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156 results for “Development and Evolution”
A quantitative assessment of ontogeny and moulting in a Cambrian radiodont and the evolution of arthropod development
<p>Radiodonta is a clade of stem euarthropods of central importance to our understanding of the evolution of this phylum. Radiodonts include some of the largest early Paleozoic animals, however little is known about their ontogeny. We present an analysis of moulting patterns and ontogeny in the radiodont <em>Stanleycaris</em> based on 263 exceptionally preserved specimens from the mid-Cambrian (Wuliuan) Burgess Shale. Ranging in size from 10 to 83mm, this constitutes the most extensive radiodont ontogenetic series known. Using a novel morphospace approach, we show that putative carcasses and exuviae can be quantitatively distinguished by the particular suites of structures preserved and their modes of preservation. We propose that <em>Stanleycaris</em>, and probably other radiodonts, moulted via a suture near the anterior of the trunk. Similar anterior moulting strategies, with a suture located at the head-trunk boundary, are shared with some Cambrian euarthropods and are potentially ancestral. Allometric analyses suggest that as <em>Stanleycaris</em> body size increases, the head sclerite and neck become relatively broader, while the trunk and flaps become slightly longer. The eyes developed precociously indicating an important role of visual processing in juveniles. Finally, we find evidence for an initial anamorphic developmental phase, where segment number increases at least from 11 or 12 up to 17, followed by an epimorphic phase, in which growth continued without segment addition. This is consistent with the hypothesis that finite post-embryonic segment addition (hemianamorphosis) is ancestral for arthropods and refines the timing of the origin of this important developmental mode. </p>
A quantitative assessment of ontogeny and moulting in a Cambrian radiodont and the evolution of arthropod development
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Data from: Habitat deterioration promotes the evolution of direct development in metamorphosing species
<p>Although metamorphosis is widespread in the animal kingdom, several species have evolved life cycle modifications to avoid complete metamorphosis. Some species, e.g., many salamanders and newts, have deleted the adult stage via a process called paedomorphosis. Others, e.g., some frog species and marine invertebrates, no longer have a distinct larval stage and reach maturation via direct development. Here we study which ecological conditions can lead to the loss of metamorphosis via the evolution of direct development. To do so, we use size-structured consumer-resource models in conjunction with the adaptive-dynamics approach. In case the larval habitat deteriorates, individuals will produce larger offspring and in concert accelerate metamorphosis. While this leads to the evolutionary transition from metamorphosis to direct development when the adult habitat is highly favourable, the population will go extinct in case the adult habitat does not provide sufficient food in order to escape metamorphosis. With a phylogenetic approach we furthermore show that among amphibians the transition of metamorphosis to direct development is indeed, in line with model predictions, conditional on and preceded by the evolution of larger egg sizes.</p>
Evolution and development at the origin of a phylum
<p class="AbstractSummary">Quantifying morphological evolution is key to determining the patterns and processes underlying the origin of phyla. We constructed a hierarchical morphological character matrix to characterize the radiation and establishment of echinoderm body plans during the early Paleozoic. This showed that subphylum-level clades diverged gradually through the Cambrian, and the distinctiveness of the resulting body plans was amplified by the extinction of transitional forms and obscured by convergent evolution during the Ordovician. Higher-order characters that define these body plans were not fixed at the origin of the phylum, countering hypotheses regarding developmental processes governing the early evolution of animals. Instead, these burdened characters were flexible enabling continued evolutionary innovation throughout the clades' history.</p>
Data for: Adaptive tail-length evolution in deer mice is associated with differential Hoxd13 expression in early development
<p>Variation in the size and number of axial segments underlies much of the diversity in animal body plans. Here, we investigate the evolutionary, genetic, and developmental mechanisms driving tail-length differences between forest and prairie ecotypes of deer mice (<em>Peromyscus maniculatus</em>). We first show that long-tailed forest mice perform better in an arboreal locomotion assay, consistent with tails being important for balance during climbing. We then identify six genomic regions that contribute to differences in tail length, three of which associate with caudal vertebra length and the other three with vertebra number. For all six loci, the forest allele increases tail length, indicative of the cumulative effect of natural selection. Two of the genomic regions associated with variation in vertebra number contain Hox gene clusters. Of those, we find an allele-specific decrease in Hoxd13 expression in the embryonic tail bud of long-tailed forest mice, consistent with its role in axial elongation. Additionally, we find that forest embryos have more presomitic mesoderm than prairie embryos, and that this correlates with an increase in the number of neuromesodermal progenitors (NMPs), which are modulated by Hox13 paralogs. Together, these results suggest a role for Hoxd13 in the development of natural variation in adaptive morphology on a microevolutionary timescale.</p>
