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Data from: Novel approaches for phylogenetic inference from morphological data and total-evidence dating in squamate reptiles (lizards, snakes, and amphisbaenians)
Here, I combine previously underutilized models and priors to perform more biologically-realistic phylogenetic inference from morphological data, with an example from squamate reptiles. When coding morphological characters, it is often possible to denote ordered states with explicit reference to observed or hypothetical ancestral conditions. Using this logic, we can integrate across character-state labels and estimate meaningful rates of forward and backwards transitions from plesiomorphy to apomorphy. I refer to this approach as MkA, for 'asymmetric.' The MkA model incorporates the biological reality of limited reversal for many phylogenetically informative characters, and significantly increases likelihoods in the empirical datasets. Despite this, the phylogeny of Squamata remains contentious. Total-evidence analyses using combined morphological and molecular data and the MkA approach tend towards recent consensus estimates supporting a nested Iguania. However, support for this topology is not unambiguous across datasets or analyses, and no mechanism has been proposed to explain the widespread incongruence between partitions, or the hidden support for various topologies in those partitions. Furthermore, different morphological datasets produced by different authors contain both different characters and different states for the same or similar characters, resulting in drastically different placements for many important fossil lineages. Effort is needed to standardize ontology for morphology, resolve incongruence, and estimate a robust phylogeny. The MkA approach provides a preliminary avenue for investigating morphological evolution while accounting for temporal evidence and asymmetry in character-state changes.
Data from: The impact of phylogenetic dating method on interpreting trait evolution: a case study of Cretaceous–Palaeogene eutherian body-size evolution
The fossil record of the earliest Cenozoic contains the first large-bodied placental mammals. Several evolutionary models have been invoked to explain the transition from small to large body sizes, but methods for determining evolutionary mode of trait change depend on input from tree topology and divergence dates. Different dating methods may therefore affect inference of evolutionary model. Here, we fit models of body mass evolution onto dated phylogenies of Cretaceous and Palaeogene mammals, comparing the effect of dating method on interpretation of evolutionary model. Among traditional palaeontological dating approaches, an Ornstein–Uhlenbeck model with high alpha parameters is recovered as best-fitting when minimum-age dating is used, while branch-sharing methods are highly sensitive to topology. Release or release–radiate models are preferred when Bayesian fossilized birth–death method is used, but when using stochastic cal3 dating of trees, a model of increased evolutionary rate without a release in constraint at the Cretaceous–Palaeogene boundary has highest support. These results demonstrate unambiguously that choice of dating method is critical for interpretation of continuous trait evolution, and that care must therefore be taken to consider these effects in macroevolutionary studies.
Data from: A total-evidence approach to dating with fossils, applied to the early radiation of the Hymenoptera
Phylogenies are usually dated by calibrating interior nodes against the fossil record. This relies on indirect methods that, in the worst case, misrepresent the fossil information. Here, we contrast such node dating with an approach that includes fossils along with the extant taxa in a Bayesian total-evidence analysis. As a test case, we focus on the early radiation of the Hymenoptera, mostly documented by poorly preserved impression fossils that are difficult to place phylogenetically. Specifically, we compare node dating using nine calibration points derived from the fossil record with total-evidence dating based on 343 morphological characters scored for 45 fossil (4–20% complete) and 68 extant taxa. In both cases we use molecular data from seven markers (about 5 kb) for the extant taxa. Because it is difficult to model speciation, extinction, sampling, and fossil preservation realistically, we develop a simple uniform prior for clock trees with fossils, and we use relaxed clock models to accommodate rate variation across the tree. Despite considerable uncertainty in the placement of most fossils, we find that they contribute significantly to the estimation of divergence times in the total-evidence analysis. In particular, the posterior distributions on divergence times are less sensitive to prior assumptions and tend to be more precise than in node dating. The total-evidence analysis also shows that four of the seven Hymenoptera calibration points used in node dating are likely to be based on erroneous or doubtful assumptions about the fossil placement. With respect to the early radiation of Hymenoptera, our results suggest that the crown group dates back to the Carboniferous, approximately 309 Ma (95% interval: 291–347 Ma), and diversified into major extant lineages much earlier than previously thought, well before the Triassic.
