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1,245 results for “dating”
Data from: Variable effects of a changing climate on lay dates and productivity across the range of the Red-cockaded Woodpecker
Many temperate bird species are breeding earlier in response to warming temperatures. We examined the effects of climate on breeding phenology and productivity in 19 populations across the range of the Red-cockaded Woodpecker (Picoides borealis), an endangered species endemic to pine (Pinus spp.) forests in the southeastern United States. Red-cockaded Woodpeckers nested earlier in warmer springs and delayed nesting in wetter springs. Earlier nesting and larger group sizes resulted in higher productivity. Spring temperatures have warmed over time across the range, but this has not led to range-wide advances in nesting date over time. Coastal and northern populations have exhibited a trend of earlier nesting over time, but the response of inland populations has been variable, including some populations in which nesting has become later over time. Geographic patterns included high and increasing productivity at higher latitudes, and declining productivity in the southwestern portion of the range, suggesting a possible shift in acceptable climate conditions for the species. Earlier nesting over time was associated with increasing productivity at higher latitudes, while elsewhere earlier nesting over time was associated with declining or stable productivity, suggesting that populations differ in their ability to adjust to a changing climate. The Red-cockaded Woodpecker is a habitat specialist heavily reliant on habitat management and has little capacity to shift its range, so its long-term viability will depend on its ability to adjust in place to changing local conditions.
A total-evidence dated phylogeny of Echinoidea combining phylogenomic and paleontological data
<p>Phylogenomic and paleontological data constitute complementary resources for unravelling the phylogenetic relationships and divergence times of lineages, yet few studies have attempted to fully integrate them. Several unique properties of echinoids (sea urchins) make them especially useful for such synthetizing approaches, including a remarkable fossil record that can be incorporated into explicit phylogenetic hypotheses. We revisit the phylogeny of crown group Echinoidea using a total-evidence dating approach that combines the largest phylogenomic dataset for the clade, a large-scale morphological matrix with a dense fossil sampling, and a novel compendium of tip and node age constraints. To this end, we develop a novel method for subsampling phylogenomic datasets that selects loci with high phylogenetic signal, low systematic biases and enhanced clock-like behavior. Our results demonstrate that combining different data sources increases topological accuracy and helps resolve conflicts between molecular and morphological data. Notably, we present a new hypothesis for the origin of sand dollars, and restructure the relationships between stem and crown echinoids in a way that implies a long stretch of unidscovered evolutionary history of the crown in the late Paleozoic. Our efforts help bridge the gap between phylogenomics and phylogenetic paleontology, providing a model example of the benefits of combining the two.</p>
The black-footed ferret sighting dates
<p>Dates of sightings (with months used as time units) of the black-footed ferret in Wyoming during January 1972 - December 1990 (from Solow 1993). For instance, numbers 5, 8 and 10 in one row mean that the species was sighted during that year in May, August and October.</p> <p>Solow, A.R. (1993) Inferring extinction in a declining population.Journal of Mathematical Biology,32, 79–82.</p> <p>* Data used with permission of Andrew Solow (WHOI) and was based on information given in the US Department of the Interior<br> records of the black-footed ferret sighting (as conveyed by Solow (1993).</p> <p> </p>
Data from: Using time series analysis to characterize evolutionary and plastic responses to environmental change: a case study of a shift toward earlier migration date in sockeye salmon
Environmental change can shift the phenotype of an organism through either evolutionary or nongenetic processes. Despite abundant evidence of phenotypic change in response to recent climate change, we typically lack sufficient genetic data to identify the role of evolution. We present a method of using phenotypic data to characterize the hypothesized role of natural selection and environmentally driven phenotypic shifts (plasticity). We modeled historical selection and environmental predictors of interannual variation in mean population phenotype using a multivariate state-space model framework. Through model comparisons, we assessed the extent to which an estimated selection differential explained observed variation better than environmental factors alone. We applied the method to a 60-year trend toward earlier migration in Columbia River sockeye salmon Oncorhynchus nerka, producing estimates of annual selection differentials, average realized heritability, and relative cumulative effects of selection and plasticity. We found that an evolutionary response to thermal selection was capable of explaining up to two-thirds of the phenotypic trend. Adaptive plastic responses to June river flow explain most of the remainder. This method is applicable to other populations with time series data if selection differentials are available or can be reconstructed. This method thus augments our toolbox for predicting responses to environmental change.
