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opencc-zeroDec 2018View details →

Data from: Neural structure mapping in human probabilistic reward learning

Humans can learn abstract concepts that describe invariances over relational patterns in data. One such concept, known as magnitude, allows stimuli to be compactly represented on a single dimension (i.e. on a mental line). Here, we measured representations of magnitude in humans by recording neural signals whilst they viewed symbolic numbers. During a subsequent reward-guided learning task, the neural patterns elicited by novel complex visual images reflected their payout probability in a way that suggested they were encoded onto the same mental number line, with 'bad' bandits sharing neural representation with 'small' numbers and 'good' bandits with 'large' numbers. Using neural network simulations, we provide a mechanistic model that explains our findings and shows how structural alignment can promote transfer learning. Our findings suggest that in humans, learning about reward probability is accompanied by structural alignment of value representations with neural codes for the abstract concept of magnitude.

Data from: Contemporary genetic structure and postglacial demographic history of the black scorpionfish, Scorpaena porcus, in the Mediterranean and the Black Seas

Understanding the distribution of genetic diversity in the light of past demographic events linked with climatic shifts will help to forecast evolutionary trajectories of ecosystems within the current context of climate change. In this study, mitochondrial sequences and microsatellite loci were analysed using traditional population genetic approaches together with Bayesian dating and the more recent approximate Bayesian computation scenario testing. The genetic structure and demographic history of a commercial fish, the black scorpionfish, Scorpaena porcus, was investigated throughout the Mediterranean and Black Seas. The results suggest that the species recently underwent population expansions, in both seas, likely concomitant with the warming period following the Last Glacial Maximum, 20 000 years ago. A weak contemporaneous genetic differentiation was identified between the Black Sea and the Mediterranean Sea. However, the genetic diversity was similar for populations of the two seas, suggesting a high number of colonizers entered the Black Sea during the interglacial period and/or the presence of a refugial population in the Black Sea during the glacial period. Finally, within seas, an east/west genetic differentiation in the Adriatic seems to prevail, whereas the Black Sea does not show any structured spatial genetic pattern of its population. Overall, these results suggest that the Black Sea is not that isolated from the Mediterranean, and both seas revealed similar evolutionary patterns related to climate change and changes in sea level.

opencc-zeroDec 2017View details →

Data from: Drought intensification drives turnover of structure and function in stream invertebrate communities

Climatic extremes are becoming more frequent and intense across much of the globe, potentially transforming the biodiversity and functioning of affected ecosystems. In freshwaters, hydrological extremes such as drought can regulate beta diversity, acting as powerful environmental filters to dictate the complement of species and functional traits found at local and landscape scales. New methods that enable beta diversity and its functional equivalent to be partitioned into turnover (replacement of species/functions) and nestedness-resultant (gain/loss of species/functions) components may offer novel insights into the parallel impacts of drought on ecosystem structure and function. Using a series of artificial channels (mesocosms) designed to mimic perennial headwater streams, we experimentally manipulated streamflows to simulate a gradient of drought intensity. We then modelled taxonomic and functional turnover and nestedness of macroinvertebrate communities along this gradient, validating direct gradient approaches (bootstrapping, Mantel tests) against null models of nestedness. Drought intensification produced significant environmental distance decay trends (i.e. communities became increasingly taxonomically and functionally dissimilar the more differentially disturbed by drought they were). Taxonomic distance decay was primarily driven by turnover, while the functional trend reflected a combination of richness differences and turnover at different points along the gradient. Taxonomic and functional distance decay slopes were not significantly different, implying that communities were functionally vulnerable to drying. The increased frequency and intensity of droughts predicted under most climate change scenarios could thus profoundly modify not only the structure of running water invertebrate communities, but also the ecosystem functions they underpin.