Data from: Total-evidence dating under the fossilized birth-death process
Bayesian total-evidence dating involves the simultaneous analysis of morphological data from the fossil record and morphological and sequence data from recent organisms, and it accommodates the uncertainty in the placement of fossils while dating the phylogenetic tree. Due to the flexibility of the Bayesian approach, total-evidence dating can also incorporate additional sources of information. Here, we take advantage of this and expand the analysis to include information about fossilization and sampling processes. Our work is based on the recently described fossilized birth-death (FBD) process, which has been used to model speciation, extinction and fossilization rates that can vary over time in a piecewise manner. So far, sampling of extant and fossil taxa has been assumed to be either complete or uniformly at random, an assumption which is only valid for a minority of datasets. We therefore extend the FBD process to accommodate diversified sampling of extant taxa, which is standard practice in studies of higher-level taxa. We verify the implementation using simulations and apply it to the early radiation of Hymenoptera (wasps, ants and bees). Previous total-evidence dating analyses of this dataset were based on a simple uniform tree prior and dated the initial radiation of extant Hymenoptera to the late Carboniferous (309 Ma). The analyses using the FBD prior under diversified sampling, however, date the radiation to the Triassic and Permian (252 Ma), slightly older than the age of the oldest hymenopteran fossils. By exploring a variety of FBD model assumptions, we show that it is mainly the accommodation of diversified sampling that causes the push towards more recent divergence times. Accounting for diversified sampling thus has the potential to close the long-discussed gap between rocks and clocks. We conclude that the explicit modeling of fossilization and sampling processes can improve divergence time estimates, but only if all important model aspects, including sampling biases, are adequately addressed.
Data from: Molecular phylogeny and dating reveal a terrestrial origin in the early Carboniferous for ascaridoid nematodes
Ascaridoids are among the commonest groups of zooparasitic nematodes (roundworms) and occur in the alimentary canal of all major vertebrate groups, including man. They have an extremely high diversity and are of major socio-economic importance. However, their evolutionary history remains poorly known. Here we performed a comprehensive phylogenetic analysis of the Ascaridoidea. Our results divided the Ascaridoidea into six monophyletic major clades, i.e. the Heterocheilidae, Acanthocheilidae, Anisakidae, Ascarididae, Toxocaridae and Raphidascarididae, among which the Heterocheilidae, rather than the Acanthocheilidae, represents the sister clade to the remaining ascaridoids. The phylogeny was calibrated using an approach that involves time priors from fossils of the co-evolving hosts, and dates the common ancestor of the Ascaridoidea back to the Early Carboniferous (approximately 360.47–325.27 Ma). The divergence dates and ancestral host types indicated by our study suggest that members of the Ascaridoidea first parasitized terrestrial tetrapods and subsequently extended their host range to elasmobranchs and teleosts. We also propose that the fundamental terrestrial-aquatic switches of these nematodes were affected by changes in sea-level during the Triassic to the Early Cretaceous.
Data from: Topology, divergence dates, and macroevolutionary inferences vary between different tip-dating approaches applied to fossil theropods (Dinosauria)
Dated phylogenies of fossil taxa allow palaeobiologists to estimate the timing of major divergences and placement of extinct lineages, and to test macroevolutionary hypotheses. Recently developed Bayesian 'tip-dating' methods simultaneously infer and date the branching relationships among fossil taxa, and infer putative ancestral relationships. Using a previously published dataset for extinct theropod dinosaurs, we contrast the dated relationships inferred by several tip-dating approaches and evaluate potential downstream effects on phylogenetic comparative methods. We also compare tip-dating analyses to maximum-parsimony trees time-scaled via alternative a posteriori approaches including via the probabilistic cal3 method. Among tip-dating analyses, we find opposing but strongly supported relationships, despite similarity in inferred ancestors. Overall, tip-dating methods infer divergence dates often millions (or tens of millions) of years older than the earliest stratigraphic appearance of that clade. Model-comparison analyses of the pattern of body-size evolution found that the support for evolutionary mode can vary across and between tree samples from cal3 and tip-dating approaches. These differences suggest that model and software choice in dating analyses can have a substantial impact on the dated phylogenies obtained and broader evolutionary inferences.
