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3,937 results for “number”
Estimating on the fly: the approximate number system in rufous hummingbirds (Selasphorus rufus)
<p></p><p>When presented with resources that differ in quantity, many animals use a numerosity system to discriminate between them. One taxonomically widespread system is the approximate number system. This is a numerosity system that allows the rapid evaluation of the number of objects in a group and which is regulated by Weber's Law. Here we investigated whether wild, free-living rufous hummingbirds (Selasphorus rufus) possess an approximate number system. The hummingbirds were presented with two experiments. In the first we investigated whether hummingbirds spontaneously chose an array containing more flowers than an alternate array. In the second we asked whether the hummingbirds could learn to use numerosity as a cue to which of two arrays contained the better reward. The birds did not spontaneously prefer an array containing more flowers. After minimal training, however, they learned to choose the more numerous array and could differentiate between arrays of five and seven flowers. These data support the presence of an approximate number system in the rufous hummingbird. It seems plausible that having such a system would enable much more efficient foraging in this species.</p><p></p>
Decisions of Number Guessing Game
<p>Subjects were asked to play a game named "Number Guessing". In the game subjects needed to figure out a integer random number in the range of 1-1000 by ask two types of question. A web-based applicaiton was deployed for data collection. Each subject's decisions (the chosen numbers) for searching targeted number were recorded. </p>
NanoString nCounter copy number variation assay
<p>The sex chromosomes often follow unusual evolutionary trajectories. In particular, the sex-limited Y and W chromosomes frequently exhibit a small but unusual gene content in numerous species, where many genes have undergone massive gene amplification. The reasons for this remain elusive with a number of recent studies implicating meiotic drive, sperm competition, genetic drift and gene conversion in the expansion of gene families. However, our understanding is primarily based on Y chromosome studies, and the W chromosome has been largely overlooked. Here, we conduct a comprehensive investigation into the abundance, variability, and evolution of ampliconic genes on the W both across and within avian species. We find a striking deficit of gene families on the duck W chromosome, as well as conservation in W-linked gene copy number across duck breeds, indicating that gene amplification may not be such a general feature of sex chromosome evolution as Y studies would initially suggest. Furthermore, we show that gene families have expanded independently in the duck and chicken. In particular, using contrasts between modern chicken and duck breeds selected for different female-specific selection regimes and their wild ancestors, we investigate the factors driving the expansion of HINTW, a prominent ampliconic gene family hypothesized to play a role in female reproduction and oogenesis. While we find that HINTW is ampliconic in both species, our results support a role of female-specific selection in driving gene amplification in the chicken but not the duck, challenging the assumption that HINTW is key for female fecundity across the avian phylogeny.</p>
TA B L E 2 Estimates of pairwise sequence divergence (cyt-b gene) in pale-bellied Micronycteris, where M. minuta is divided in three clades. Below the diagonal: pairwise distance using the Kimura 2-parameter model (percentage). On the diagonal: within-clade distance using the Kimura 2-parameter model (percentage). Above the diagonal: pairwise p-distance values. Number of specimens sequenced in parenthesis. *Chimeric sequence obtained from two paratypes (Siles et al., 2013). in Revision of the pale-bellied Micronycteris Gray, 1866 (Chiroptera, Phyllostomidae) with descriptions of two new species
TA B L E 2 Estimates of pairwise sequence divergence (cyt-b gene) in pale-bellied Micronycteris, where M. minuta is divided in three clades. Below the diagonal: pairwise distance using the Kimura 2-parameter model (percentage). On the diagonal: within-clade distance using the Kimura 2-parameter model (percentage). Above the diagonal: pairwise p-distance values. Number of specimens sequenced in parenthesis. *Chimeric sequence obtained from two paratypes (Siles et al., 2013).
Phyton scripts to generate Figure 9.1: Rarefaction curves of twenty biggest genera (i.e., having the most number of available genomes) from the global analysis of 1.2 million BGCs.
