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9,882 results for “Scale”
Data from: Broad-scale variation in sexual dichromatism in songbirds is not explained by sex differences in exposure to predators during incubation
The evolution of sexual dichromatism provoked one of the greatest disagreements between Charles Darwin and Alfred Russel Wallace. According to Darwin the main driving force is sexual selection, whereby choosy females prefer showy males, leading to the evolution of conspicuous male plumage. On the other hand, Wallace suggested that dichromatism may arise because nest predation favors more cryptic females. To test the role of natural selection in the evolution of dichromatism we combined quantitative data on differences in parental share in nest attentiveness (representing the strength of natural selection on males vs. females) with spectrophotometric measurements of dichromatism in 412 species of songbirds from 69 families. We expected to find stronger dichromatism in open-nesting species with more divergent parental roles and in body parts exposed during incubation. Dichromatism was not related to the differences in parental share during incubation, but it was most pronounced in lekking species, migrants, and small species. Our results thus suggest that Wallace's hypothesis is not able to explain broad-scale variation in the dichromatism of songbirds, but point to a role for sexual selection, mutual mate choice, and migration strategy in shaping the extraordinary variation in dichromatism exhibited by songbirds.
Data from: Drosophila embryogenesis scales uniformly across temperature in developmentally diverse species
Temperature affects both the timing and outcome of animal development, but the detailed effects of temperature on the progress of early development have been poorly characterized. To determine the impact of temperature on the order and timing of events during Drosophila melanogaster embryogenesis, we used time-lapse imaging to track the progress of embryos from shortly after egg laying through hatching at seven precisely maintained temperatures between 17.5°C and 32.5°C. We employed a combination of automated and manual annotation to determine when 36 milestones occurred in each embryo. D. melanogaster embryogenesis takes 33 hours at 17.5°C, and accelerates with increasing temperature to a low of 16 hours at 27.5°C, above which embryogenesis slows slightly. Remarkably, while the total time of embryogenesis varies over two fold, the relative timing of events from cellularization through hatching is constant across temperatures. To further explore the relationship between temperature and embryogenesis, we expanded our analysis to cover ten additional Drosophila species of varying climatic origins. Six of these species, like D. melanogaster, are of tropical origin, and embryogenesis time at different temperatures was similar for them all. D. mojavensis, a sub-tropical fly, develops slower than the tropical species at lower temperatures, while D. virilis, a temperate fly, exhibits slower development at all temperatures. The alpine sister species D. persimilis and D. pseudoobscura develop as rapidly as tropical flies at cooler temperatures, but exhibit diminished acceleration above 22.5°C and have drastically slowed development by 30°C. Despite ranging from 13 hours for D. erecta at 30°C to 46 hours for D. virilis at 17.5°C, the relative timing of events from cellularization through hatching is constant across all species and temperatures examined here, suggesting the existence of a previously unrecognized timer controlling the progress of embryogenesis that has been tuned by natural selection as each species diverges.
Data from: Direct and indirect genetic and fine-scale location effects on breeding date in song sparrows
Quantifying direct and indirect genetic effects of interacting females and males on variation in jointly expressed life-history traits is central to predicting microevolutionary dynamics. However, accurately estimating sex-specific additive genetic variances in such traits remains difficult in wild populations, especially if related individuals inhabit similar fine-scale environments. Breeding date is a key life-history trait that responds to environmental phenology and mediates individual and population responses to environmental change. However, no studies have estimated female (direct) and male (indirect) additive genetic and inbreeding effects on breeding date, and estimated the cross-sex genetic correlation, while simultaneously accounting for fine-scale environmental effects of breeding locations, impeding prediction of microevolutionary dynamics. We fitted animal models to 38 years of song sparrow (Melospiza melodia) phenology and pedigree data to estimate sex-specific additive genetic variances in breeding date, and the cross-sex genetic correlation, thereby estimating the total additive genetic variance while simultaneously estimating sex-specific inbreeding depression. We further fitted three forms of spatial animal model to explicitly estimate variance in breeding date attributable to breeding location, overlap among breeding locations and spatial autocorrelation. We thereby quantified fine-scale location variances in breeding date and quantified the degree to which estimating such variances affected the estimated additive genetic variances. The non-spatial animal model estimated nonzero female and male additive genetic variances in breeding date (sex-specific heritabilities: 0·07 and 0·02, respectively) and a strong, positive cross-sex genetic correlation (0·99), creating substantial total additive genetic variance (0·18). Breeding date varied with female, but not male inbreeding coefficient, revealing direct, but not indirect, inbreeding depression. All three spatial animal models estimated small location variance in breeding date, but because relatedness and breeding location were virtually uncorrelated, modelling location variance did not alter the estimated additive genetic variances. Our results show that sex-specific additive genetic effects on breeding date can be strongly positively correlated, which would affect any predicted rates of microevolutionary change in response to sexually antagonistic or congruent selection. Further, we show that inbreeding effects on breeding date can also be sex specific and that genetic effects can exceed phenotypic variation stemming from fine-scale location-based variation within a wild population.