Data from: Inflation of molecular clock rates and dates: molecular phylogenetics, biogeography, and diversification of a global cicada radiation from Australasia (Hemiptera: Cicadidae: Cicadettini)
Dated phylogenetic trees are important for studying mechanisms of diversification, and molecular clocks are important tools for studies of organisms lacking good fossil records. However, studies have begun to identify problems in molecular clock dates caused by uncertainty of the modeled molecular substitution process. Here we explore Bayesian relaxed-clock molecular dating while studying the biogeography of ca. 200 species from the global cicada tribe Cicadettini. Because the available fossils are few and uninformative, we calibrate our trees in part with a cytochrome oxidase I (COI) clock prior encompassing a range of literature estimates for arthropods. We show that tribe-level analyses calibrated solely with the COI clock recover extremely old dates that conflict with published estimates for two well-studied New Zealand subclades within Cicadettini. Additional subclade analyses suggest that COI relaxed-clock rates and maximum-likelihood branch lengths become inflated relative to EF-1α intron and exon rates and branch lengths as clade age increases. We present corrected estimates derived from (1) an extrapolated EF-1α exon clock derived from COI-calibrated analysis within the largest New Zealand subclade, (2) post-hoc scaling of the tribe-level chronogram using results from subclade analyses, and (3) exploitation of a geological calibration point associated with New Caledonia. We caution that considerable uncertainty is generated due to dependence of substitution estimates on both the taxon sample and the choice of model, including gamma category number and the choice of empirical versus estimated base frequencies. Our results suggest that diversification of the tribe Cicadettini commenced in the early- to mid-Cenozoic and continued with the development of open, arid habitats in Australia and worldwide. We find that Cicadettini is a rare example of a global terrestrial animal group with an Australasian origin, with all non-Australasian genera belonging to two distal clades. Within Australia, we show that Cicadettini is more widely distributed than any other cicada tribe, diverse in temperate, arid and monsoonal habitats, and nearly absent from rainforests. We comment on the taxonomic implications of our findings for thirteen cicada genera.
Data from: Phylogeny of salmonids (salmoniformes: Salmonidae) and its molecular dating: analysis of mtDNA data
Phylogenetic relationships among 41 species of salmonid fish and some aspects of their diversification-time history were studied using the GenBank and original mtDNA data. The position of the root of the Salmonidae phylogenetic tree was uncertain. Among the possible variants, the most reasonable seems to be that in which thymallins are grouped into the same clade as coregonins and the lineage of salmonins occupied a basal position relative to this clade. The genera of Salmoninae formed two distinct clades, i.e., (Brachymystax, Hucho) and (Salmo, Parahucho, (Salvelinus, (Parasalmo, Oncorhynchus)). Furthermore, the genera Parasalmo and Oncorhynchus were reciprocally monophyletic. The congruence of Salmonidae phylogenetic trees obtained using different types of phylogenetic markers is discussed. According to Bayesian dating, ancestral lineages of salmonids and their sister esocoids diverged about 106 million years ago. Sometime after, probably 100–70 million years ago, the salmonid-specific whole genome duplication took place. The divergence of salmonid lineages on the genus level occurred much later, within the time interval of 42–20 million years ago. The main wave of the diversification of salmonids at the species level occurred during the last 12 million years. The possible effect of genome duplication on the Salmonidae diversification pattern is discussed.