Genome evolution is associated with nutrition-responsive regulatory development in horned dung beetles
<p>The Scarabaeinae, or true dung beetles, are a hyper-diverse clade of insects of ecological, evolutionary, and agricultural significance and have long served as informative models of evolutionary ecology and development. Perhaps the most conspicuous of their unique traits are head horns, novel structures that serve as secondary sexual weapons, exhibit extraordinary developmental plasticity, and have fueled one of the most dramatic morphological radiations in the animal kingdom. In this study, we investigate the evolutionary basis for dung beetle traits - including horns - via comparative genomic and developmental assays. We present chromosome-level genome assemblies of three dung beetle species in the species-rich Onthophagini tribe (> 2500 extant species) including <em>Onthophagus taurus</em>, <em>Onthophagus sagittarius</em>, and <em>Digitonthophagus gazella</em>. Contrasting these assemblies with seven other species across the order Coleoptera identifies rapidly evolving gene families associated with metabolic regulation of developmental plasticity and metamorphosis. Intraspecific comparisons of chromatin accessibility in developing head horns of <em>O. taurus</em> identify distinct cis-regulatory architectures underlying sex- and nutrition-responsive development of this novel trait, including a large proportion of recently evolved regulatory elements sensitive to horn morph determination. Binding motifs of diverse developmental transcription factors are enriched in these nutrition-responsive open chromatin regions, including the early embryonic patterning gene <em>twist</em>. Using RNA interference (RNAi), we show <em>twist</em> has been co-opted into the beetle horn regulatory network to mediate differential horn morphogenesis in alternate male morphs via its interactions with nutrition-sensitive DNA-binding sites, highlighting the utility of this approach in identifying new developmental regulators of morphological evolution. These results demonstrate gene networks are highly evolvable transducers of environmental and genetic signals critical for the formation and diversification of developmental traits, established in part by condition-responsive chromatin accessibility. Further, this work provides new reference-quality genome assemblies of three dung beetles that will bolster future developmental, ecological, and evolutionary studies of this insect group.</p>
Evolution of mate harm resistance in females from Drosophila melanogaster populations selected for faster development and early reproduction
<p><span>These images are part of the study titled "<strong>Evolution of mate harm resistance in females from <em>Drosophila melanogaster </em>populations selected for faster development and early reproduction</strong>". The study uses thorax length of study fruit flies as a measure of body size. The images are of the individual fruit fly thorax. These images are used on ImageJ to measure thorax length. The details of the method can be found in the manuscript, which is now accepted for publication in the Journal of Evolutionary Biology. The same can also be found in a <a href="https://doi.org/10.1101/2022.12.25.521905">pre-print</a> version. </span></p> <p><span>The abstract of the article is mentioned below: </span></p> <p> </p> <p><strong><span>Abstract</span></strong></p> <p><span>Interlocus sexual conflict is predicted to result in sexually antagonistic coevolution between male competitive traits, which are also female-detrimental, and mate harm resistance (MHR) in females. Little is known about the connection between life-history evolution and sexually antagonistic coevolution. Here, we investigated the evolution of MHR in a set of experimentally evolved populations, where mate-harming ability has been shown to have substantially reduced in males as a correlated response to the selection for faster development and early reproduction. We measured mortality and fecundity of females of these populations and those of their matched controls, under different male exposure conditions. We observed that the evolved females were more susceptible to mate harm - suffering from significantly higher mortality under continuous exposure to control males within the twenty-day assay period. Though these evolved females are known to have shorter lifespan, substantially higher mortality was not observed under virgin and single-mating conditions. We used fecundity data to show that this higher mortality in the experimentally evolved females was not due to the cost of egg production, and hence can only be attributed to reduced MHR. Further analysis indicated that this decreased MHR is unlikely to be due purely to the smaller size of these females. Instead, it is more likely to be an indirect experimentally evolved response attributable to the changed breeding ecology, and/or male trait evolution. Our results underline the implications of changes in life history traits, including lifespan, to the evolution of MHR in females. </span></p>