Data from: Quantifying pursuit-diving seabirds' associations with fine-scale physical features in tidal stream environments
The rapid increase in the number of tidal stream turbine arrays will create novel and unprecedented levels of anthropogenic activity within habitats characterized by horizontal current speeds exceeding 2 ms−1. However, the potential impacts on pursuit-diving seabirds exploiting these tidal stream environments remain largely unknown. Identifying similarities between the fine-scale physical features (100s of metres) suitable for array installations, and those associated with foraging pursuit-diving seabirds, could identify which species are most vulnerable to either collisions with moving components, or displacement from these installations. A combination of vessel-based observational surveys, Finite Volume Community Ocean Model outputs and hydroacoustic seabed surveys provided concurrent measures of foraging distributions and physical characteristics at a fine temporal (15 min) and spatial (500 m) resolution across a tidal stream environment suitable for array installations, during both breeding and non-breeding seasons. These data sets were then used to test for associations between foraging pursuit-diving seabirds (Atlantic puffins Fratercula arctica, black guillemots Cepphus grylle, common guillemots Uria aalge, European shags Phalacrocorax aristotelis) and physical features. These species were associated with areas of fast horizontal currents, slow horizontal currents, high turbulence, downward vertical currents and also hard–rough seabeds. The identity and strength of associations differed among species, and also within species between seasons, indicative of interspecific and intraspecific variations in habitat use. However, Atlantic puffins were associated particularly strongly with areas of fast horizontal currents during breeding seasons, and European shags with areas of rough–hard seabeds and downward vertical currents during non-breeding seasons. Synthesis and applications. Atlantic puffins' strong association with fast horizontal current speeds indicates that they are particularly likely to interact with installations during breeding seasons. Any post-installation monitoring and mitigation measures should therefore focus on this species and season. The multi-species associations with high turbulence and downward vertical currents, which often coincide with fast horizontal current speeds, also highlight useful pre-installation mitigation measures via the omission of devices from these areas, reducing the overall likelihood of interactions. Environmental impact assessments (EIA) generally involve once-a-month surveys across 2-year periods. However, the approaches used in this study show that more focussed surveys can greatly benefit management strategies aiming to reduce the likelihood of negative impacts by facilitating the development of targeted mitigation measures. It is therefore recommended that these approaches contribute towards EIA within development sites.
Data from: Multi-scale model of CRISPR-induced coevolutionary dynamics: diversification at the interface of Lamarck and Darwin
The CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) system is a recently discovered type of adaptive immune defense in bacteria and archaea that functions via directed incorporation of viral and plasmid DNA into host genomes. Here, we introduce a multi-scale model of dynamic coevolution between hosts and viruses in an ecological context that incorporates CRISPR immunity principles. We analyze the model to test whether and how CRISPR immunity induces host and viral diversification and the maintenance of many coexisting strains. We show that hosts and viruses coevolve to form highly diverse communities. We observe the punctuated replacement of extant strains, so that populations have very low similarity compared over the long term. However in the short term, we observe evolutionary dynamics consistent with both incomplete selective sweeps of novel strains and the recurrence of previously rare strains. Coalitions of multiple dominant host strains are predicted to arise because host strains can have nearly identical immune phenotypes mediated by CRISPR defense albeit with different genotypes. We close by discussing how our explicit eco-evolutionary model of CRISPR immunity can help guide efforts to understand the drivers of diversity seen in microbial communities where CRISPR systems are active.