Data from: Shifts in hatch dates do not provide pied flycatchers with a rapid ontogenetic route to adjust offspring time schedules to climate change
1. Environments change rapidly, and it is unclear whether organisms with complex life-styles, such as avian migrants, are able to adjust sufficiently. For understanding human impacts on ecosystem functioning, it is crucial to understand how well, and by which mechanisms species are able to adapt. 2. To improve the understanding of migrants' ability to adjust their annual timing to climate change, we investigated ontogenetic hatch date effects on adult spring migration timing and female egg laying dates. We experimentally delayed hatch dates of pied flycatchers Ficedula hypoleuca by one week in three breeding seasons by delaying incubation onset. We investigate if natural and experimental (shifts in) hatch date affected timing of recruiting individuals up to at least three years after the manipulation. 3. Spring arrival dates were positively correlated to natural variation in hatch dates in three of the five years considered, but no such effects were found in egg laying. Experiments showed that delayed hatching resulted in delayed arrival and laying only in one-year old and not in older birds. These effects were mostly observed during one of the study years. 4. The discrepancy between experimental and natural hatch date effects indicate that a causal hatch date effect is not generally responsible for the correlation between hatch date and timing during adulthood. Instead, we propose that natural hatch date effects on spring arrival arise from genetic variation in migration schedules, while delays in hatching induced carry-over effects on arrival and laying dates in offspring (e.g. the experimental effect in 2010). Strong support for year-specific expression of hatch date and delay effects on time schedules imply that trait-variation can be easily obscured. The latter may explain the lack of hatch date effects on female egg laying. 5. Our results imply that plasticity in breeding phenology does not provide pied flycatchers with a non-genetic inheritance route to rapidly advance annual cycles. Instead, plasticity may rather masks (genetic) trait-variation for selection to act on, and thereby slow down micro-evolutionary adaptation to changing environments.
Data from: From gene trees to a dated allopolyploid network: insights from the angiosperm genus Viola (Violaceae)
Allopolyploidisation acounts for a significant fraction of speciation events in many eukaryotic lineages. However, existing phylogenetic and dating methods require tree-like topologies and are unable to handle the network-like phylogenetic relationships of lineages containing allopolyploids. No explicit framework has so far been established for evaluating competing network topologies, and few attempts have been made to date phylogenetic networks. We used a four-step approach to generate a dated polyploid species network for the cosmopolitan angiosperm genus Viola L. (Violaceae Batch.). The genus contains ca 600 species and both recent (neo-) and more ancient (meso-) polyploid lineages distributed over 16 sections. First, we obtained DNA sequences of three low-copy nuclear genes and one chloroplast region, from 42 species representing all 16 sections. Second, we obtained fossil-calibrated chronograms for each nuclear gene marker. Third, we determined the most parsimonious multilabelled genome tree and its corresponding network, resolved at the section (not the species) level. Reconstructing the 'correct' network for a set of polyploids depends on recovering all homoeologs, i.e. all subgenomes, in these polyploids. Assuming the presence of Viola subgenome lineages that were not detected by the nuclear gene phylogenies ('ghost subgenome lineages'), significantly reduced the number of inferred polyploidisation events. We identified the most parsimonious network topology from a set of five competing scenarios differing in the interpretation of homoeolog extinctions and lineage sorting, based on (1) fewest possible ghost subgenome lineages, (2) fewest possible polyploidisation events, and (3) least possible deviation from expected ploidy as inferred from available chromosome counts of the involved polyploid taxa. Finally, we estimated the homoploid and polyploid speciation times of the most parsimonious network. Homoploid speciation times were estimated by coalescent analysis of gene tree node ages. Polyploid speciation times were estimated by comparing branch lengths and speciation rates of lineages with and without ploidy shifts. Our analyses recognise Viola as an old genus (crown age 31 Ma) whose evolutionary history has been profoundly affected by allopolyploidy. Between 16 and 21 allopolyploidisations are necessary to explain the diversification of the 16 major lineages (sections) of Viola, suggesting that allopolyploidy has accounted for a high percentage – between 67% and 88% – of the speciation events at this level. The theoretical and methodological approaches presented here for (1) constructing networks and (2) dating speciation events within a network, have general applicability for phylogenetic studies of groups where allopolyploidisation has occurred. They make explicit use of a hitherto underexplored source of ploidy information from chromosome counts to help resolve phylogenetic cases where incomplete sequence data hampers network inference. Importantly, the coalescent-based method used herein circumvents the assumption of tree-like evolution required by most techniques for dating speciation events.
