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Data from: Synonymous genetic variation in natural isolates of Escherichia coli does not predict where synonymous substitutions occur in a long-term experiment
Synonymous genetic differences vary by more than 20-fold among genes in natural isolates of Escherichia coli. One hypothesis to explain this heterogeneity is that genes with high levels of synonymous variation mutate at higher rates than genes with low synonymous variation. If so, then one would expect to observe similar mutational patterns in evolution experiments. In fact, however, the pattern of synonymous substitutions in a long-term evolution experiment with E. coli does not support this hypothesis. In particular, the extent of synonymous variation across genes in that experiment does not reflect the variation observed in natural isolates of E. coli. Instead, gene length alone predicts with high accuracy the prevalence of synonymous changes in the experimental populations. We hypothesize that patterns of synonymous variation in natural E. coli populations are instead caused by differences across genomic regions in their effective population size that, in turn, reflect different histories of recombination, horizontal gene transfer, selection, and population structure.
Data from: Booming far: the long-range vocal strategy of a lekking bird
The pressures of selection acting on transmission of information by acoustic signals are particularly high in long-distance communication networks. Males of the North African houbara bustard (Chlamydotis undulata undulata) produce extremely low-frequency vocalizations called 'booms' as a component of their courtship displays. These displays are performed on sites separated by a distance of on average 550 m, constituting exploded leks. Here, we investigate the acoustic features of booms involved in species-specific identity. We first assessed the modifications of acoustic parameters during boom transmission at long range within the natural habitat of the species, finding that the frequency content of booms was reliably transmitted up to 600 m. Additionally, by testing males' behavioural responses to playbacks of modified signals, we found that the presence of the second harmonic and the frequency modulation are the key parameters for species identification, and also that a sequence of booms elicited stronger responses than a single boom. Thus, the coding-decoding process relies on redundant and propagation-resistant features, making the booms particularly well adapted for the long-range transmission of information between males. Moreover, by experimentally disentangling the presentation of visual and acoustic signals, we showed that during the booming phase of courtship, the two sensory modalities act in synergy. The acoustic component is dominant in the context of intra-sexual competition. While the visual component is not necessary to induce agonistic response, it acts as an amplifier and reduces the time of detection of the signaller. The utilization of these adaptive strategies allows houbara males to maximize the active space of vocalizations emitted in exploded leks.
Data from: Maternal age at birth shapes offspring life-history trajectory across generations in long-lived Asian elephants
1. Advanced maternal age at birth can have pronounced consequences for offspring health, survival and reproduction. If carried over to the next generation, such fitness effects could have important implications for population dynamics and the evolution of ageing, but these remain poorly understood. While many laboratory studies have investigated maternal age effects, relatively few studies have been conducted in natural populations, and they usually only present a "snapshot" of an offspring's lifetime. 2. In the present study, we focus on how maternal age influences offspring life-history trajectories and performance in a long-lived mammal. 3. We use a multigenerational demographic dataset of semi-captive Asian elephants to investigate maternal age effects on several offspring life-history traits: condition, reproductive success, and overall survival. 4. We show that offspring born to older mothers display reduced overall survival but higher reproductive success, and reduced survival of their own progeny. Our results show evidence of a persistent effect of maternal age on fitness across generations in a long-lived mammal. 5. By highlighting transgenerational effects on the fitness of the next generation associated with maternal age, the present study helps increase our understanding of factors contributing to individual variation in ageing rates and fitness.