<p>Phyton scripts to generate Figure 9.1: Rarefaction curves of twenty biggest genera (i.e., having the most number of available genomes) from the global analysis of 1.2 million BGCs.</p>
Dataset for Testing the Number of Floor Detector Module
<p>Dataset for testing the performance of the number of floor detection model posted <a href="https://zenodo.org/record/4421613#.YBm3uuhKiUl">here</a>.</p>
Data from: Interannual variation in effective number of breeders and estimation of effective population size in long-lived iteroparous lake sturgeon (Acipenser fulvescens)
Quantifying interannual variation in effective adult breeding number (Nb) and relationships between Nb, effective population size (Ne), adult census size (N) and population demographic characteristics are important to predict genetic changes in populations of conservation concern. Such relationships are rarely available for long-lived iteroparous species like lake sturgeon (Acipenser fulvescens). We estimated annual Nb and generational Ne using genotypes from 12 microsatellite loci for lake sturgeon adults (n = 796) captured during ten spawning seasons and offspring (n = 3925) collected during larval dispersal in a closed population over 8 years. Inbreeding and variance Nb estimated using mean and variance in individual reproductive success derived from genetically identified parentage and using linkage disequilibrium (LD) were similar within and among years (interannual range of Nb across estimators: 41–205). Variance in reproductive success and unequal sex ratios reduced Nb relative to N on average 36.8% and 16.3%, respectively. Interannual variation in Nb/N ratios (0.27–0.86) resulted from stable N and low standardized variance in reproductive success due to high proportions of adults breeding and the species' polygamous mating system, despite a 40-fold difference in annual larval production across years (437–16 417). Results indicated environmental conditions and features of the species' reproductive ecology interact to affect demographic parameters and Nb/N. Estimates of Ne based on three single-sample estimators, including LD, approximate Bayesian computation and sibship assignment, were similar to annual estimates of Nb. Findings have important implications concerning applications of genetic monitoring in conservation planning for lake sturgeon and other species with similar life histories and mating systems.
Data from: Numbers and distribution of the Great Cormorant in Iceland: limitation at the regional and metapopulation level
We studied a metapopulation of great cormorant (Phalacrocorax carbo) in Iceland, using complete aerial censuses of nests in 25 years during 1975–2015. Age composition was estimated in 1998–2014 by ground surveys in September and February. Brood size was estimated from aerial photographs in 2007–2015. Weather, food, breeding habitat, and density were considered as explanatory variables when examining numerical and distributional changes in the cormorant metapopulation. In 1975–1990 total nest numbers changed little, very low numbers about 1992 were followed by an annual increase of 3.5% in 1994–2015. Total nest numbers were positively correlated with estimates of spawning stocks of cod and saithe and inversely related to the subpolar gyre index (SPG‐I). During the increase in 1994–2015, average colony size at first increased and then declined. Habitat use also changed: the proportion of nests on small rocky islets (skerries) at first declined, from 69% to 44% in 1995–2003 and then increased again to about 58% in 2012–2014. Habitat changes were probably a response to changed patterns of human disturbance. Breeding density, as nests per km2 sea <20 m deep, was rather uniform among five defined regions in 1975–1996. Thereafter, densities became much higher in two sheltered regions with kelp forests and in one mostly exposed region. A second exposed region remained low and in the third nest numbers declined markedly. Thus, carrying capacity was higher in sheltered regions where cormorant breeding had historically been depressed by human disturbance. Brood size varied little among regions but declined with the years from about 2.5 to 1.8. The proportion of juveniles in September (fecundity) declined in 1998–2015 from over 0.4 to 0.3 and was inversely correlated with year and nest numbers, if outlier years were excluded, suggesting resource limitation. Survival of juvenile cormorants in September–February was estimated at 0.471 ± 0.066 SE. Commercial fish stocks and climate indices were not correlated with the proportion of juveniles. Annual survival of adults (breeding and nonbreeding) was estimated from nest counts and age composition 1999–2014, as 0.850 ± 0.026 SE and showed no trend in 1998–2014. We conclude that the metapopulation of cormorants in Iceland was resource‐limited at two levels: fecundity at the regional and winter survival at the total level.
