

Authors:

Simpson, SD, Purser, J & Radford, AN

Year:

2015

Journal:

Global Change Biology

Weblink:

https://dx.doi.org/10.1111/gcb.12685

Abstract:

Increases in noise‐generating human activities since the Industrial Revolution have changed the acoustic landscape of many terrestrial and aquatic ecosystems. Anthropogenic noise is now recognized as a major pollutant of international concern, and recent studies have demonstrated impacts on, for instance, hearing thresholds, communication, movement and foraging in a range of species. However, consequences for survival and reproductive success are difficult to ascertain. Using a series of laboratory‐based experiments and an open‐water test with the same methodology, we show that acoustic disturbance can compromise antipredator behaviour – which directly affects survival likelihood – and explore potential underlying mechanisms. Juvenile European eels (Anguilla anguilla) exposed to additional noise (playback of recordings of ships passing through harbours), rather than control conditions (playback of recordings from the same harbours without ships), performed less well in two simulated predation paradigms. Eels were 50% less likely and 25% slower to startle to an ‘ambush predator’ and were caught more than twice as quickly by a ‘pursuit predator’. Furthermore, eels experiencing additional noise had diminished spatial performance and elevated ventilation and metabolic rates (indicators of stress) compared with control individuals. Our results suggest that acoustic disturbance could have important physiological and behavioural impacts on animals, compromising life‐or‐death responses.

Citations:

65

Citations per year:

14.7

Title:

A step change in the transfer of interspecific variation into wheat from Amblyopyrum muticum

Authors:

King, J, Grewal, S, Yang, CY, Hubbart, S, Scholefield, D, Ashling, S, Edwards, KJ, Allen, AM, Burridge, A, Bloor, C, Davassi, A, Da Silva, GJ, Chalmers, K & King, IP

Year:

2017

Journal:

Plant Biotechnology Journal

Weblink:

https://dx.doi.org/10.1111/pbi.12606

Abstract:

Despite some notable successes, only a fraction of the genetic variation available in wild relatives has been utilized to produce superior wheat varieties. This is as a direct result of the lack of availability of suitable high‐throughput technologies to detect wheat/wild relative introgressions when they occur. Here, we report on the use of a new SNP array to detect wheat/wild relative introgressions in backcross progenies derived from interspecific hexaploid wheat/Ambylopyrum muticum F1 hybrids. The array enabled the detection and characterization of 218 genomewide wheat/Am. muticum introgressions, that is a significant step change in the generation and detection of introgressions compared to previous work in the field. Furthermore, the frequency of introgressions detected was sufficiently high to enable the construction of seven linkage groups of the Am. muticum genome, thus enabling the syntenic relationship between the wild relative and hexaploid wheat to be determined. The importance of the genetic variation from Am. muticum introduced into wheat for the development of superior varieties is discussed.

Citations:

30

Citations per year:

12.4

Title:

Quantitative analysis of harmonic convergence in mosquito auditory interactions

Authors:

Aldersley, A, Champneys, A, Homer, M & Robert, D

Year:

2016

Journal:

Journal of The Royal Society Interface

Weblink:

https://dx.doi.org/10.1098/rsif.2015.1007

Abstract:

This article analyses the hearing and behaviour of mosquitoes in the context of inter-individual acoustic interactions. The acoustic interactions of tethered live pairs of Aedes aegypti mosquitoes, from same and opposite sex mosquitoes of the species, are recorded on independent and unique audio channels, together with the response of tethered individual mosquitoes to playbacks of pre-recorded flight tones of lone or paired individuals. A time-dependent representation of each mosquito's non-stationary wing beat frequency signature is constructed, based on Hilbert spectral analysis. A range of algorithmic tools is developed to automatically analyse these data, and used to perform a robust quantitative identification of the ‘harmonic convergence’ phenomenon. The results suggest that harmonic convergence is an active phenomenon, which does not occur by chance. It occurs for live pairs, as well as for lone individuals responding to playback recordings, whether from the same or opposite sex. Male–female behaviour is dominated by frequency convergence at a wider range of harmonic combinations than previously reported, and requires participation from both partners in the duet. New evidence is found to show that male–male interactions are more varied than strict frequency avoidance. Rather, they can be divided into two groups: convergent pairs, typified by tightly bound wing beat frequencies, and divergent pairs, that remain widely spaced in the frequency domain. Overall, the results reveal that mosquito acoustic interaction is a delicate and intricate time-dependent active process that involves both individuals, takes place at many different frequencies, and which merits further enquiry.