Data from: Local biotic environment shapes the spatial scale of bacteriophage adaptation to bacteria
The ecological, epidemiological, and evolutionary consequences of host-parasite interactions are critically shaped by the spatial scale at which parasites adapt to hosts. The scale of interaction between hyperparasites and their parasites is likely to be influenced by the host of the parasite and potentially likely to differ among within-host environments. Here we examine the scale at which bacteriophages adapt to their host bacteria by studying natural isolates from the surface or interior of horse chestnut leaves. We find that phages are more infective to bacteria from the same tree relative to those from other trees but do not differ in infectivity to bacteria from different leaves within the same tree. The results suggest that phages target common bacterial species, including an important plant pathogen, within plant host tissues; this result has important implications for therapeutic phage epidemiology. Furthermore, we show that phages from the leaf interior are more infective to their local hosts than phages from the leaf surface are to theirs, suggesting either increased resistance of bacteria on the leaf surface or increased phage adaptation within the leaf. These results highlight that biotic environment can play a key role in shaping the spatial scale of parasite adaptation and influencing the outcome of coevolutionary interactions.
Data from: Allometric scaling of long-distance seed dispersal by migratory birds
Migratory birds are often suggested to be important vectors for long-distance dispersal (LDD) of plant and animal propagules. The scale of such dispersal events (hundreds to thousands of kilometers) can influence landscape-level biological processes and species distributions. However, the few vector species studied and the lack of proper integration of their migratory movement in models of LDD has precluded the study of their potential as long-distance biotic dispersers. By means of a mechanistic model parameterized with empirical data, we first investigated the properties of seed dispersal curves generated by migratory birds and then analyzed the effect of bird size on model parameters and consequent seed dispersal patterns. Seed dispersal curves showed in most cases large and heavy tails, resulting in relatively frequent LDD (up to 3.5% of dispersal distances longer than 100 km). Bird size mediated trade-offs between bird movement and seed retention time that, in turn, determined seed dispersal patterns and the potential of each bird species as an LDD vector. Our modeling framework builds on a mechanistic understanding of seed dispersal by migratory birds and may thus be a useful tool to estimate the scale and frequency of bird-mediated, large-scale transport of native, invasive, and pathogenic organisms.
Data from: Large-scale natural disturbance alters genetic population structure of the sailfin molly, Poecilia latipinna
Many inferences about contemporary rates of gene flow are based on the assumption that the observed genetic structure among populations is stable. Recent studies have uncovered several cases in which this assumption is tenuous. Most of those studies have focused on the effects that regular environmental fluctuations can have on genetic structure and gene flow patterns. Occasional catastrophic disturbances could also alter either the distribution of habitat or the spatial distribution of organisms in a way that affects population structure. However, evidence of such effects is sparse in the literature because it is difficult to obtain. Hurricanes, in particular, have the potential to exert dramatic effects on population structure of organisms found on islands or coral reefs or in near shore and coastal habitats. Here we draw on a historic genetic data set and new data to suggest that the genetic structure of sailfin molly (Poecilia latipinna) populations in north Florida was altered dramatically by an unusually large and uncommon type of storm surge associated with Hurricane Dennis in 2005. We compare the spatial pattern of genetic variation in these populations after Hurricane Dennis to the patterns described in an earlier study in this same area. We use comparable genetic data from another region of Florida, collected in the same two periods, to estimate the amount of change expected from typical temporal variation in population structure. The comparative natural history of sailfin mollies in these two regions indicates that the change in population structure produced by the storm surge is not the result of many local extinctions with recolonization from a few refugia but emerged from a pattern of mixing and redistribution.