Data from: Bayesian tip dating reveals heterogeneous morphological clocks in Mesozoic birds
Recently, comprehensive morphological datasets including nearly all the well-recognized Mesozoic birds became available, making it feasible for statistically rigorous methods to unveil finer evolutionary patterns during early avian evolution. Here, we exploited the advantage of Bayesian tip dating under relaxed morphological clocks to estimate both the divergence times and evolutionary rates while accounting for their uncertainties. We further subdivided the characters into six body regions (i.e., skull, axial skeleton, pectoral girdle and sternum, forelimb, pelvic girdle, and hindlimb) to assess evolutionary rate heterogeneity both along the lineages and across partitions. We observed extremely high rates of morphological character changes during early avian evolution and the clock rates are quite heterogeneous among the six regions. The branch subtending Pygostylia shows extremely high rate in the axial skeleton, while the branches subtending Ornithothoraces and Enantiornithes show notably high rates in the pectoral girdle and sternum, and moderately high rates in the forelimb. The extensive modifications in these body regions largely correspond to refinement of the flight capability. This study reveals the power and flexibility of Bayesian tip dating implemented in MrBayes to investigate evolutionary dynamics in deep time.
Data from: A simulation-based evaluation of tip-dating under the fossilized birth-death process
Bayesian molecular dating is widely used to study evolutionary timescales. This procedure usually involves phylogenetic analysis of nucleotide sequence data, with fossil-based calibrations applied as age constraints on internal nodes of the tree. An alternative approach is tip-dating, which explicitly includes fossil data in the analysis. This can be done, for example, through the joint analysis of molecular data from present-day taxa and morphological data from both extant and fossil taxa. In the context of tip-dating, an important development has been the fossilized birth-death process, which allows non-contemporaneous tips and sampled ancestors while providing a model of lineage diversification for the prior on the tree topology and internal node times. However, tip-dating with fossils faces a number of considerable challenges, especially those associated with fossil sampling and evolutionary models for morphological characters. We conducted a simulation study to evaluate the performance of tip-dating using the fossilized birth-death model. We simulated fossil occurrences and the evolution of nucleotide sequences and morphological characters under a wide range of conditions. Our analyses of these data show that the number and the maximum age of fossil occurrences have a greater influence than the degree of among-lineage rate variation or the number of morphological characters on estimates of node times and the tree topology. Tip-dating with the fossilized birth-death model generally performs well in recovering the relationships among extant taxa, but has difficulties in correctly placing fossil taxa in the tree and identifying the number of sampled ancestors. The method yields accurate estimates of the ages of the root and crown group, although the precision of these estimates varies with the probability of fossil occurrence. The exclusion of morphological characters results in a slight overestimation of node times, whereas the exclusion of nucleotide sequences has a negative impact on inference of the tree topology. Our results provide an overview of the performance of tip-dating using the fossilized birth-death model, which will inform further development of the method and its application to key questions in evolutionary biology.