RNASeq fastq files associated with the manuscript entitled 'Interspecies transcriptome analyses identify genes that control the development and evolution of limb skeletal proportion'
<p>This next-generation sequencing dataset is associated with the research manuscript entitled ‘<em>Interspecies transcriptome analyses identify genes that control the development and evolution of limb skeletal proportion</em>’ (https://www.biorxiv.org/content/10.1101/754002v2).</p> <p>The folder ‘<strong>Zenodo_Saxena_etal_2021_RNASeq_FastqFiles</strong>’ contains raw/unprocessed RNASeq Fatsq read files for postnatal day 5 (P5) mouse (Mus) and jerboa (Jac) cartilage samples (Metatarsal = MT; Radius/Ulna = RU).</p> <p>> The <strong>Jac_P5</strong> subfolder contains single-end reads (R1) for five jerboa metatarsals (MT1-5) and radius/ulna (RU1-5) biological replicates. Jac_MT1-3 and Jac_RU1-3 were used in the primary differential expression analysis (n=3). Jac_MT4-5 and Jac_RU4-5 were used for independent validation (n=2) of the the primary analysis. </p> <p>> The <strong>Mus_P5</strong> subfolder contains single-end reads (R1) for five mouse metatarsals (MT1-5) and radius/ulna (RU1-5) biological replicates. Mus_MT1-3 and Mus_RU1,3 & 4 were used in the primary differential expression analysis (n=3). Mus_MT4-5 and Mus_RU4 & 5 were used for independent validation (n=2) of the the primary analysis. </p>
Evolution of Teamwork Quality Instruments in Agile Software Development: A Systematic Literature Review
<p>Suplemmentary Material of the article: Evolution of Teamwork Quality Instruments in Agile Software Development: A Systematic Literature Review</p>
Dataset: Evolution Of Computational Ontologies: Assessing Development Processes Using Metrics
<p>Ontologies facilitate meaning between human and computational actors. On the one hand, the underlying technology can be considered mature. It has a standardized language, established tools for editing and sharing, and broad adoption in practice and research. On the other hand, we still know little about how these artifacts evolve over their lifetime, even though knowledge of the development process could influence quality control. It would enable us to give knowledge engineers better modeling or selection guidelines.</p> <p>This paper examines the evolution of computational ontologies using ontology metrics. First, we gathered hypotheses on the ontology development process. We assume that groups of ontologies follow a similar development pattern and that a stereotypical development process exists. Afterward, these hypotheses are tested against historical metric data from 7053 versions from 69 dormant ontologies.</p> <p>We will show that ontology development processes are highly heterogeneous. While the made hypotheses are partly true for a slight majority of ontologies, concluding the bigger picture of ontology development down to the individual ontologies is mostly not possible. Further, the data revealed that most ontologies have disruptive change events for most of the measures attributes. These disruptive events are further examined regarding their occurrences, combinations, and sizes.</p>
Data from: Habitat deterioration promotes the evolution of direct development in metamorphosing species
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Data from: Cellular and molecular mechanisms that shape the development and evolution of tail vertebral proportion in mice and jerboas
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Evolution and development at the origin of a phylum
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Data for: Adaptive tail-length evolution in deer mice is associated with differential Hoxd13 expression in early development
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Data from: Comparative transcriptomic analysis of the evolution and development of flower size in Saltugilia (Polemoniaceae)
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Data from: Relaxed selection in evolution of genes regulating limb development gives clue to variation in forelimb morphology of cetaceans and other mammals
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Genome evolution is associated with nutrition-responsive regulatory development in horned dung beetles
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Reticulate evolution and rapid development of reproductive barriers upon secondary contact in a forest fungus
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Data from: Laboratory culture of the California Sea Firefly Vargula tsujii (Ostracoda: Cypridinidae): developing a model system for the evolution of marine bioluminescence
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Data from: Modifications during early plant development promote the evolution of nature’s most complex woods
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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.