Data from: Long-term effect of social interactions on behavioral plasticity and lifetime mating success
Behavioral traits often change over an individual's lifetime. Experience, physiological senescence, and age-dependent differences in optimal behavior can, in theory, all cause longitudinal behavioral changes. Yet most studies of behavioral plasticity and selection on behavior focus on short-term population-level responses to social factors such as conspecific density or sex ratio. Longer-term effects of social interactions on individual behavior have rarely been tested. Here we tested these effects by exposing male water striders (Hemiptera: Gerridae) to two different social conditions throughout their lifetime; we call these the nonsocial and social treatments. We then measured each male's lifetime mating success and individual behavioral plasticity by observing four different behaviors (exploring a novel environment, dispersal ability, sex-recognition sensitivity, and tendency to remount a resistant female after being dislodged) every 2 weeks. The social environment influenced individual variation in behavioral plasticity as well as population-level behavioral plasticity. Moreover, when we calculated linear selection gradients of individual behavioral traits and their plasticities on lifetime mating success, male remounting tendency and individual plasticity in exploration ability were likely to be the most important factors explaining variation in male lifetime mating success. In conclusion, the variation in social interactions throughout an individual's lifetime contributes to the individual variation in behavioral plasticity, which can significantly affect a male's lifetime fitness.
Data from: Reconstructing the phylogenetic history of long-term effective population size and life-history traits using patterns of amino acid replacement in mitochondrial genomes of mammals and birds
The nearly neutral theory, which proposes that most mutations are deleterious or close to neutral, predicts that the ratio of nonsynonymous over synonymous substitution rates (dN/dS), and potentially also the ratio of radical over conservative amino acid replacement rates (Kr/Kc), are negatively correlated with effective population size. Previous empirical tests, using life-history traits (LHT) such as body-size or generation-time as proxies for population size, have been consistent with these predictions. This suggests that large-scale phylogenetic reconstructions of dN/dS or Kr/Kc might reveal interesting macroevolutionary patterns in the variation in effective population size among lineages. In this work, we further develop an integrative probabilistic framework for phylogenetic covariance analysis introduced previously, so as to estimate the correlation patterns between dN/dS, Kr/Kc, and three LHT, in mitochondrial genomes of birds and mammals. Kr/Kc displays stronger and more stable correlations with LHT than does dN/dS, which we interpret as a greater robustness of Kr/Kc, compared with dN/dS, the latter being confounded by the high saturation of the synonymous substitution rate in mitochondrial genomes. The correlation of Kr/Kc with LHT was robust when controlling for the potentially confounding effects of nucleotide compositional variation between taxa. The positive correlation of the mitochondrial Kr/Kc with LHT is compatible with previous reports, and with a nearly neutral interpretation, although alternative explanations are also possible. The Kr/Kc model was finally used for reconstructing life-history evolution in birds and mammals. This analysis suggests a fairly large-bodied ancestor in both groups. In birds, life-history evolution seems to have occurred mainly through size reduction in Neoavian birds, whereas in placental mammals, body mass evolution shows disparate trends across subclades. Altogether, our work represents a further step toward a more comprehensive phylogenetic reconstruction of the evolution of life-history and of the population-genetics environment.
Data from: A long PCR based approach for DNA enrichment prior to next-generation sequencing for systematic studies
Premise of the study: We present an alternative approach for molecular systematic studies that combines long PCR and next-generation sequencing (NGS). Our approach can be used to generate templates from any DNA source for NGS. Here we test our approach by amplifying complete chloroplast genomes and we present a set of 58 potentially universal primers for angiosperms to do so. Additionally, this approach is likely to be particularly useful for nuclear regions. Methods and Results: Chloroplast genomes of 30 species across angiosperms were amplified to test our approach. Amplification success varied depending on whether PCR conditions were optimized for a given taxon. To further test our approach, some amplicons were sequenced on an Illumina HiSeq 2000. Conclusions: Although here we tested this approach by sequencing plastomes, long PCR amplicons could be generated using DNA from any genome, expanding the possibilities of this approach for molecular systematic studies.
Data from: Cultural flies: conformist social learning in fruit flies predicts long-lasting mate-choice traditions
Despite theoretical justification for the evolution of animal culture, there is still scant empirical evidence for it beyond mammals and birds, and we still know little about the process of cultural inheritance. Here, we propose a mechanism-driven definition of animal culture and test it in the fruit fly. We found that fruit flies have five cognitive capacities that enable them to transmit mating preferences culturally across generations, potentially fostering persistent traditions (the main marker of culture) in mating preference. A transmission chain experiment validates a model of the emergence of local traditions indicating that such social transmission may lead initially neutral traits to become adaptive, hence strongly selecting for copying and conformity, a situation that, although suggested decades ago, still had little empirical support.