Data from: Environmental effects on the structure of the G-matrix

Genetic correlations between traits determine the multivariate response to selection in the short term, and thereby play a causal role in evolutionary change. While individual studies have documented environmentally induced changes in genetic correlations, the nature and extent of environmental effects on multivariate genetic architecture across species and environments remain largely uncharacterized. We reviewed the literature for estimates of the genetic variance-covariance (G) matrix in multiple environments, and compared differences in G between environments to the divergence in G between conspecific populations (measured in a common garden). We found that the predicted evolutionary trajectory differed as strongly between environments as it did between populations. Between-environment differences in the underlying structure of G (total genetic variance and the relative magnitude and orientation of genetic correlations) were equal to or greater than between-population differences. Neither environmental novelty nor the difference in mean phenotype predicted these differences in G. Our results suggest that environmental effects on multivariate genetic architecture may be comparable to the divergence that accumulates over dozens or hundreds of generations between populations. We outline avenues of future research to address the limitations of existing data and characterize the extent to which lability in genetic correlations shapes evolution in changing environments.

Data from: Population structure, gene flow, and historical demography of a small coastal shark (Carcharhinus isodon) in US waters of the Western Atlantic Ocean

Patterns of population structure, genetic demographics, and gene flow in the small coastal shark Carcharhinus isodon (finetooth shark) sampled from two discrete nurseries along the southeastern US coast (Atlantic) and three nurseries in the northern Gulf of Mexico (Gulf), were assessed using 16 nuclear-encoded microsatellites and 1077 base pairs of the mitochondrial DNA (mtDNA) control region. Significant heterogeneity in microsatellite allele distributions was detected among all localities except between the two in the Atlantic. Significant heterogeneity in mtDNA haplotypes was not detected, a result likely due to extremely low mtDNA diversity. The genetic discontinuities combined with seasonal movement patterns, a patchy distribution of appropriate nursery habitat, the apparent absence of sex-biased gene flow, and the occurrence of mating in the vicinity of nursery areas, suggest that both male and female finetooth sharks display regional philopatry to discrete nursery areas. Global and local tests of neutrality, using mtDNA haplotypes, and demographic model testing, using Approximate Bayesian Computation of microsatellite alleles, supported a range-wide expansion of finetooth sharks into US waters occurring less than ∼9000 years ago. These findings add to the growing number of studies in a variety of coastally distributed marine fishes documenting significant barriers to gene flow around peninsular Florida and in the eastern Gulf. The findings also provide further evidence that the traditional model of behavioural ecology, based on large coastal sharks, may not be appropriate for understanding and conserving small coastal sharks.

Data from: Life-history evolution in response to changes in metapopulation structure in an arthropod herbivore

The persistence and dynamics of populations largely depends on the way they are configured and integrated into space and the ensuing eco-evolutionary dynamics. We manipulated spatial and temporal variation in patch size in replicated experimental metapopulations of the herbivore mite Tetranychus urticae and followed evolutionary dynamics over approximately 30 generations. A significant divergence in life history traits, physiological endpoints and gene expression was recorded in the spatially and spatiotemporally variable metapopulation, but also a remarkable convergence relative to the stable reference metapopulation in traits related to size and fecundity and in its transcriptional regulation. The observed evolutionary dynamics are tightly linked to demographic changes, more specifically frequent episodes of resource shortage that increased the reproductive performance of mites on tomato, a challenging host plant. This points towards a general, adaptive stress response in stable spatial variable and spatiotemporal variable metapopulations that pre-adapts a herbivore arthropod to novel environmental stressors.

opencc-zeroDec 2016View details →

Data from: Computer assisted detection of axonal bouton structural plasticity in in vivo time-lapse images