Data from: First dating of a recombination event in mammalian tick-borne flaviviruses
The mammalian tick-borne flavivirus group (MTBFG) contains viruses associated with important human and animal diseases such as encephalitis and hemorrhagic fever. In contrast to mosquito-borne flaviviruses where recombination events are frequent, the evolutionary dynamic within the MTBFG was believed to be essentially clonal. This assumption was challenged with the recent report of several homologous recombinations within the Tick-borne encephalitis virus TBEV. We performed a thorough analysis of publicly available genomes in this group and found no compelling evidence for the previously identified recombinations. However, our results show for the first time that demonstrable recombination (i.e., with large statistical support and strong phylogenetic evidences) has occurred in the MTBFG, more specifically within the Louping ill virus lineage. Putative parents, recombinant strains and breakpoints were further tested for statistical significance using phylogenetic methods. We investigated the time of divergence between the recombinant and parental strains in a Bayesian framework. The recombination was estimated to have occurred during a window period of 282 to 76 years before the present. By unravelling the temporal setting of the event, we adduce hypotheses
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: Geomolecular dating and the origin of placental mammals
In modern evolutionary divergence analysis the role of geological information extends beyond providing a timescale, to informing molecular rate variation across the tree. Here I consider the implications of this development. I use fossil calibrations to test the accuracy of models of molecular rate evolution for placental mammals, and reveal substantial misspecification associated with life history rate correlates. Adding further calibrations to reduce dating errors at specific nodes unfortunately tends to transfer underlying rate errors to adjacent branches. Thus, tight calibration across the tree is vital to buffer against rate model errors. I argue that this must include allowing maximum bounds to be tight when good fossil records permit, otherwise divergences deep in the tree will tend to be inflated by the interaction of rate errors and asymmetric confidence in minimum and maximum bounds. In the case of placental mammals I sought to reduce the potential for transferring calibration and rate model errors across the tree by focusing on well-supported calibrations with appropriately conservative maximum bounds. The resulting divergence estimates are younger than others published recently, and provide the long-anticipated molecular signature for the placental mammal radiation observed in the fossil record near the 66 Ma Cretaceous-Paleogene extinction event.
Data from: No speed dating please! Patterns of social preference in male and female house mice
Background: In many animal species, interactions between individuals of different sex often occur in the context of courtship and mating. During these interactions, a specific mating partner can be chosen. By discriminating potential mates according to specific characteristics, individuals can increase their evolutionary fitness in terms of reproduction and offspring survival. In this study, we monitored the partner preference behaviour of female and male wild house mice (Mus musculus domesticus) from populations in Germany (G) and France (F) in a controlled cage setup for 5 days and six nights. We analysed the effects of individual factors (e.g. population origin and sex) on the strength of preference (selectivity), as well as dyadic factors (e.g. neutral genetic distance and major histocompatibility complex (MHC) dissimilarity) that direct partner preferences. Results: Selectivity was stronger in mice with a pure population background than mixed individuals. Furthermore, female mice with a father from the German population had stronger selectivity than other mice. In this group, we found a preference for partners with a larger dissimilarity of their father's and their partner's MHC, as assessed by sequencing the H2-Eß locus. In all mice, selectivity followed a clear temporal pattern: it was low in the beginning and reached its maximum only after a whole day in the experiment. After two days, mice seemed to have chosen their preferred partner, as this choice was stable for the remaining four days in the experiment. Conclusions: Our study supports earlier findings that mate choice behaviour in wild mice can be paternally influenced. In our study, preference seems to be potentially associated with paternal MHC distance. To explain this, we propose familial imprinting as the most probable process for information transfer from father to offspring during the offspring's early phase of life, which possibly influences its future partner preferences. Furthermore, our experiments show that preferences can change after the first day of encounter, which implies that extended observation times might be required to obtain results that allow a valid ecological interpretation.
FIGURE 4 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 4. Title page of volume 4 of the Histoire Naturelle. Insectes. Laporte separate edition.
FIGURE 2 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 2. Timeline of production for all the dictionnaires of the EM.
Data from: TipDatingBeast: an R package to assist the implementation of phylogenetic tip-dating tests using BEAST
Molecular tip-dating of phylogenetic trees is a growing discipline that uses DNA sequences sampled at different points in time to co-estimate the timing of evolutionary events with rates of molecular evolution. In this context, BEAST, a program for Bayesian analysis of molecular sequences, is the most widely used phylogenetic tool. Here, we introduce TipDatingBeast, an R package built to assist the implementation of various phylogenetic tip-dating tests using BEAST. TipDatingBeast currently contains two main functions. The first one allows preparing date-randomization analyses, which assess the temporal signal of a dataset. The second function allows performing leave-one-out analyses, which test for the consistency between independent calibration sequences and allow pinpointing those leading to potential bias. We apply those functions to an empirical dataset and supply practical guidance for results interpretation.