Data from: Simulated moult reduces flight performance but overlap with breeding does not affect breeding success in a long-distance migrant
1. Long-distance migrants are time-constrained as they need to incorporate many annual cycle stages within a year. Migratory passerines moult in the short interval between breeding and migration. To widen this interval, moult may start while still breeding, but this results in flying with moulting wings when food provisioning. 2. We experimentally simulated wing gaps in breeding male pied flycatchers by plucking 2 primary feathers from both wings. We quantified the nest visitations of both parents, proportion of high-quality food brought to the nestlings and adults and nestlings condition. Differences in oxidative damage caused by a possible reduction in flight efficiency were measured in amounts of ROMs and OXY in the blood. We also measured how flight performance was affected with recordings of the male`s escape flight using high-speed cameras. Finally, we collected data on adult survival, clutch size and laying date in the following year. 3. "Plucked" males travelled a 5% shorter distance per wingbeat, showing that our treatment reduced flight performance. In line with this, "plucked" males visited their nests less often. Females of "plucked" males, however, visited the nest more often than controls, and fully compensated their partner's reduced visitation rate. As a result, there were no differences between treatments in food quality brought to the nest, adult or chick mass or number of successfully fledged chicks. Males did not differ in their oxidative damage or local survival to the following year. In contrast, females paired with plucked males tended to return less often to breed in the next year in comparison to controls, but this difference was not significant. For the birds that did return there were no effects on breeding. 5. Our results reveal that wing gaps in male pied flycatchers reduce their flight performance, but when it occurs during breeding they prioritise their future reproduction by reducing parental care. As a result, there is no apparent detriment to their condition during breeding. Because non-moulting females are able to compensate their partner's reduced care, there is also no immediate costs to the offspring, but females may pay the cost suffering from a reduced survival.
Data from: Food availability and predation risk, rather than intrinsic attributes are the main factors shaping the reproductive decisions of a long-lived predator
Deciphering the causes of variation in reproductive success is a fundamental issue in ecology, as the number of offspring produced is an important driver of individual fitness and population dynamics. Little is known however, about how different factors interact to drive variation in reproduction, such as whether an individual's response to extrinsic conditions (e.g. food availability or predation) varies according to its intrinsic attributes (e.g. age, previous allocation of resources towards reproduction). We used 29 years of reproductive data from marked female tawny owls and natural variation in food availability (field vole) and predator abundance (northern goshawk) to quantify the extent to which extrinsic and intrinsic factors interact to influence owl reproductive traits (breeding propensity, clutch size and nest abandonment). Extrinsic and intrinsic factors appeared to interact to affect breeding propensity (which accounted for 83% of the variation in owl reproductive success). Breeding propensity increased with vole density, although increasing goshawk abundance reduced the strength of this relationship. Owls became slightly more likely to breed as they aged, although this was only apparent for individuals who had fledged chicks the year before. Owls laid larger clutches when food was more abundant. When owls were breeding in territories less exposed to goshawk predation, 99.5% of all breeding attempts reached the fledging stage. In contrast, the probability of breeding attempts reaching the fledging stage in territories more exposed to goshawk predation depended on the amount of resources an owl had already allocated towards reproduction (averaging 87.7% for owls with clutches of 1-2 eggs compared to 97.5% for owls with clutches of 4-6 eggs). Overall, our results suggested that changes in extrinsic conditions (predominantly food availability, but also predator abundance) had the greatest influence on owl reproduction. In response to deteriorating extrinsic conditions (fewer voles and more goshawks) owls appeared to breed more frequently, but allocated fewer resources per breeding attempt. However, intrinsic attributes also appeared to have a relatively small influence on how an individual responded to variation in extrinsic conditions, which indicates that reproductive decisions were shaped by a complex series of extrinsic and intrinsic trade-offs.
