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94 results for “Evolutionary Biology”
Figure 2 in The suprageneric groups of the Pimplinae (Hymenoptera: Ichneumonidae): a cladistic re-evaluation and evolutionary biological study
Figure 2. Cladogram resulting from primary analysis: section 2 (of 13), Delomeristini. Note that each of the three genera, Atractogaster, Delomerista and Perithous is strongly monophyletic.
Figure 4 in The suprageneric groups of the Pimplinae (Hymenoptera: Ichneumonidae): a cladistic re-evaluation and evolutionary biological study
Figure 4. Cladogram resulting from primary analysis: section 4 (of 13), the higher Pimplini. Note the strongly monophyletic nature of the Xanthopimpla and Pimpla genus-groups, and of the two genera, Lissopimpla and Xanthopimpla, comprising the former group.
Figure 1 in The suprageneric groups of the Pimplinae (Hymenoptera: Ichneumonidae): a cladistic re-evaluation and evolutionary biological study
Figure 1. Cladogram resulting from primary analysis: section 1 (of 13), outgroups and tribes of Pimplini, showing characters supporting both the monophyly of the subfamily and the several tribes. Autapomorphies are represented by black rectangles, postulated parallelisms by stippled rectangles, and reversals by white rectangles. This convention is adopted in all subsequent cladograms.
Figure 3 in The suprageneric groups of the Pimplinae (Hymenoptera: Ichneumonidae): a cladistic re-evaluation and evolutionary biological study
Figure 3. Cladogram resulting from primary analysis: section 3 (of 13), the basal Pimplini (the Theronia genus-group). Note that the Theronia group is paraphyletic with respect to the Pimpla and Xanthopimpla genus-groups, and that the more restricted genera, Theronia and Neotheronia, are polyphyletic.
Overcoming the pitfalls of categorizing continuous variables in ecology and evolutionary biology
<ol> <li><span>Many metrics in biological research – from body size to life history timing to environmental metrics – are measured continuously (e.g., body size in grams) but analyzed as categories (e.g., large versus small). The pitfalls of categorization are well-recognized in statistics, but many scientists in the fields of ecology, evolution, and behavior may not be aware of this literature. These fields lack a review of common examples and feasible solutions to avoid the hazards of categorizing continuous data. </span></li> <li><span>Our goal was to summarize current practices of categorizing continuous predictors in ecology and evolutionary biology and provide guidance for overcoming those pitfalls. We conducted a mini-review of 72 recent publications in six popular journals to quantify the prevalence of categorization. We then summarized commonly categorized metrics and simulated a dataset to demonstrate the drawbacks of categorization using common metrics and realistic examples from ecology and evolutionary biology. </span></li> <li><span>We show that categorizing continuous variables is common (31% of publications reviewed), especially in the animal behavior field, and underscore that predictor variables – including abiotic, morphological, physiological, behavioral, and demographic metrics – can and should be collected and analyzed continuously. Our analysis of the simulated field dataset demonstrates how categorizing continuous variables can lower statistical power and change interpretation, especially when arbitrary breakpoints are used. Finally, we provide recommendations on how to keep variables continuous throughout the entire scientific process. </span></li> <li><span>Together, these pieces comprise an actionable guide to increasing statistical power and facilitating large synthesis studies by simply leaving continuous variables alone. Overcoming the pitfalls of categorizing continuous variables will allow ecologists and evolutionary biologists to continue making trustworthy conclusions about natural processes, along with predictions about their responses to climate change and other environmental contexts. We hope that this manuscript and its associated code will provide a useful lab practical for students and teachers to develop programming skills including data simulation, plotting, and model comparisons, as well as research skills including reporting and interpretation. </span></li> </ol>
Terminology in ecology and evolutionary biology disproportionately harms marginalized groups
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Two leaves that cannot die: the genome sequence of Welwitschia mirabilis reveals its unique biology and evolutionary history
<p>Welwitschia mirabilis (hereafter Welwitschia), the sole species in Welwitschiales, belongs to gnetophytes, an ancient, enigmatic gymnosperm lineage. It is a strikingly bizarre plant with distinctive morphology of just two large ever-elongating leaves and is remarkable in being able to survive extreme environmental stresses of the Namibian and Angolan deserts. Here, we provide a chromosome-level assembly of its genome (6.8 Gb/1C) and extensive methylome and transcriptome data to reveal the genetics underpinning its intriguing biology. The Welwitschia genome has been shaped by a lineage-specific ancient whole genome duplication ~ 86 million years ago, and more recently (within 10 million years) by bursts of retrotransposon activity. In addition, high levels of cytosine methylation, extremely so for CHH motifs, are associated with retrotransposons, whilst their long-term deamination has resulted in an exceptionally GC-poor genome. High levels of methylation are likely to be responses to maintain genomic integrity in the face of stress-induced retroelement mobility while reduced GC content will confer a genomic advantage under nutrient limitation. Changes in the copy number and/or expression of key gene families and specific transcription factors (e.g. R2R3MYB, SAUR) controlling cell growth, differentiation and metabolism underpin the plant's extreme longevity under increasing temperature, nutrient and water stress. The Welwitschia chromosome level assembly here, along with a new high-quality assembly for Gnetum montanum, enhances our understanding of genome evolution in gnetophytes. It also provides critical new insights into the extraordinary development of Welwitschia's ever-growing leaves, enabling its survival in such hostile conditions.</p>
Figure 15 in The suprageneric groups of the Pimplinae (Hymenoptera: Ichneumonidae): a cladistic re-evaluation and evolutionary biological study
Figure 15. Cladogram resulting from secondary analysis: section 2 (of 9), Delomeristini.