Drivers of amphibian population dynamics and asynchrony at local and regional scales
<ol> <li>Identifying the drivers of population fluctuations in spatially distinct populations remains a significant challenge for ecologists. Whereas regional climatic factors may generate population synchrony (i.e., the Moran effect), local factors including the level of density-dependence may reduce the level of synchrony. Although divergences in the scaling of population synchrony and spatial environmental variation have been observed, the regulatory factors that underlie such mismatches are poorly understood.</li> <li>Few previous studies have investigated how density-dependent processes and population-specific responses to weather variation influence spatial synchrony at both local and regional scales. We addressed this issue in a pond-breeding amphibian, the great crested newt (<i>Triturus cristatus</i>). We used capture-recapture data collected through long-term surveys in five <i>T. cristatus</i> populations in Western Europe.</li> <li>In all populations – and subpopulations within metapopulations – population size, annual survival and recruitment fluctuated over time. Likewise, there was considerable variation in these demographic rates between populations and within metapopulations. These fluctuations and variations appear to be context-dependent and more related to site-specific characteristics than local or regional climatic drivers. We found a low level of demographic synchrony at both local and regional levels. Weather has weak and spatially variable effects on survival, recruitment and population growth rate. In contrast, density-dependence was a common phenomenon (at least for population growth) in almost all populations and subpopulations.</li> <li>Our findings support the idea that the Moran effect is low in species where the population dynamics more closely depends on local factors (e.g. population density and habitat characteristics) than on large-scale environmental fluctuation (e.g. regional climatic variation). Such responses may have far-reaching consequences for the long-term viability of spatially structured populations and their ability to response to large-scale climatic anomalies.</li> </ol>
Data from: Spatio-temporal scaling of biodiversity in acoustic tropical bird communities
Automated analysis of acoustic communities is a rapidly emerging approach for the characterization and monitoring of biodiversity. To evaluate its utility, we should verify that such "bioacoustics" can accurately detect ecological signal in spatiotemporal acoustic data. Targeting the Biological Dynamics of Forest Fragments Project sites in Brazil, we ask: What is the relative contribution of the spatial, temporal and habitat dimension to variation in bird acoustic communities in a previously fragmented tropical rainforest? Does the functional diversity of bird communities scale similarly to space and time as does species diversity, when both are recorded by bioacoustics means? Overall, is the imprint of landscape fragmentation 30 years ago still audible in the present‐day soundscape? We sampled forty‐four sites in secondary forest and 107 sites in old‐growth forest, resulting in 11,000 hours of audio recordings. We detected 60 bird species with satisfactory precision and recovered a linear log‐log relation between sampling time and species diversity. Sites in primary forest host more species than sites in secondary forest, but the difference decreased with sampling time, as the slope was slightly higher in secondary than primary forests. Functional diversity, as exposed by vocalizing birds, accumulates faster than does species diversity. The similarity among local communities decreases with distance in both time and space, but stability in time is remarkably high: two acoustic samples from the same site one year (or more) apart prove more similar than two samples taken at the same time but from sites situated just a few hundred meters apart. These findings suggest that habitat modification can be heard as a long‐lasting imprint on the soundscape of regenerating habitats and identify Soundscape–Area and Soundscape–Time Relations as a promising tool for biodiversity research, applied biomonitoring and restoration ecology.
Data from: Large-scale genotyping of highly polymorphic loci by next generation sequencing: how to overcome the challenges to reliably genotype individuals?
Studying the different roles of adaptive genes is still a challenge in evolutionary ecology and requires reliable genotyping of large numbers of individuals. Next-generation sequencing (NGS) techniques enable such large-scale sequencing, but stringent data processing is required. Here, we develop an easy to use methodology to process amplicon-based NGS data and we apply this methodology to reliably genotype four major histocompatibility complex (MHC) loci belonging to MHC class I and II of Alpine marmots (Marmota marmota). Our post-processing methodology allowed us to increase the number of retained reads. The quality of genotype assignment was further assessed using three independent validation procedures. A total of 3069 high-quality MHC genotypes were obtained at four MHC loci for 863 Alpine marmots with a genotype assignment error rate estimated as 0.21%. The proposed methodology could be applied to any genetic system and any organism, except when extensive copy-number variation occurs (that is, genes with a variable number of copies in the genotype of an individual). Our results highlight the potential of amplicon-based NGS techniques combined with adequate post-processing to obtain the large-scale highly reliable genotypes needed to understand the evolution of highly polymorphic functional genes.
Data from: Changeable camouflage: how well can flounder resemble the colour and spatial scale of substrates in their natural habitats?