Data from: Distribution models and a dated phylogeny for Chilean Oxalis species reveal occupation of new habitats by different lineages, not rapid adaptive radiation
Among the World's most challenging environments for plant life is the Atacama Desert, an arid zone extending over 1300 km and from sea level to 2000/3000 m along the southwestern Andean foothills. Plants there and in the adjacent Mediterranean zone exhibit striking adaptations, and we here use a species-rich such group to address the question whether adaptations arose in parallel, at different times, or simultaneously. Answering this type of question has been a major concern of evolutionary biology over the past few years, with a growing consensus that lineages tend to be conservative in their vegetative traits and niche requirements. Combined nuclear and chloroplast DNA sequences for 112 species of Oxalidales (4900 aligned nucleotides) yielded a fossil-calibrated phylogeny that includes 43 of the 54 species of Oxalis occurring in Chile. Distribution models (SDMs) for these species that included precipitation, temperature, fog and/or vegetation types and the phylogeny were used to reconstruct ancestral habitat preferences, relying on likelihood and Bayesian techniques. Since uneven collecting can reduce the power of SDMs, we used a background sample from 1224 Chilean Oxalis collections to correct models for collecting effort. Models with just 10 of 19 bioclim parameters did as well as more parameter-rich models. Results reveal that the Oxalis flora of Chile consists of seven distant lineages that originated at different times prior to the last Andean uplift pulse and some of which had features pre-adapting them to seasonally arid or xeric conditions. The Mediterranean core zone, south of the Atacama, offered an ecological refuge for insufficiently arid-adapted species and harbors a mix of ancient and young groups. There is no evidence of rapid adaptive radiation.
Data from: Baseline immune activity is associated with date rather than with moult stage in the Arctic-breeding barnacle goose (Branta leucopsis)
Variation in immune defence in birds is often explained either by external factors such as food availability and disease pressure or by internal factors such as moult and reproductive effort. We explored these factors together in one sampling design by measuring immune activity over the time frame of the moulting period of Arctic-breeding barnacle geese (Branta leucopsis). We assessed baseline innate immunity by measuring levels of complement-mediated lysis and natural antibody-mediated agglutination together with total and differential leukocyte counts. Variation in immune activity during moult was strongly associated with calendar date and to a smaller degree with the growth stage of wing feathers. We suggest that the association with calendar date reflected temporal changes in the external environment. This environmental factor was further explored by comparing the immune activity of geese in the Arctic population with conspecifics in the temperate climate zone at comparable moult stages. In the Arctic environment, which has a lower expected disease load, geese exhibited significantly lower values of complement-mediated lysis, their blood contained fewer leukocytes, and levels of phagocytic cells and reactive leukocytes were relatively low. This suggests that lower baseline immune activity could be associated with lower disease pressure. We conclude that in our study species, external factors such as food availability and disease pressure have a greater effect on temporal variation of baseline immune activity than internal factors such as moult stage.
Data from: Arrival date and microorganisms in barn swallows
Migration between breeding sites and winter quarters constitute a major life history strategy in birds. The benefits of such migrations must at least equal the costs for such behavior to evolve and be maintained. We tested whether there was a relationship between abundance and diversity of microorganisms on nest lining feathers and timing of arrival by barn swallows Hirundo rustica. Nest lining feathers are chosen and transported by adult barn swallows to their nests just before and during egg laying, at a time when barn swallows have arrived weeks earlier, implying that any heterogeneity in abundance and diversity of microorganisms on feathers in nests must arise from feather preferences. There was a negative relationship between arrival date and the total number of fledglings showing that early arrival is advantageous. The arrival date of adult barn swallows was significantly positively correlated with the abundance of specific bacteria (Bacillus licheniformis) and positively correlated with the abundance of the fungus Trichoderma reesei and negatively correlated with the abundance of the fungus Mucor circinelloides. Moreover, we found a significant positive relationship between arrival date and mean total number of bacterial colonies in TSA medium. There was a significant negative relationship between arrival date and mean total number of bacterial colonies in FMA medium, and Simpson's diversity index of the abundance of bacteria in FMA medium. Such heterogeneity may arise from some microorganisms being beneficial, others detrimental and yet others benign and of no significant importance. In contrast, there was no significant relationship between arrival date and age of individuals. These findings are consistent with the hypothesis that early arriving barn swallows differ in abundance and diversity of microorganisms from late arriving conspecifics, and that they choose feathers for their nests that differ in terms of microorganisms from those chosen by late arrival individuals.