Arctic sea ice snow melt onset dates from the Advanced Horizontal Range Algorithm, version 5 (1979 - 2022)
<h2>Data</h2><p>This data set includes one NetCDF (.nc) file containing the full set of annual Arctic sea ice melt onset dates and statistical summaries for the 1979 - 2022 period derived with the Advanced Horizontal Range Algorithm (AHRA) V5. The remaining .png files include browse images of each data layer contained within the primary NetCDF file.</p><p>A full description of the data provided herein can be found in the following publication: </p><p>Bliss, A. C. (submitted 2023), Passive microwave observations of Arctic sea ice melt onset from the Advanced Horizontal Range Algorithm 1979 – 2022, <i>Scientific Data</i>.</p><h2>Future updates</h2><p>This data set is distributed on an ongoing basis by the NASA Distributed Active Archive Center at the National Snow and Ice Data Center. Future updates to the AHRA V5 data set including annual updates of the data product will be available at the NSIDC archive below:</p><p>Bliss, A. C., M. Anderson, and S. Drobot. (2022). Snow Melt Onset Over Arctic Sea Ice from SMMR and SSM/I-SSMIS Brightness Temperatures, Version 5. Boulder, Colorado USA. NASA National Snow and Ice Data Center Distributed Active Archive Center. <a href="https://doi.org/10.5067/TRGWQ0ONTQG5">https://doi.org/10.5067/TRGWQ0ONTQG5</a>.</p>
Date Fruit Detection Dataset for Computer Vision-Based Automatic Harvesting.
<p>The "Date Fruit Detection Dataset for Computer Vision-Based Automatic Harvesting" is a collection of videos and images showcasing date fruits from four Moroccan varieties, namely Majhoul, Boufagous, Bouisthami, and Khoult. This dataset is specifically designed to detect and classify date fruits, with the primary goal being the automation of the harvesting process.</p><p>All the images in this dataset were captured in two orchards located in Morocco, with the first orchard situated in the southeast of Errachidia and the second in Tismoumine, Alnif, Tinghir. These images were taken under various natural conditions, encompassing differing lighting, contrast, shadows, and instances where the dates were concealed by bags or hidden beneath palm leaves.</p><p>The dataset was meticulously compiled over the period spanning from June to September 2022, ensuring comprehensive coverage of all four maturity stages of date fruits, which include immature, khalal, rutab, and tamer. The dataset is intended for both object detection and classification purposes, and it includes a YOLO annotation txt file for each image. These annotations have been tailored to precisely recognize not only the date fruit but also to distinguish the specific variety and its maturity stage.</p>
Diachronic semantics: changes of meaning of words over time and the consequences for keeping classification systems up to date
<p>Meanings of words in a natural language are changing over time under the influences of different factors. Words adapt to new meanings, lose old meanings, rearrange current meanings and change some parts of previous meanings, etc. The language as a living organism needs to be able to accept and adapt to those changes. Like natural languages, artificial languages such as classification systems or subject indexing systems have to adjust to those changes too. Linguist F. de Saussure defines language as a 'system of signs'. If we transfer this definition into the artificial language such as a classification system (e.g., Universal Decimal Classification (UDC)) and define it also as a 'system of signs' which has a vocabulary, a grammar and a syntax, we could draw parallels between phenomena which occur in natural and in artificial languages. The young linguistic discipline which deals with changes in meanings over time is called diachronic semantics and this paper explores how its mechanisms can be used to analyze the changes that occur in classification systems over time. Diachronic semantics uses various mechanisms to describe adapting and changing meanings of words. These mechanisms include: metaphor, metonymy, specialization, generalization, analogy and splitting. This paper also aims to explain the borrowing and adjusting of the theory from the field of linguistics into the field of information sciences.</p>
Origon date and video
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Radiocarbon dates from houses of Fosie type
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