Flounder change colour and pattern for camouflage. We used a spectrometer to measure reflectance spectra and a digital camera to capture body patterns of two flounder species camouflaged on four natural backgrounds of different spatial scale (sand, small gravel, large gravel and rocks). We quantified the degree of spectral match between flounder and background relative to the situation of perfect camouflage in which flounder and background were assumed to have identical spectral distribution. Computations were carried out for three biologically relevant observers: monochromatic squid, dichromatic crab and trichromatic guitarfish. Our computations present a new approach to analysing datasets with multiple spectra that have large variance. Furthermore, to investigate the spatial match between flounder and background, images of flounder patterns were analysed using a custom program originally developed to study cuttlefish camouflage. Our results show that all flounder and background spectra fall within the same colour gamut and that, in terms of different observer visual systems, flounder matched most substrates in luminance and colour contrast. Flounder matched the spatial scales of all substrates except for rocks. We discuss findings in terms of flounder biology; furthermore, we discuss our methodology in light of hyperspectral technologies that combine high-resolution spectral and spatial imaging.
Data from: Organic farming enhances parasitoid diversity at the local and landscape scale
1. The magnitude of the benefits derived from organic farming within contrasting managed landscapes remains unclear and, in particular, the potential scale-dependent response of insect parasitoids is relatively unexplored. Identifying the scale at which parasitoids are affected by organic farming will be an important step to enhance their conservation. 2. We sampled tachinid parasitoids at the centre and margin of arable and grassland fields on paired organic and conventional farms located in landscapes with different proportions of organic land. A total of 192 fields were sampled in two biogeographical regions of the UK. 3. We found that the positive effect of organic farming on tachinid parasitoid diversity can be observed at multiple spatial scales. At the local scale, we found higher abundance and species richness of tachinid parasitoids on organic than on conventional farms and on field margins than on field centres. At the landscape scale, the diversity of tachinids was higher in landscapes with higher proportions of organic land. At both scales, the positive effect of organic farming was clear for arable fields, while it was almost neutral for grasslands. 4. Synthesis and applications. Any attempt to enhance parasitoid diversity in agricultural landscapes needs to consider the local management in relation to the habitat type, location within the field and agricultural management in the surrounding landscape. To restore parasitoid diversity, the promotion of organic agriculture should aim to increase both the total extent of organic farming and the connectivity of individual farms. As the benefits of organic farming to biodiversity clearly spread beyond individual farm boundaries, any assessment of organic farming should consider these positive externalities.
Data from: Crowdsourced geometric morphometrics enable rapid large-scale collection and analysis of phenotypic data
1. Advances in genomics and informatics have enabled the production of large phylogenetic trees. However, the ability to collect large phenotypic datasets has not kept pace. 2. Here, we present a method to quickly and accurately gather morphometric data using crowdsourced image-based landmarking. 3. We find that crowdsourced workers perform similarly to experienced morphologists on the same digitization tasks. We also demonstrate the speed and accuracy of our method on seven families of ray-finned fishes (Actinopterygii). 4. Crowdsourcing will enable the collection of morphological data across vast radiations of organisms, and can facilitate richer inference on the macroevolutionary processes that shape phenotypic diversity across the tree of life.
Data from: General models for the spectra of surface area scaling strategies of cells and organisms: fractality, geometric dissimilitude, and internalization
Surface areas and volumes of biological systems—from molecules to organelles, cells, and organisms—affect their biological rates and kinetics. Therefore, surface-area-to-volume ratios and the scaling of surface area with volume profoundly influences ecology, physiology, and evolution. The zeroth-order geometric expectation is that surface area scales with body mass or volume as a power law with an exponent of two-thirds, with consequences for surface-area-to-volume (SA:V) ratios and constraints on size; however, organisms have adaptations for altering the surface area scaling and SA:V ratios of their bodies and structures. The strategies fall into three groups: (i) fractal-like surface convolutions and crinkles; (ii) classic geometric dissimilitude through elongating, flattening, fattening, and hollowing; and (iii) internalization of surfaces. Here I develop general quantitative theory to model the spectra of effects of these strategies on SA:V ratios and surface area scaling, from exponents of less than two-thirds to superlinear scaling and mixed-power laws. Applying the theory to cells helps quantitatively evaluate the effects of membrane fractality, shape-shifting, vacuoles, vesicles, and mitochondria on surface area scaling, informing understanding of cell allometry, morphology, and evolution. Analysis of compiled data indicates that through hollowness and surface internalization eukaryotic phytoplankton increase their effective surface area scaling, attaining near-linear scaling in larger cells. This unifying theory highlights the fundamental role of biological surfaces in metabolism and morphological evolution.