Data from: Birth date predicts alternative life-history pathways in a fish with sequential reproductive tactics
In species with plastic expression of alternative reproductive tactics (ARTs), individuals of the same sex, usually males, can adopt different reproductive tactics depending on factors such as body size. The 'birth date hypothesis' proposes that condition-dependent expression of ARTs may ultimately depend on birth date, because individuals born at different times of the year may achieve different sizes and express different reproductive tactics accordingly. However, this has rarely been tested. Here, we tested this hypothesis in a fish with ARTs, the peacock blenny (Salaria pavo). A long-term (6 years) mark–recapture study demonstrated that ARTs in the peacock blenny were sequential and that males may follow at least two alternative life-history pathways: a nest-holder pathway, in which males express the nest-holder tactic from their first breeding season onwards, and a parasitic pathway, where males reproduce on their first breeding season as sneaker males and subsequently as nest-holders. We have found evidence of a birth date effect on the expression of ARTs in the peacock blenny. Males following the nest-holder pathway are born earlier and are larger at the first breeding season than males following the parasitic pathway, but they have similar growth curves. The mechanisms underlying a birth date effect are far from clear and might be diverse. We have not found support for a mechanism of body size threshold triggering sexual maturation and subsequent ARTs. A mechanism of tactic determination that is strictly based on timing of first maturation is also unlikely. A proxy of lifetime reproductive success shows crossing (body size associated) fitness curves for the two main life-history pathways.
Data from: New crinoids from the Baltic region (Estonia): fossil tip-dating phylogenetics constrains the origin and Ordovician–Silurian diversification of the Flexibilia (Echinodermata)
This study documents previously unknown taxonomic and morphological diversity among early Palaeozoic crinoids. Based on highly complete, well preserved crown material, we describe two new genera from the Ordovician and Silurian of the Baltic region (Estonia) that provide insight into two major features of the geological history of crinoids: the early evolution of the flexible clade during the Great Ordovician Biodiversification Event (GOBE), and their diversification history surrounding the end-Ordovician mass extinction. The unexpected occurrence of a highly derived sagenocrinid, Tintinnabulicrinus estoniensis gen. et. sp. nov., from Upper Ordovician (lower Katian) rocks of the Baltic palaeocontinent provides high-resolution temporal, taxonomic and palaeobiogeographical constraints on the origin and early evolution of the Flexibilia. The Silurian (lower Rhuddanian, Llandovery) Paerticrinus arvosus gen. et sp. nov. is the oldest known Silurian crinoid from Baltica and thus provides the earliest Baltic record of crinoids following the aftermath of the end-Ordovician mass extinction. A Bayesian 'fossil tip-dating' analysis implementing the fossilized birth–death process and a relaxed morphological clock model suggests that flexibles evolved c. 3 million years prior to their oldest fossil record, potentially involving an ancestor–descendant relationship (via 'budding' cladogenesis or anagenesis) with the paraphyletic cladid Cupulocrinus. The sagenocrinid subclade rapidly diverged from 'taxocrinid' grade crinoids during the final stages of the GOBE, culminating in maximal diversity among Ordovician crinoid faunas on a global scale. Remarkably, diversification patterns indicate little taxonomic turnover among flexibles across the Late Ordovician mass extinction. However, the elimination of closely related clades may have helped pave the way for their subsequent Silurian diversification and increased ecological role in post-Ordovician Palaeozoic marine communities. This study highlights the significance of studies reporting faunas from undersampled palaeogeographical regions for clade-based phylogenetic studies and improving estimates of global biodiversity through geological time.