Data from: Estimating the number of pulses in a mass extinction
Most previous work on the Signor-Lipps effect has focused on testing whether taxa in a mass extinction went extinct simultaneously or gradually. However, many authors have proposed scenarios in which taxa go extinct in distinct pulses. Little methodology has been developed for quantifying characteristics of such pulsed extinction events. Here we introduce a method for estimating the number of pulses in a mass extinction, based on the positions of fossil occurrences in a stratigraphic section. Rather than using a hypothesis test and assuming simultaneous extinction as the default, we reframe the question by asking what number of pulses best explains the observed fossil record. Using a two-step algorithm, we are able to estimate not just the number of extinction pulses, but also a confidence level or posterior probability for each possible number of pulses. In the first step, we find the maximum likelihood estimate for each possible number of pulses. In the second step, we calculate the Akaike Information Criterion (AIC) and Bayesian Information Criterion (BIC) weights for each possible number of pulses, and then apply a k-Nearest Neighbor classifier to these weights. This gives us a vector of confidence levels for the number of extinction pulses — for instance, we might be 80% confident that there was a single extinction pulse, 15% confident that there were two pulses, and 5% confidence that there were three pulses. Equivalently, we can state that we are 95% confidence that the number of extinction pulses is 1 or 2. Using simulation studies, we show that the method performs well in a variety of situations, although it has difficulty in the case of decreasing fossil recovery potential, and it is most effective for small numbers of pulses unless the sample size is large. We demonstrate the method using a dataset of Late Cretaceous ammonites.
Data from: The jack-of-all-trades is master of none: a pathogen's ability to infect a greater number of host genotypes comes at a cost of delayed reproduction.
A trade-off between a pathogen's ability to infect many hosts and its reproductive capacity on each host genotype is predicted to limit the evolution of an expanded host range, yet few empirical results provide evidence for the magnitude of such trade-offs. Here, we test the hypothesis for a trade-off between the number of host genotypes that a fungal pathogen can infect (host genotype range) and its reproductive capacity on susceptible plant hosts. We utilized strains of the oat crown rust fungus that carried widely varying numbers of virulence (avr) alleles known to determine host genotype range. We quantified total spore production and the expression of four pathogen life history stages: infection efficiency, time until reproduction, pustule size, and spore production per pustule. In support of the trade-off hypothesis, we found that virulence level, the number of avr alleles per pathogen strain, was correlated with significant delays in the onset of reproduction and with smaller pustule sizes. Modeling from our results, we conclude that trade-offs have the capacity to constrain the evolution of host genotype range in local populations. In contrast, long term trends in virulence level suggests that the continued deployment of resistant host lines over wide regions of the USA has generated selection for increased host genotype range.
Data from: An artificial delay in emergence influences the number but not the fitness of adult emerald ash borer emerging from infested ash wood
Emerald ash borer, Agrilus planipennis Fairmaire (Buprestidae) is the most significant invasive forest pest in North America. Laboratory research on this species requires a source of adult and larval insects that are of the same fitness as those present in the wild. Production of adult emerald ash borer relies on flushing adults from logs which are subject to cold storage for some period prior to use. The effect of this storage on the number of insects emerging or the fitness of those that emerge has not been investigated. We subjected logs of EAB-infested white ash, Fraxinus americana L. to 7–14 month of cold storage and quantified the number of insects that emerged, time to emergence, and the body condition of adults as a measure of fitness. Body condition was evaluated using Soxhlet fat extraction and water weight. No published methods for Soxhlet fat extraction were available for this species so we developed extraction protocols. The number of insects emerging decreased with time, but fitness (i.e., fat content, water content) did not decrease. Time to emergence did increase but only in the longest-storage treatment while a comparison of male versus female emergence provides evidence for protandry in emerald ash borer. Rearing programs for emerald ash borer using wood from cold storage should adjust the amount used to produce a given number of insects but the quality of those individuals emerging will not be affected. We suggest that those insects that perished during storage were of lower quality when entering diapause and thus would serve as poor-quality host in rearing programs for natural enemies of emerald ash borer. These data also provide evidence for one pathway of introduction for emerald ash borer, suggesting that refrigeration in transit was required for EAB to remain viable and establish its beachhead in North America.