Data from: High-throughput identification of informative nuclear loci for shallow-scale phylogenetics and phylogeography
One of the major challenges for researchers studying phylogeography and shallow-scale phylogenetics is the identification of highly-variable and informative nuclear loci for the question of interest. Previous approaches to marker generation have generally required extensive testing of loci of unknown utility from other systems or development of markers from the nearest model organism with genomic resources. Here, we present a fast and economical approach to generating thousands of variable, single-copy nuclear loci for any system using next-generation sequencing. We performed Illumina paired-end sequencing of three reduced-representation libraries (RRLs) in chorus frogs (Pseudacris) to identify orthologous, single-copy loci across libraries and to estimate sequence divergence at multiple taxonomic levels. We also conducted PCR testing of these loci across the genus Pseudacris and outgroups to determine whether loci developed for phylogeography can be extended to deeper phylogenetic levels. Prior to sequencing, we conducted in silico digestion of the most closely-related reference genome (Xenopus tropicalis) to generate expectations for the number of loci and degree of coverage for a particular experimental design. Using the RRL approach, we: (1) identified >100,000 single-copy nuclear loci, 6,339 of which were shared across individuals within species and 904 of which were shared between species, (2) estimated average nuclear sequence divergence at 0.1% between alleles within an individual, 1.1% between conspecific individuals, and 1.8% between species, and (3) determined from PCR testing that 53% of the loci successfully amplify within-species and also many amplify to the genus-level and beyond (16%). Our study effectively identified nuclear loci present in the genome that have levels of sequence divergence on par with mitochondrial markers commonly used in phylogeography. Specifically, we estimated that ~7% of loci in the chorus frog genome are >3% divergent within species; this translates to ~50,000 single-copy loci in the genome with >3% divergence. Moreover, successful amplification of many loci at deeper phylogenetic levels indicates that the RRL approach represents an efficient method for rapid generation of informative markers for both phylogenetics and phylogeography. We conclude by making recommendations for minimizing the cost and maximizing the efficiency of marker development for future studies in this field.
Data from: Assessing spatio-temporal priorities for species' recovery in broad-scale dynamic landscapes
1. As threats to biodiversity from environmental change increase, assessing priorities for mitigation action becomes increasingly important. However, there have been few attempts to schedule actions across broad spatial extents that explicitly account for dynamic ecological processes and threats. 2. We combined a dynamic occupancy model with a decision analysis framework to spatially allocate multiple recovery actions to maximize species' probability of occupancy under threats posed by climate and land-use change. We used the koala Phascolarctos cinereus across the Australian state of New South Wales (810 000 km2) to illustrate this approach. We considered four actions implemented on a 10 × 10 km2 grid: reduce domestic dog attacks through dog control, reduce vehicle collisions through fencing highways, protect habitat through land acquisitions and restore Eucalyptus forest. We used the occupancy model to predict ecological responses to recovery actions and simulated annealing to identify spatio-temporal priorities for each action. We contrasted the results against priorities generated using a traditional static distribution model. 3. To maximize the probability of koala occupancy in 50 years' time, with an annual budget of up to AU$20 million, investment priorities were located in the eastern part of koala's range, focusing on dog control with some investment in habitat protection and restoration. With higher budgets, investment priorities shifted towards habitat protection and restoration in the western part of the range. However, priorities based on the static distribution model, which had a lower predictive accuracy than the dynamic model, were different. Regardless of budget, priorities derived from the static model were predominantly located in the western part of koala's range, focusing on highway fencing with some investment in dog control. 4. Synthesis and applications. Our approach for integrating spatio-temporal dynamics into conservation prioritization across broad spatial extents provides a significant advance on existing approaches based on static distribution models. The finding that the inferior static model produced different priorities to the dynamic model cautions against the use of static models for conservation planning in dynamic landscapes. Additionally, the substantial changes in priorities with budget indicate that conservation planning under dynamic landscape and climate change must carefully consider priority actions and locations relative to the conservation resources available.