Data from: Birth dates vary with fixed and dynamic maternal features, offspring sex, and extreme climatic events in a high-latitude marine mammal
Reproductive synchrony tends to be widespread in diverse species of plants and animals, especially at higher latitudes. However, for long-lived mammals, birth dates for different individuals can vary by weeks within a population. A mother's birth timing can reveal useful information about her reproductive abilities and have important implications for the characteristics and survival of her offspring. Despite this, our current knowledge of factors associated with variation in birth dates is modest. We used long-term data for known-age Weddell seals in Antarctica and a Bayesian hierarchical modeling approach to study how birth dates varied with fixed and temporally varying features of mothers, whether sex allocation varied with birth timing, and annual variation in birth dates. Based on birth dates for 4465 pups born to 1117 mothers aged 4–31, we found that diverse features of mothers were associated with variation in birth dates. Maternal identity was the most important among these. Unlike most studies, which have reported that birth dates occur earlier as mothers age, we found that birth dates progressively occurred earlier in the year in the early part of a mother's reproductive life, reached a minimum at age 16, and then occurred later at later ages. Birth dates were positively related to a mother's age at primiparity and recent reproductive effort. The earliest birth dates were for pups born to prime-age mothers who did not reproduce in the previous year but began reproduction early in life, suggesting that females in the best condition gave birth earlier than others. If so, our finding that male pups tended to be born earlier than females provides support for the Trivers–Willard sex-allocation model. Average birth dates were quite consistent across years, except for 2 years that had notable delays and occurred during the period when massive icebergs were present and disrupted the ecosystem.
Data from: Influence of gene flow on divergence dating – implications for speciation history of Takydromus grass lizards
Dating the time of divergence and understanding speciation processes are central to the study of the evolutionary history of organisms but are notoriously difficult. The difficulty is largely rooted in variations in the ancestral population size or in the genealogy variation across loci. To depict the speciation processes and divergence histories of three monophyletic Takydromus species endemic to Taiwan, we sequenced 20 nuclear loci and combined with one mitochondrial locus published in GenBank. They were analyzed by a multispecies coalescent approach within a Bayesian framework. Divergence dating based on the gene tree approach showed high variation among loci, and the divergence was estimated at an earlier date than when derived by the species tree approach. To test whether variations in the ancestral population size accounted for the majority of this variation, we conducted computer inferences using isolation-with-migration (IM) and approximate Bayesian computation (ABC) frameworks. The results revealed that gene flow during the early stage of speciation was strongly favored over the isolation model, and the initiation of the speciation process was far earlier than the dates estimated by gene- and species-based divergence dating. Due to their limited dispersal ability, it is suggested that geographic isolation may have played a major role in the divergence of these Takydromus species. Nevertheless, the current study reveals a more complex situation and demonstrates that gene flow during the speciation process cannot be overlooked and may have a great impact on divergence dating. By using multilocus data and incorporating Bayesian coalescence approaches, we provide a more biologically realistic framework for delineating the divergence history of Takydromus.
Data from: Biogeographic dating of speciation times using paleogeographically informed processes
Standard models of molecular evolution cannot estimate absolute speciation times alone, and require external calibrations to do so, such as fossils. Because fossil calibration methods rely on the incomplete fossil record, a great number of nodes in the tree of life cannot be dated precisely. However, many major paleogeographical events are dated, and since biogeographic processes depend on paleogeographical conditions, biogeographic dating may be used as an alternative or complementary method to fossil dating. I demonstrate how a time-stratified biogeographic stochastic process may be used to estimate absolute divergence times by conditioning on dated paleogeographical events. Informed by the current paleogeographical literature, I construct an empirical dispersal graph using 25 areas and 26 epochs for the past 540 Ma of Earth's history. Simulations indicate biogeographic dating performs well so long as paleogeography imposes constraint on biogeographic character evolution. To gauge whether biogeographic dating may be of practical use, I analyzed the well-studied turtle clade (Testudines) to assess how well biogeographic dating fares when compared to fossil-calibrated dating estimates reported in the literature. Fossil-free biogeographic dating estimated the age of the most recent common ancestor of extant turtles to be from the Late Triassic, which is consistent with fossil-based estimates. Dating precision improves further when including a root node fossil calibration. The described model, paleogeographical dispersal graph, and analysis scripts are available for use with RevBayes.