Data from: Large chromosomal rearrangements during a long-term evolution experiment with Escherichia coli
Large-scale rearrangements may be important in evolution because they can alter chromosome organization and gene expression in ways not possible through point mutations. In a long-term evolution experiment, twelve Escherichia coli populations have been propagated in a glucose-limited environment for over 25 years. We used whole-genome mapping (optical mapping) combined with genome sequencing and PCR analysis to identify the large-scale chromosomal rearrangements in clones from each population after 40,000 generations. A total of 110 rearrangement events were detected, including 82 deletions, 19 inversions, and 9 duplications, with lineages having between 5 and 20 events. In three populations, successive rearrangements impacted particular regions. In five populations, rearrangements affected over a third of the chromosome. Most rearrangements involved recombination between insertion sequence (IS) elements, illustrating their importance in mediating genome plasticity. Two lines of evidence suggest that at least some of these rearrangements conferred higher fitness. First, parallel changes were observed across the independent populations, with ~65% of the rearrangements affecting the same loci in at least two populations. For example, the ribose-utilization operon and the manB-cpsG region were deleted in 12 and 10 populations, respectively, suggesting positive selection, and this inference was previously confirmed for the former case. Second, optical maps from clones sampled over time from one population showed that most rearrangements occurred early in the experiment, when fitness was increasing most rapidly. However, some rearrangements likely occur at high frequency and may have simply hitchhiked to fixation. In any case, large-scale rearrangements clearly influenced genomic evolution in these populations.
Data from: Is telomere length a molecular marker of individual quality? insights from a long-lived bird
1. In wild vertebrates, some individuals survive and reproduce better than others and this has led to the concept of individual quality. Despite its importance when studying ecological processes and life-history trade-offs, measuring individual quality is complex because individuals must be followed during a large part of their life. 2. Recently, telomere biology has been successfully brought into ecology and telomere length has been suggested to be a promising molecular tool to evaluate individual quality in wild vertebrates ('the telomere – individual quality hypothesis'). 3. In this study, we tested this hypothesis in a long-lived species, the Black-browed albatross (Thalassarche melanophrys) by simultaneously measuring telomere length and several potential complementary phenotypic proxies of individual quality in a single year. In addition, we followed the return rate and the reproductive performance of these same albatrosses for a decade. 4. We found that long telomeres were associated with several markers of high individual quality (foraging behaviour, body size, and stress hormone levels). Furthermore, we found that a single measure of telomere length could predict future offspring productivity, for at least several years following telomere measurement (better productivity being associated with longer telomeres). 5. Altogether, these results support the 'telomere – individual quality hypothesis' and suggest that telomere length can be useful to estimate individual quality in long-lived seabirds.
Data from: An approach to estimate short-term, long-term, and reaction norm repeatability
Evolutionary ecologists increasingly study reaction norms that are expressed repeatedly within the same individual's lifetime. For example, foragers continuously alter anti-predator vigilance in response to moment-to-moment changes in predation risk. Variation in this form of plasticity occurs both among and within individuals. Among-individual variation in plasticity (individual by environment interaction or I×E) is commonly studied; by contrast, despite increasing interest in its evolution and ecology, within-individual variation in phenotypic plasticity is not. We outline a study design based on repeated measures and a multi-level extension of random regression models that enables quantification of variation in reaction norms at different hierarchical levels (such as among- and within-individuals). The approach enables the calculation of repeatability of reaction norm intercepts (average phenotype) and slopes (level of phenotypic plasticity); these indices are not specific to measurement or scaling and are readily comparable across data sets. The proposed study design also enables calculation of repeatability at different temporal scales (such as short- and long-term repeatability) thereby answering calls for the development of approaches enabling scale-dependent repeatability calculations. We introduce a simulation package in the R statistical language to assess power, imprecision and bias for multi-level random regression that may be utilised for realistic datasets (unequal sample sizes across individuals, missing data, etc). We apply the idea to a worked example to illustrate its utility. We conclude that consideration of multi-level variation in reaction norms deepens our understanding of the hierarchical structuring of labile characters and helps reveal the biology in heterogeneous patterns of within-individual variance that would otherwise remain 'unexplained' residual variance.