Data from: Numbers and population trends of large herbivores in Mole National Park, Ghana
<p>Mole National Park (MNP) is Ghana's oldest and largest wildlife preserve. Eight large herbivores were counted in four different seasons in 2013/2014 on transects covering 4.7% of the park to estimate their population sizes and trends after changes in park management; all species were more abundant than previously reported. Averaging counts across seasons, and including all age classes, gave an estimated population of 1595 elephants, which is likely to be a substantial proportion of the west African elephant population. Kob were the most abundant herbivore, with an estimated population of 9092, followed by bushbuck (6758), warthog (6247) and hartebeest (6039). Roan, buffalo and waterbuck population estimates were 4382, 4272 and 4140 respectively. The impact of widespread burning on herbivore populations is currently unknown, but probably helps maintain both numbers and diversity. While all herbivore populations were higher than previously estimated, it was hard to determine the extent of recent increases due to methodological limitations of earlier aerial surveys. However, the distribution of large herbivores seems to be little changed, suggesting that both numbers and distribution are still limited by poaching and seasonal water availability.</p>
Data from: The impact of reconstruction methods, phylogenetic uncertainty and branch lengths on inference of chromosome number evolution in American daisies (Melampodium, Asteraceae)
Chromosome number change (polyploidy and dysploidy) plays an important role in plant diversification and speciation. Investigating chromosome number evolution commonly entails ancestral state reconstruction performed within a phylogenetic framework, which is, however, prone to uncertainty, whose effects on evolutionary inferences are insufficiently understood. Using the chromosomally diverse plant genus Melampodium (Asteraceae) as model group, we assess the impact of reconstruction method (maximum parsimony, maximum likelihood, Bayesian methods), branch length model (phylograms versus chronograms) and phylogenetic uncertainty (topological and branch length uncertainty) on the inference of chromosome number evolution. We also address the suitability of the maximum clade credibility (MCC) tree as single representative topology for chromosome number reconstruction. Each of the listed factors causes considerable incongruence among chromosome number reconstructions. Discrepancies between inferences on the MCC tree from those made by integrating over a set of trees are moderate for ancestral chromosome numbers, but severe for the difference of chromosome gains and losses, a measure of the directionality of dysploidy. Therefore, reliance on single trees, such as the MCC tree, is strongly discouraged and model averaging, taking both phylogenetic and model uncertainty into account, is recommended. For studying chromosome number evolution, dedicated models implemented in the program ChromEvol and ordered maximum parsimony may be most appropriate. Chromosome number evolution in Melampodium follows a pattern of bidirectional dysploidy (starting from x = 11 to x = 9 and x = 14, respectively) with no prevailing direction.
Data from: A few large roads or many small ones? How to accommodate growth in vehicle numbers to minimise impacts on wildlife
Roads and vehicular traffic are among the most pervasive of threats to biodiversity because they fragmenting habitat, increasing mortality and opening up new areas for the exploitation of natural resources. However, the number of vehicles on roads is increasing rapidly and this is likely to continue into the future, putting increased pressure on wildlife populations. Consequently, a major challenge is the planning of road networks to accommodate increased numbers of vehicles, while minimising impacts on wildlife. Nonetheless, we currently have few principles for guiding decisions on road network planning to reduce impacts on wildlife in real landscapes. We addressed this issue by developing an approach for quantifying the impact on wildlife mortality of two alternative mechanisms for accommodating growth in vehicle numbers: (1) increasing the number of roads, and (2) increasing traffic volumes on existing roads. We applied this approach to a koala (Phascolarctos cinereus) population in eastern Australia and quantified the relative impact of each strategy on mortality. We show that, in most cases, accommodating growth in traffic through increases in volumes on existing roads has a lower impact than building new roads. An exception is where the existing road network has very low road density, but very high traffic volumes on each road. These findings have important implications for how we design road networks to reduce their impacts on biodiversity.