Data from: The geographical variation of network structure is scale dependent: understanding the biotic specialization of host-parasitoid networks
Research on the structure of ecological networks suggests that a number of universal patterns exist. Historically, biotic specialization has been thought to increase towards the Equator. Yet, recent studies have challenged this view showing non-conclusive results. Most studies analysing the geographical variation in biotic specialization focus, however, only on the local scale. Little is known about how the geographical variation of network structure depends on the spatial scale of observation (i.e., from local to regional spatial scales). This should be remedied, as network structure changes as the spatial scale of observation changes, and the magnitude and shape of these changes can elucidate the mechanisms behind the geographical variation in biotic specialization. Here we analyse four facets of biotic specialization in host-parasitoid networks along gradients of climatic constancy, classifying the networks according to their spatial extension (local or regional). Namely, we analyse network connectance, consumer diet overlap, consumer diet breadth, and resource vulnerability at both local and regional scales along the gradients of both current climatic constancy and historical climatic change. While at the regional scale none of the climatic variables are associated to biotic specialization, at the local scale, network connectance, consumer diet overlap, and resource vulnerability decrease with current climatic constancy, whereas consumer generalism increases (i.e., broader diet breadths in tropical areas). Similar patterns are observed along the gradient of historical climatic change. We provide an explanation based on different beta-diversity for consumers and resources across the geographical gradients. Our results show that the geographical gradient of biotic specialization is not universal. It depends on both the facet of biotic specialization and the spatial scale of observation.
Data from: Interrogating genomic-scale data for Squamata (lizards, snakes, and amphisbaenians) shows no support for key traditional morphological relationships
Genomics is narrowing uncertainty in the phylogenetic structure for many amniote groups. For one of the most diverse and species-rich groups, the squamate reptiles (lizards and snakes, amphisbaenians), an inverse correlation between the number of taxa and loci sampled still persists across all publications using DNA sequence data and reaching a consensus on the relationships among them has been highly problematic. Here, we use high-throughput sequence data from 289 samples covering 75 families of squamates to address phylogenetic affinities, estimate divergence times, and characterize residual topological uncertainty in the presence of genome scale data. Importantly, we address genomic support for the traditional taxonomic groupings Scleroglossa and Macrostomata using novel machine-learning techniques. We interrogate genes using various metrics inherent to these loci, including parsimony-informative sites, phylogenetic informativeness, length, gaps, number of substitutions, and site concordance to understand why certain loci fail to find previously well-supported molecular clades and how they fail to support species-tree estimates. We show that both incomplete lineage sorting and poor gene-tree estimation (due to a few undesirable gene properties, such as an insufficient number of parsimony informative sites), may account for most gene and species-tree discordance. We find overwhelming signal for Toxicofera, and also show that none of the loci included in this study supports Scleroglossa or Macrostomata. We comment on the origins and diversification of Squamata throughout the Mesozoic and underscore remaining uncertainties that persist in both deeper parts of the tree (e.g., relationships between Dibamia, Gekkota, and remaining squamates; and between the three toxiferan clades Iguania, Serpentes, and Anguiformes) and within specific clades (e.g., affinities among gekkotan, pleurodont iguanians, and colubroid families).
Data from: Fine-Scale Mapping of Recombination Rate in Drosophila Refines its Correlation to Diversity and Divergence
Regional rates of recombination often correlate with levels of nucleotide diversity, and either selective or neutral hypotheses can explain this relationship. Regional recombination rates also correlate with nucleotide differences between human and chimpanzee, consistent with models where recombination is mutagenic; however, a lack of correlation is observed in the Drosophila melanogaster group, consistent with models invoking natural selection. Here, we revisit the relationship among recombination, diversity, and interspecies difference by generating empirical estimates of these parameters in Drosophila pseudoobscura. To measure recombination rate, we genotyped 1,294 backcross hybrids at 50 markers across the largest assembled linkage group in this species. Genome-wide diversity was estimated by sequencing a second isolate of D. pseudoobscura at shallow coverage. Alignment to the sequenced genome of the closely related species, Drosophila persimilis, provided nucleotide site orthology. Our findings demonstrate that scale is critical in determining correlates to recombination rate: fine-scale cross-over rate estimates are far stronger predictors of both diversity and interspecies difference than broad-scale estimates. The correlation of fine-scale recombination rate to diversity and interspecies difference appears to be genome-wide, evidenced by examination of an X-linked region in greater detail. Because we observe a strong correlation of cross-over rate with interspecies difference, even after correcting for segregating ancestral variation, we suggest that both mutagenic and selective forces generate these correlations, the latter in regions of low crossing over. We propose that it is not cross-overs per se that are mutagenic, but rather repair of DNA double-strand break precursors via crossing over and gene conversion.
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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.