Data from: Estimating species colonization dates using DNA in lake sediment
1. Detection of DNA in lake sediments holds promise as a tool to study processes like extinction, colonization, adaptation and evolutionary divergence. However, low concentrations make sediment DNA difficult to detect, leading to high false negative rates. Additionally, contamination could potentially lead to high false positive rates. Careful laboratory procedures can reduce false positive and negative rates, but should not be assumed to completely eliminate them. Therefore, methods are needed that identify potential false positive and negative results, and use this information to judge the plausibility of different interpretations of DNA data from natural archives. 2. We developed a Bayesian algorithm to infer the colonization history of a species using records of DNA from lake-sediment cores, explicitly labelling some observations as false positive or false negative. We illustrate the method by analysing DNA of whitefish (Coregonus lavaretus. L) from sediment cores covering the past 10,000 years from two central Swedish lakes. We provide the algorithm as an R-script, and the data from this study as example input files. 3. In one lake, Stora Lögdasjön, where connectivity with the proto-Baltic Sea and the degree of whitefish ecotype differentiation suggested colonization immediately after deglaciation, DNA was indeed successfully recovered and amplified throughout the postglacial sediment. For this lake we found no loss of detection probability over time, but a high false negative rate. In the other lake, Hotagen, where connectivity and ecotype differentiation suggested colonization long after deglaciation, DNA was amplified only in the upper part of the sediment, and colonization was estimated at 2,200 BP based on the assumption that successful amplicons represent whitefish presence. Here the earliest amplification represents a false positive with a posterior probability of 41%, which increases the uncertainty in the estimated time of colonization. 4. Complementing careful laboratory procedures aimed at preventing contamination, our method estimates contamination rates from the data. By combining these results with estimates of false negative rates, our models facilitate unbiased interpretation of data from natural DNA archives.
FIGURE 1 in Corrections and additions to the dating of the "Histoire Naturelle des Vers" and the Tableau Encyclopédie (Vers, coquilles, mollusques et polypiers) portions of the Encyclopédie Méthodique
FIGURE 1. "Corrected" 1792 front matter showing the verso of the half title page (left) and the title page (right) of volume one of the Vers section of the Histoire Naturelle dictionary of the Encyclopédie Méthodique.
FIGURE 3 in Dating and publication of the Encyclopédie Méthodique (1782- 1832), with special reference to the parts of the Histoire Naturelle and details on the Histoire Naturelle des Insectes
FIGURE 3. Title page of volume 4 of the Histoire Naturelle. Insectes. Panckoucke and Plomteux edition.
Data from: Inferring node dates from tip dates in fossil Canidae: the importance of tree priors
Tip-dating methods are becoming popular alternatives to traditional node calibration approaches for building time-scaled phylogenetic trees, but questions remain about their application to empirical datasets. We compared the performance of the most popular methods against a dated tree of fossil Canidae derived from previously published monographs. Using a canid morphology dataset, we performed tip-dating using BEAST v. 2.1.3 and MrBayes v. 3.2.5. We find that for key nodes (Canis, approx. 3.2 Ma, Caninae approx. 11.7 Ma) a non-mechanistic model using a uniform tree prior produces estimates that are unrealistically old (27.5, 38.9 Ma). Mechanistic models (incorporating lineage birth, death and sampling rates) estimate ages that are closely in line with prior research. We provide a discussion of these two families of models (mechanistic versus non-mechanistic) and their applicability to fossil datasets.
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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.