Too much is bad: increasing numbers of livestock and conspecifics reduce body mass in an avian scavenger
Individual traits such as body mass can serve as early warning signals of changes in the fitness prospects of animal populations facing environmental impacts. Here, taking advantage of a 19-year monitoring, we assessed how individual, population and environmental factors modulate long-term changes in the body mass of Canarian Egyptian vultures. Individual vulture body mass increased when primary productivity was highly variable, but decreased in years with a high abundance of livestock. We hypothesized that carcasses of wild animals, a natural food resource that can be essential for avian scavengers, could be more abundant in periods of weather instability but depleted when high livestock numbers lead to over-grazing. In addition, increasing vulture population numbers also negatively affect body mass suggesting density-dependent competition for food. Interestingly, the relative strength of individual, population and resource availability factors on body mass changed with age and territorial status, a pattern presumably shaped by differences in competitive abilities and/or age-dependent environmental knowledge and foraging skills. Our study supports that individual plastic traits may be extremely reliable tools to better understand the response of secondary consumers to current and future natural and human-induced environmental changes.
Data from: Reliable effective number of breeders/adult census size ratios in seasonal-breeding species: opportunity for integrative demographic inferences based on capture-mark-recapture data and multilocus genotypes
The ratio of the effective number of breeders (Nb) to the adult census size (Na), Nb/ Na, approximates the departure from the standard capacity of a population to maintain genetic diversity in one reproductive season. This information is relevant for assessing population status, understanding evolutionary processes operating at local scales and unraveling how life-history traits affect these processes. However, our knowledge on Nb/Na ratios in nature is limited because estimation of both parameters is challenging. The sibship frequency (SF) method is adequate for reliable Nb estimation because it is based on sibship and parentage reconstruction from genetic marker data, thereby providing demographic inferences that can be compared with field-based information. In addition, capture-mark-recapture (CMR) robust design methods are well suited for Na estimation in seasonal-breeding species. We used tadpole genotypes of three pond-breeding amphibian species (Epidalea calamita, Hyla molleri and Pelophylax perezi, n = 73-96 single-cohort tadpoles / species genotyped at 15-17 microsatellite loci) and candidate parental genotypes (n = 94-300 adults / species) to estimate Nb by the SF method. To assess the reliability of Nb estimates, we compared sibship and parentage inferences with field-based information and checked for the convergence of results in replicated subsampled analyses. Finally, we used CMR data from a 6-year monitoring program to estimate annual Na in the three species and calculate the Nb/Na ratio. Reliable ratios were obtained for E. calamita (Nb/Na = 0.18-0.28) and P. perezi (0.5), but in H. molleri Na could not be estimated and genetic information proved insufficient for reliable Nb estimation. Integrative demographic studies taking full advantage of SF and CMR methods can provide accurate estimates of the Nb/Na ratio in seasonal-breeding species. Importantly, the SF method provides results that can be readily evaluated for reliability. This represents a good opportunity for obtaining robust demographic inferences with wide applications for evolutionary and conservation research.
Data from: Timing and number of colonizations but not diversification rates affect diversity patterns in hemosporidian lineages on a remote oceanic archipelago
Parasite diversity on remote oceanic archipelagos is determined by the number and timing of colonizations, and in-situ diversification rate. In this study we compare intra-archipelago diversity of two hemosporidian parasite genera, Plasmodium and Leucocytozoon, infecting birds of the Mascarene archipelago. Despite the generally higher vagility of Plasmodium parasites, we report a much lower diversity of Plasmodium cytochrome-b haplotypes in the archipelago compared to Leucocytozoon. Using phylogenetic data, we find that this difference in diversity is consistent with differences in the timing and the number of colonizations, while rates of diversification do not vary significantly between the two genera. The prominence of immigration history in explaining current diversity patterns highlights the importance of historical contingencies in driving disparate biogeographic patterns in potentially harmful blood parasites infecting island birds.