Data from: Genetic uniformity and long-distance clonal dispersal in the invasive androgenetic Corbicula clams
The clam genus Corbicula is an interesting model system to study the evolution of reproductive modes since it includes both sexual and asexual (androgenetic) lineages. While the sexual populations are restricted to the native Asian areas, the androgenetic lineages are widely distributed being also found in America and Europe where they form a major aquatic invasive pest. We investigated the genetic diversity of native and invasive Corbicula populations through a worldwide sampling. The use of mitochondrial and nuclear (microsatellite) markers revealed an extremely low diversity in the invasive populations with only four, undiversified, genetic lineages distributed across Europe and America. On the contrary, in the native populations, both sexual and androgenetic lineages exhibited much higher genetic diversity. Remarkably the most abundant and widely distributed invasive forms, the so-called form A and form R found in America and Europe respectively, are fixed for the same single COI (cytochrome c oxydase subunit I) haplotype and same multilocus genotype. This suggests that form R, observed in Europe since the 1980s, derived directly from form A found in America since the 1920s. In addition, this form shares alleles with some Japanese populations indicating a Japanese origin for this invasive lineage. Finally, our study suggests that few androgenetic Corbicula individuals successfully invaded the non-native range and then dispersed clonally. This is one striking case of genetic paradox raising the issue of invasive and evolutionary success of genetically undiversified populations.
Impact of prognostic nutritional index on long-term outcomes in patients with breast cancer
<p>raw data for PNI</p>
FIGURE 2 in Long-legged flies (Diptera: Dolichopodidae) in the collection of the Natal Museum: A review of C. H. Curran's types, new synonyms, and new combinations
FIGURE 2. Acropsilus vorax (Curran), hypopygium, left lateral view. Scale bar: 0.1 mm
FIGURE 1 in Long-legged flies (Diptera: Dolichopodidae) in the collection of the Natal Museum: A review of C. H. Curran's types, new synonyms, and new combinations
FIGURE 1. Acropsilus vorax (Curran), wing. Scale bar: 0.5 mm.
Figure 2 in Description of a new long-snouted beaked whale from the Late Miocene of Denmark: evolution of suction feeding and sexual dimorphism in the Ziphiidae (Cetacea: Odontoceti)
Figure 2. Reconstruction of MSM1001x (holotype), Dagonodum mojnum gen. nov., sp. nov., dorsal view: A, skull; B, mandible. Dotted lines correspond to reconstructed areas. Scale bar = 100 mm.
Figure 19 in Description of a new long-snouted beaked whale from the Late Miocene of Denmark: evolution of suction feeding and sexual dimorphism in the Ziphiidae (Cetacea: Odontoceti)
Figure 19. Boxplot of the ratio AL/TL between the length from the posterior end of the alveolar groove to the posterior end of the mandible (AL) and the total length of the mandible (TL). The circled data correspond to the two long-snouted fossil ziphiids Messapicetus gregarius and Ninoziphius platyrostris, the most similar in size to Dagonodum mojnum gen. nov., sp. nov.
Figure 17 in Description of a new long-snouted beaked whale from the Late Miocene of Denmark: evolution of suction feeding and sexual dimorphism in the Ziphiidae (Cetacea: Odontoceti)
Figure 17. The most parsimonious tree obtained with maximum of parsimony to decipher the relationships of MSM1001x, Dagonodum mojnum gen. nov., sp. nov., among Ziphiidae. Tree length = 215; consistency index = 0.474; retention index = 0.698. Numbers above the branches = bootstrap values; numbers below the branches = absolute Bremer support values. Values of Bootstrap under 50% are not presented. †Fossil species.
Figure 1 in Description of a new long-snouted beaked whale from the Late Miocene of Denmark: evolution of suction feeding and sexual dimorphism in the Ziphiidae (Cetacea: Odontoceti)
Figure 1. Current extension of the Gram Formation in Denmark (shaded area). The type locality is situated in the Gram claypit, 1.5 km north of Gram. Modified from Rasmussen (1966).
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
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.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.