The ability to measure minute structural changes in neural circuits is essential for long-term in vivo imaging studies. Here, we propose a methodology for detection and measurement of structural changes in axonal boutons imaged with time-lapse two-photon laser scanning microscopy (2PLSM). Correlative 2PLSM and 3D electron microscopy (EM) analysis, performed in mouse barrel cortex, showed that the proposed method has low fractions of false positive/negative bouton detections (2/0 out of 18), and that 2PLSM-based bouton weights are correlated with their volumes measured in EM (r=0.93). Next, the method was applied to a set of axons imaged in quick succession to characterize measurement uncertainty. The results were used to construct a statistical model in which bouton addition, elimination, and size changes are described probabilistically, rather than being treated as deterministic events. Finally, we demonstrate that the model can be used to quantify significant structural changes in boutons in long-term imaging experiments.

opencc-zeroDec 2016View details →

Data from: The consequences of polyandry for sibship structures, distributions of relationships and relatedness, and potential for inbreeding in a wild population

The evolutionary benefits of simultaneous polyandry (female multiple mating within a single reproductive event) remain elusive. One potential benefit could arise if polyandry alters sibship structures and consequent relationships and relatedness among females' descendants, and thereby intrinsically reduces future inbreeding risk (the 'indirect inbreeding avoidance hypothesis'). However such effects have not been quantified in naturally complex mating systems that also encompass iteroparity, overlapping generations, sequential polyandry, and polygyny. We used long-term social and genetic pedigree data from song sparrows (Melospiza melodia) to quantify cross-generational consequences of simultaneous polyandry for offspring sibship structures and distributions of relationships and relatedness among possible mates. Simultaneous polyandry decreased full-sibships and increased half-sibships on average, but such effects varied among females and were smaller than would occur in the absence of sequential polyandry or polygyny. Further, while simultaneous polyandry decreased the overall frequencies of possible matings among adult full-sibs, it increased the frequencies of possible matings among adult half-sibs and more distant relatives. These results imply that the intrinsic consequences of simultaneous polyandry for inbreeding risk could cause weak indirect selection on polyandry, but the magnitude and direction of such effects will depend on complex interactions with other mating system components and the form of inbreeding depression.

opencc-zeroDec 2018View details →

Data from: Structurally assisted super black in colorful peacock spiders

Male peacock spiders (Maratus, Salticidae) compete to attract female mates using elaborate, sexually-selected displays. They evolved both brilliant color and velvety black. Here we use scanning electron microscopy (SEM), hyperspectral imaging, and finite-difference time-domain (FDTD) optical modeling to investigate the deep black surfaces of peacock spiders. We found that super black regions reflect <0.5% of light (for a 30° collection angle) in Maratus speciosus (0.44%) and Maratus karrie (0.35%) due to microscale structures. Both species evolved unusually high, tightly packed cuticular bumps (microlens arrays), and M. karrie has an additional dense covering of black brush-like scales atop the cuticle. Our optical models show that the radius and height of spider microlenses achieve a balance between (i) decreased surface reflectance and (ii) enhanced melanin absorption (through multiple scattering, diffraction out of the acceptance cone of female eyes, and increased path length of light through absorbing melanin pigments). The birds-of-paradise (Paradiseidae), ecological analogues of peacock spiders, also evolved super black near bright color patches. Super black locally eliminates white specular highlights, reference points used to calibrate color perception, making nearby colors appear brighter, even luminous, to vertebrates. We propose that this pre-existing, qualitative sensory experience—"sensory bias"—is also found in spiders, leading to the convergent evolution of super black for mating displays in jumping spiders.

Data from: Multiple processes drive genetic structure of humpback whale (Megaptera novaeangliae) populations across spatial scales