Data from: Bayesian analysis of biogeography when the number of areas is large
Historical biogeography is increasingly studied from an explicitly statistical perspective, using stochastic models to describe the evolution of species range as a continuous-time Markov process of dispersal between and extinction within a set of discrete geographic areas. The main constraint of these methods is the computational limit on the number of areas that can be specified. We propose a Bayesian approach for inferring biogeographic history that extends the application of biogeographic models to the analysis of more realistic problems that involve a large number of areas. Our solution is based on a 'data-augmentation' approach, in which we first populate the tree with a history of biogeographic events that is consistent with the observed species ranges at the tips of the tree. We then calculate the likelihood of a given history by adopting a mechanis- tic interpretation of the instantaneous-rate matrix, which specifies both the exponential waiting times between biogeographic events and the relative probabilities of each biogeographic change. We develop this approach in a Bayesian framework, marginalizing over all possible biogeographic histories using Markov chain Monte Carlo (MCMC). Besides dramatically increasing the number of areas that can be accommodated in a biogeographic analysis, our method allows the parameters of a given biogeographic model to be estimated and different biogeographic models to be objectively compared. Our approach is implemented in the program, BayArea.
Data from: Bidirectional shifts in colony queen number in a socially polymorphic ant population
The breeding system of social organisms affects many important aspects of social life. Some species vary greatly in the number of breeders per group, but the mechanisms and selective pressures contributing to the maintenance of this polymorphism in social structure remain poorly understood. Here, we take advantage of a genetic dataset that spans 15 years to investigate the dynamics of colony queen number within a socially polymorphic ant species. Our study population of Formica selysi has single- and multiple-queen colonies. We found that the social structure of this species is somewhat flexible: on average, each year 3.2% of the single-queen colonies became polygynous, and conversely 1.4% of the multiple-queen colonies became monogynous. The annualized queen replacement rates were 10.3 and 11.9% for single- and multiple-queen colonies, respectively. New queens were often but not always related to previous colony members. At the population level, the social polymorphism appeared stable. There was no genetic differentiation between single- and multiple-queen colonies at eight microsatellite loci, suggesting ongoing gene flow between social forms. Overall, the regular and bidirectional changes in queen number indicate that social structure is a labile trait in F. selysi, with neither form being favoured within a time-frame of 15 years.
Data from: Acknowledging differences: number, characteristics, and distribution of marine benthic communities along Taiwan coast
Our knowledge of the ability of coral reefs to face contemporary challenges disregards the wide variety of benthic communities (BCs) that could be associated with contrasted dynamics when facing stressors. Accordingly, this study investigates the number, characteristics, and distribution of BCs responsible for the development of coastal three‐dimensional structures in Taiwan. A total of 89 transects among three regions (north, east, and south) and two depths (−10 and −40 m) were characterized using a morpho‐functional categorization of benthic organisms. Using an unsupervised learning algorithm, k‐means cluster, an optimal number of k groups were identified among transects in order to minimize total intra‐group variance and represent a first level of organization, mirroring the number of BCs. Each BC was then described into prevailing categories and typified by an association with significant indicator groups. Their distributions were further examined and tested among regions and depths. Seven BCs were identified as having different composition and indicator categories. Their distributions suggest that, while sea surface temperature and light regime may be associated with a panel of available BCs, local conditions may have the final say on whether a BC eventually thrives at a given location. Overall, this study proposes an innovative and simple analytical framework for acknowledging differences among BCs. Our results encourage greater consideration of these shades in coral reef ecology studies, as they could conceal a variety of roles and dynamics important for the conservation of these endangered ecosystems.
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Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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