Citations:

11

Citations per year:

3.4

Title:

Human preferences for sexually dimorphic faces may be evolutionarily novel

Authors:

Scott, IM, Clark, AP, Josephson, SC, Boyette, AH, Cuthill, IC, Fried, RL, Gibson, MA, Hewlett, BS, Jamieson, M, Jankowiak, W, Honey, PL, Huang, Z, Liebert, MA, Purzycki, BG, Shaver, JH, Snodgrass, JJ, Sosis, R, Sugiyama, LS, Swami, V, Yu, DW, Zhao, Y & Penton-Voak, IS

Year:

2014

Journal:

PNAS

Weblink:

https://dx.doi.org/10.1073/pnas.1409643111

Abstract:

A large literature proposes that preferences for exaggerated sex typicality in human faces (masculinity/femininity) reflect a long evolutionary history of sexual and social selection. This proposal implies that dimorphism was important to judgments of attractiveness and personality in ancestral environments. It is difficult to evaluate, however, because most available data come from large-scale, industrialized, urban populations. Here, we report the results for 12 populations with very diverse levels of economic development. Surprisingly, preferences for exaggerated sex-specific traits are only found in the novel, highly developed environments. Similarly, perceptions that masculine males look aggressive increase strongly with development and, specifically, urbanization. These data challenge the hypothesis that facial dimorphism was an important ancestral signal of heritable mate value. One possibility is that highly developed environments provide novel opportunities to discern relationships between facial traits and behavior by exposing individuals to large numbers of unfamiliar faces, revealing patterns too subtle to detect with smaller samples.

Citations:

56

Citations per year:

11.8

Title:

Virus Infection of Plants Alters Pollinator Preference: A Payback for Susceptible Hosts?

Authors:

Groen, SC, Jiang, S, Murphy, AM, Cunniffe, NJ, Westwood, JH, Davey, MP, Bruce, TJA, Caulfield, JC, Furzer, OJ, Reed, A, Robinson, SI, Miller, E, Davis, CN, Pickett, JA, Whitney, HM, Glover, BJ & Carr, JP

Year:

2016

Journal:

PLOS Pathogens

Weblink:

https://dx.doi.org/10.1371/journal.ppat.1005790

Abstract:

Plant volatiles play important roles in attraction of certain pollinators and in host location by herbivorous insects. Virus infection induces changes in plant volatile emission profiles, and this can make plants more attractive to insect herbivores, such as aphids, that act as viral vectors. However, it is unknown if virus-induced alterations in volatile production affect plant-pollinator interactions. We found that volatiles emitted by cucumber mosaic virus (CMV)-infected tomato (Solanum lycopersicum) and Arabidopsis thaliana plants altered the foraging behaviour of bumblebees (Bombus terrestris). Virus-induced quantitative and qualitative changes in blends of volatile organic compounds emitted by tomato plants were identified by gas chromatography-coupled mass spectrometry. Experiments with a CMV mutant unable to express the 2b RNA silencing suppressor protein and with Arabidopsis silencing mutants implicate microRNAs in regulating emission of pollinator-perceivable volatiles. In tomato, CMV infection made plants emit volatiles attractive to bumblebees. Bumblebees pollinate tomato by ‘buzzing’ (sonicating) the flowers, which releases pollen and enhances self-fertilization and seed production as well as pollen export. Without buzz-pollination, CMV infection decreased seed yield, but when flowers of mock-inoculated and CMV-infected plants were buzz-pollinated, the increased seed yield for CMV-infected plants was similar to that for mock-inoculated plants. Increased pollinator preference can potentially increase plant reproductive success in two ways: i) as female parents, by increasing the probability that ovules are fertilized; ii) as male parents, by increasing pollen export. Mathematical modeling suggested that over a wide range of conditions in the wild, these increases to the number of offspring of infected susceptible plants resulting from increased pollinator preference could outweigh underlying strong selection pressures favoring pathogen resistance, allowing genes for disease susceptibility to persist in plant populations. We speculate that enhanced pollinator service for infected individuals in wild plant populations might provide mutual benefits to the virus and its susceptible hosts.

Citations:

19

Citations per year:

6.6

Title:

The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference

Authors:

Tarver, JE, Dos Reis, M, Mirarab, S, Moran, RJ, Parker, S, O’Reilly, JE, King, BL, O’Connell, MJ, Asher, RJ, Warnow, T, Peterson, KJ, Donoghue, PCJ & Pisani, D

Year:

2016

Journal:

Genome Biology and Evolution

Weblink:

https://dx.doi.org/10.1093/gbe/evv261

Abstract:

Placental mammals comprise three principal clades: Afrotheria (e.g., elephants and tenrecs), Xenarthra (e.g., armadillos and sloths), and Boreoeutheria (all other placental mammals), the relationships among which are the subject of controversy and a touchstone for debate on the limits of phylogenetic inference. Previous analyses have found support for all three hypotheses, leading some to conclude that this phylogenetic problem might be impossible to resolve due to the compounded effects of incomplete lineage sorting (ILS) and a rapid radiation. Here we show, using a genome scale nucleotide data set, microRNAs, and the reanalysis of the three largest previously published amino acid data sets, that the root of Placentalia lies between Atlantogenata and Boreoeutheria. Although we found evidence for ILS in early placental evolution, we are able to reject previous conclusions that the placental root is a hard polytomy that cannot be resolved. Reanalyses of previous data sets recover Atlantogenata + Boreoeutheria and show that contradictory results are a consequence of poorly fitting evolutionary models; instead, when the evolutionary process is better-modeled, all data sets converge on Atlantogenata. Our Bayesian molecular clock analysis estimates that marsupials diverged from placentals 157–170 Ma, crown Placentalia diverged 86–100 Ma, and crown Atlantogenata diverged 84–97 Ma. Our results are compatible with placental diversification being driven by dispersal rather than vicariance mechanisms, postdating early phases in the protracted opening of the Atlantic Ocean.

Citations:

60

Citations per year:

17.5

Title:

Assessment of ecological status in UK lakes using benthic diatoms

Authors:

Bennion, H, Kelly, MG, Juggins, S, Yallop, ML, Burgess, A, Jamieson, J & Krokowski, J

Year:

2014

Journal:

Freshwater Science

Weblink:

https://dx.doi.org/10.1086/675447

Abstract:

The European Union’s Water Framework Directive (WFD) requires that all water bodies in Europe achieve good ecological status (GES) by 2015. We developed an ecological classification tool for UK lakes based on benthic diatoms, a key component of the biological-quality element macrophytes and phytobenthos. A database of 1079 epilithic and epiphytic diatom samples and matching environmental data was assembled from 228 UK lakes. The data set was divided into 3 lake types: low, medium, and high alkalinity. A lake trophic diatom index (LTDI) was developed based on modification of the trophic diatom index (TDI) for rivers, and ecological quality ratios (EQRs) were generated for each lake type. The high/good status boundary was defined as the 25th percentile of EQRs of all reference sites (identified based on independent sedimentary-diatom-assemblage data or catchment point-source and landuse data), whereas the good/moderate boundary was set at the point at which nutrient-sensitive and nutrient-tolerant taxa were present in equal relative abundance. The moderate/poor and poor/bad boundaries were defined by equal division of the remaining EQR gradient. Samples from reference sites were used to predict the expected LTDI value for each sample, and these values were compared with the classifications derived from the LTDI. For lakes identified as reference sites, 68% were classified as having high status and 32% as having good. The model predicted 81% of nonreference lakes to have good or worse status. The model was applied to 17 English lakes (10 low- and 7 medium-alkalinity) for which classification based on other WFD tools was available. The classifications based on LTDI gave the same status (within 1 class) as other biological elements for 11 of the 17 lakes (65%). Thus, the LTDI gives a reliable assessment of the condition of the littoral biofilm and is a key component of a WFD-compliant tool kit for classifying UK standing waters.

Citations:

26

Citations per year:

5.1

Title:

How to catch more prey with less effective traps: explaining the evolution of temporarily inactive traps in carnivorous pitcher plants

Authors:

Bauer, U, Federle, W, Seidel, H, Grafe, TU & Ioannou, CC

Year:

2015

Journal:

Proceedings of The Royal Society B

Weblink:

https://dx.doi.org/10.1098/rspb.2014.2675

Abstract:

Carnivorous Nepenthes pitcher plants capture arthropods with specialized slippery surfaces. The key trapping surface, the pitcher rim (peristome), is highly slippery when wetted by rain, nectar or condensation, but not when dry. As natural selection should favour adaptations that maximize prey intake, the evolution of temporarily inactive traps seems paradoxical. Here, we show that intermittent trap deactivation promotes ‘batch captures' of ants. Prey surveys revealed that N. rafflesiana pitchers sporadically capture large numbers of ants from the same species. Continuous experimental wetting of the peristome increased the number of non-recruiting prey, but decreased the number of captured ants and shifted their trapping mode from batch to individual capture events. Ant recruitment was also lower to continuously wetted pitchers. Our experimental data fit a simple model that predicts that intermittent, wetness-based trap activation should allow safe access for ‘scout’ ants under dry conditions, thereby promoting recruitment and ultimately higher prey numbers. The peristome trapping mechanism may therefore represent an adaptation for capturing ants. The relatively rare batch capture events may particularly benefit larger plants with many pitchers. This explains why young plants of many Nepenthes species additionally employ wetness-independent, waxy trapping surfaces.

Citations:

15

Citations per year:

3.4