Elucidating patterns of population structure for species with complex life histories, and disentangling the processes driving such patterns, remains a significant analytical challenge. Humpback whale (Megaptera novaeangliae) populations display complex genetic structures that have not been fully resolved at all spatial scales. We generated a data set of nuclear markers for 3,575 samples spanning the seven breeding stocks and substocks found in the South Atlantic and western and northern Indian Oceans. For the total sample, and males and females separately, we assessed genetic diversity, tested for genetic differentiation between putative populations and isolation by distance, estimated the number of genetic clusters without a priori population information, and estimated rates of gene flow using maximum likelihood and Bayesian approaches. At the ocean basin scale, structure is governed by geographic distance (IBD p<0.05) and female fidelity to breeding areas, in line with current understanding of the drivers of broad-scale population structure. Consistent with previous studies, the Arabian Sea breeding stock was highly genetically differentiated (FST 0.034-0.161; p<0.01 for all comparisons). However, the breeding stock boundary between west South Africa and east Africa was more porous than expected based on genetic differentiation, cluster, and gene flow analyses. Instances of male-fidelity to breeding areas and relatively high rates of dispersal for females were also observed between the three substocks in the western Indian Ocean. This mismatch between demographic units and current management boundaries may have ramifications for assessments of the status and continued protections of populations still in recovery from commercial whaling.

Data from: Adaptive and neutral markers both show continent-wide population structure of mountain pine beetle (Dendroctonus ponderosae)

Assessments of population genetic structure and demographic history have traditionally been based on neutral markers while explicitly excluding adaptive markers. In this study, we compared the utility of putatively adaptive and neutral single-nucleotide polymorphisms (SNPs) for inferring mountain pine beetle population structure across its geographic range. Both adaptive and neutral SNPs, and their combination, allowed range-wide structure to be distinguished and delimited a population that has recently undergone range expansion across northern British Columbia and Alberta. Using an equal number of both adaptive and neutral SNPs revealed that adaptive SNPs resulted in a stronger correlation between sampled populations and inferred clustering. Our results suggest that adaptive SNPs should not be excluded prior to analysis from neutral SNPs as a combination of both marker sets resulted in better resolution of genetic differentiation between populations than either marker set alone. These results demonstrate the utility of adaptive loci for resolving population genetic structure in a nonmodel organism.

Data from: Genetic structure in village dogs reveals a Central Asian domestication origin

Dogs were the first domesticated species, originating at least 15,000 y ago from Eurasian gray wolves. Dogs today consist primarily of two specialized groups—a diverse set of nearly 400 pure breeds and a far more populous group of free-ranging animals adapted to a human commensal lifestyle (village dogs). Village dogs are more genetically diverse and geographically widespread than purebred dogs making them vital for unraveling dog population history. Using a semicustom 185,805-marker genotyping array, we conducted a large-scale survey of autosomal, mitochondrial, and Y chromosome diversity in 4,676 purebred dogs from 161 breeds and 549 village dogs from 38 countries. Geographic structure shows both isolation and gene flow have shaped genetic diversity in village dog populations. Some populations (notably those in the Neotropics and the South Pacific) are almost completely derived from European stock, whereas others are clearly admixed between indigenous and European dogs. Importantly, many populations—including those of Vietnam, India, and Egypt—show minimal evidence of European admixture. These populations exhibit a clear gradient of short-range linkage disequilibrium consistent with a Central Asian domestication origin.

opencc-zeroDec 2016View details →

Data from: Robust extraction of quantitative structural information from high-variance histological images of livers from necropsied Soay sheep

Quantitative information is essential to the empirical analysis of biological systems. In many such systems, spatial relations between anatomical structures is of interest, making imaging a valuable data acquisition tool. However, image data can be difficult to analyse quantitatively. Many image processing algorithms are highly sensitive to variations in the image, limiting their current application to fields where sample and image quality may be very high. Here, we develop robust image processing algorithms for extracting structural information from a dataset of high-variance histological images of inflamed liver tissue obtained during necropsies of wild Soay sheep. We demonstrate that features of the data can be measured in a fully automated manner, providing quantitative information which can be readily used in statistical analysis. We show that these methods provide measures that correlate well with a manual, expert operator-led analysis of the same images, that they provide advantages in terms of sampling a wider range of information and that information can be extracted far more quickly than in manual analysis.

Data from: Linkage disequilibrium network analysis (LDna) gives a global view of chromosomal inversions, local adaptation and geographic structure

Recent advances in sequencing allow population-genomic data to be generated for virtually any species. However, approaches to analyse such data lag behind the ability to generate it, particularly in nonmodel species. Linkage disequilibrium (LD, the nonrandom association of alleles from different loci) is a highly sensitive indicator of many evolutionary phenomena including chromosomal inversions, local adaptation and geographical structure. Here, we present linkage disequilibrium network analysis (LDna), which accesses information on LD shared between multiple loci genomewide. In LD networks, vertices represent loci, and connections between vertices represent the LD between them. We analysed such networks in two test cases: a new restriction-site-associated DNA sequence (RAD-seq) data set for Anopheles baimaii, a Southeast Asian malaria vector; and a well-characterized single nucleotide polymorphism (SNP) data set from 21 three-spined stickleback individuals. In each case, we readily identified five distinct LD network clusters (single-outlier clusters, SOCs), each comprising many loci connected by high LD. In A. baimaii, further population-genetic analyses supported the inference that each SOC corresponds to a large inversion, consistent with previous cytological studies. For sticklebacks, we inferred that each SOC was associated with a distinct evolutionary phenomenon: two chromosomal inversions, local adaptation, population-demographic history and geographic structure. LDna is thus a useful exploratory tool, able to give a global overview of LD associated with diverse evolutionary phenomena and identify loci potentially involved. LDna does not require a linkage map or reference genome, so it is applicable to any population-genomic data set, making it especially valuable for nonmodel species.

opencc-zeroSep 2019View details →

Data from: Differential female sociality is linked with the fine-scale structure of sexual interactions in replicate groups of red junglefowl, Gallus gallus

Recent work indicates that social structure has extensive implications for patterns of sexual selection and sexual conflict. However, little is known about the individual variation in social behaviours linking social structure to sexual interactions. Here, we use network analysis of replicate polygynandrous groups of red junglefowl (Gallus gallus) to show that the association between social structure and sexual interactions is underpinned by differential female sociality. Sexual dynamics are largely explained by a core group of highly social, younger females, which are more fecund and more polyandrous, and thus associated with more intense postcopulatory competition for males. In contrast, less fecund females from older cohorts, which tend to be socially dominant, avoid male sexual attention by clustering together and perching on branches, and preferentially reproduce with dominant males by more exclusively associating and mating with them. Collectively, these results indicate that individual females occupy subtly different social niches, and demonstrate that female sociality can be an important factor underpinning the landscape of intra-sexual competition and the emergent structure of animal societies.

Data from: We happy few: using structured population models to identify the decisive events in the lives of exceptional individuals

In any population, some individuals make it big: they are among the few that produce many offspring, grow to large size, and so on. What distinguishes the lives of these happy few? We present three approaches for identifying what factors distinguish those "lucky" individuals who come to dominate reproduction in a population without fixed differences between individuals (genotype, site quality, etc.): comparing life-history trajectories for lucky and unlucky individuals and calculating the elasticity of the probability of becoming lucky to perturbations in demographic rates at a given size or a given age. As examples we consider published size-structured integral projection models for the tropical tree Dacrydium elatum and the semiarid shrub Artemisia ordosica and an age-size-structured matrix model for the tropical tree Cedrela ordosica. We find that good fortune (e.g., rapid growth) when small and young matters much more than good fortune when older and larger. Becoming lucky is primarily a matter of surviving while others die. For species with more variable growth (such as Cedrela and Ordosica), it is also a matter of growing fast. We focus on reproductive skew, but our methods are broadly applicable and can be used to investigate how individuals come to be exceptional in any aspect.

opencc-zeroDec 2017View details →

Data from: Inconsistent use of multiple comparison corrections in studies of population genetic structure: are some type I errors more tolerable than others?

Studies of genetic population structure often involve numerous tests of Hardy-Weinberg equilibrium (HWE), linkage disequilibrium (LD), and genetic differentiation. Tests of HWE or LD are important precursors to population structure assessments. When conducting multiple related statistical tests, type 1 error increases, e.g., familywise error rate (FWER) inflation. FWER inflation can alter the results of statistical tests and thus the conclusions. Authors are aware of the need to control for FWER inflation, but there has been low consistency of use. Furthermore, there is a potential for the choice of correction methods to be exploited to selectively use FWER corrections to avoid data exclusion or to result in increased the rejection of null hypotheses. We surveyed literature from 2011-2013 to determine if studies of population structure assess LD and HWE and if FWER corrections were applied consistently across different types of genetic differentiation, linkage disequilibrium, and Hardy-Weinberg equilibrium tests. We found a lack of documentation of FWER corrections in studies, and we advocate for authors to be more cognizant in reporting their corrections. We also found significantly inconsistent FWER corrections, with a bias towards less restrictive correction on genetic differentiation and more restrictive corrections with LD and HWE. While varied adjustments of FWER for different types of analyses might be justified, papers with inconsistent usage across tests of HWE, LD and genetic differentiation did not present rationale for their FWER corrections. We also found a lack of documentation of HWE, LD and FWER corrections in studies. We encourage authors to report statistical tests and related FWER corrections, use FWER corrections consistently or justify their different methods in the same study.

opencc-zeroDec 2018View details →

Data from: Warming at the population level: effects on age structure, density, and generation cycles.

The impact of climate change on strongly age-structured populations is poorly understood, despite the central role of temperature in determining developmental rates in ectotherms. Here we examine the effect of warming and its interactions with resource availability on the population dynamics of the pyralid moth Plodia interpunctella, populations of which normally show generation cycles, a consequence of strong and asymmetric age-related competition. . Warming by 3°C above the standard culture temperature led to substantial changes in population density, age structure and population dynamics. Adult populations were some 50% larger in warmed populations, probably because the reduced fecundity associated with warming leads to reduced larval competition, allowing more larvae to develop to adulthood. Warming also interacted with resource availability to alter population dynamics, with the generation cycles typical of this species breaking down in the 30° populations when standard lab. diet was provided but not when a reduced nutrient poor diet was used. Warming by 6° led to either rapid extinction or the persistence of populations at low densities for the duration of the experiment. We conclude that even moderate warming can have considerable effects on population structure and dynamics, potentially leading to complete changes in dynamics in some cases. These results are particularly relevant given the large number of economically important species that exhibit generation cycling, in many cases arising from similar mechanisms to those operating in P. interpunctella.

opencc-zeroNov 2019View details →

Data from: ENIGMATIC HOOK-LIKE STRUCTURES IN MESOZOIC AMMONITES (SCAPHITIDAE)

In the last few decades, hook-like structures have been reported in the Mesozoic ammonite family Scaphitidae. Despite their exceptional preservation and debates about their function, no detailed reconstruction of them has yet been made. For the first time, we describe the composition and detailed morphology of these structures in the body chambers of six specimens of the Campanian ammonite Rhaeboceras halli (Meek and Hayden) using high resolution X-ray imaging. The hook-like structures are composed of a thin layer of brushite. The base of the hooks is open on one side forming an internal cavity, now filled with sediments. The tips of the hooks end in one or two cusps or, rarely, none at all. We used geometric morphometrics to capture the morphological disparity of the bicuspidate morphotypes comprising 98% of the hooks. Principal component analysis revealed chirality among the hooks and a cluster analysis (Gaussian mixture) recognized five main morphologies. Contrary to previous interpretation of these structures, we conclude that they are not radular teeth. They are much larger and more variable in size and shape than any known ammonite radulae and completely out of proportion with respect to the size of the jaw. The chirality, the hook-like shape, and the absence of a size relationship between the hooks and the body chambers in which they occur, lead us to propose that these hooks could represent elements of the brachial crown related to copulatory behavior. If so, these would be the first reported remnants of brachial crowns in ammonites.