Data from: Morphological integration during postnatal ontogeny: Implications for evolutionary biology
<p>How covariance patterns of phenotypes change during development is fundamental for a broader understanding of evolution. There is compelling evidence that mammalian cranium covariance patterns change during ontogeny. However, it is unclear to what extent variation in covariance patterns during ontogeny can impact the response to selection. To tackle this question we explored: i) the extent to which covariance patterns change during postnatal ontogeny; ii) in which ontogenetic stages covariance patterns differ the most, and iii) the extent to which the phenotypic covariance pattern at different ontogenetic stages can be explained by the same processes determining additive genetic covariance. We sampled postnatal ontogenetic series for both marsupials, and placentals. Within each ontogenetic series, we compared covariance matrices (<strong>P</strong>-matrices) at different ontogenetic stages. Furthermore, we compared these <strong>P</strong>-matrices to two target matrices [adult <strong>P</strong>-matrix and an additive genetic covariance matrix (<strong>G</strong>-matrix)]. Our results show that for all ontogenetic series, covariance patterns from weaning onward are conserved and probably shaped by the same processes determining the <strong>G</strong>-matrix. We conclude that irrespective of eventual differences in how selection operates during most of postnatal ontogeny, the net response to such pressures will probably not be affected by ontogenetic differences in the covariance pattern.</p>
Two leaves that cannot die: the genome sequence of Welwitschia mirabilis reveals its unique biology and evolutionary history
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Data from: Morphological integration during postnatal ontogeny: Implications for evolutionary biology
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Data from: Evidence for rapid evolutionary change in an invasive plant in response to biological control
We present evidence that populations of an invasive plant species that have become re-associated with a specialist herbivore in the exotic range through biological control have rapidly evolved increased anti-herbivore defences compared to populations not exposed to biocontrol. We grew half-sib families of the invasive plant Lythrum salicaria sourced from 17 populations near Ottawa, Canada, that differed in their history of exposure to a biocontrol agent, the specialist beetle Neogalerucella calmariensis. In a greenhouse experiment, we manipulated larval and adult herbivory to examine whether a population's history of biocontrol influenced plant defence and growth. Plants sourced from populations with a history of biocontrol suffered lower defoliation than naïve, previously unexposed populations, strongly suggesting they had evolved higher resistance. Plants from biocontrol-exposed populations were also larger and produced more branches in response to herbivory, regrew faster even in the absence of herbivory, and were better at compensating for the impacts of herbivory on growth (i.e., they exhibited increased tolerance). Furthermore, resistance and tolerance were positively correlated among genotypes with a history of biocontrol but not among naïve genotypes. Our findings suggest that biocontrol can rapidly select for increased defences in an invasive plant, and may favour a mixed defence strategy of resistance and tolerance without an obvious cost to plant vigour. While rarely studied, such evolutionary responses in the target species have important implications for the long-term efficacy of biocontrol programmes.
Data for "Heuristic algorithms in Evolutionary Computations and modular organization of biological macromolecules: applications to in vitro evolution"
<p>This publication contains data for the construction of the figures and tables for the paper "Heuristic algorithms in Evolutionary Computations and modular organization of biological macromolecules: applications to in vitro evolution" accepted to publication in PLOS ONE.</p>
Supplementary File to "Both binding strength and evolutionary accessibility affect the population frequency of transcription factor binding sequences in Arabidopsis thaliana" (Genome Biology and Evolution)
<p>This data is supplementary file 1 of the following publication:</p> <p>Schweizer G, Wagner A. "Both binding strength and evolutionary accessibility affect the population frequency of transcription factor binding sequences in Arabidopsis thaliana" (Genome Biology and Evolution)</p>
Discussions of the not-so-fit: how ableism limits diverse thought and investigative potential in evolutionary biology
<p>Evolutionary biology and many of its foundational concepts are grounded in a history of ableism and eugenics. The field has not made a concerted effort to divest our concepts and investigative tools from this fraught history and as a result, an ableist investigative lens has persisted into present-day evolutionary research, limiting the scope of research and harming the ability to communicate and synthesize knowledge about evolutionary processes. This failure to divest from our eugenicist and ableist history has harmed progress in evolutionary biology and allowed principles from evolutionary biology to continue to be weaponized against marginalized communities in the modern-day. To rectify this problem, scholars in evolutionary research must come to terms with how the history of the field has influenced their investigations and work to establish a new framework for defining and investigating concepts, such as selection and fitness.</p>
Selective and non-selective evolutionary signatures found in the simplest replicative biological entities
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Fig. 2 in The phylogeny, evolutionary developmental biology, and paleobiology of the Deuterostomia: 25 years of new techniques, new discoveries, and new ideas
Fig. 2 The phylogeny and divergence times of the major deuterostome taxa. Shown is the consensus tree discussed in the text with each node labeled according to its relative support (see key). Most nodes are supported by abundant types of independent data (see text), but a few (e.g., Asterozoa), although supported by phylogenomics, are only weakly
Fig. 3 in The hypothesis of adaptive radiation in evolutionary biology: hard facts about a hazy concept
Fig. 3 Systematic characteristics of the groups having possibly radiated. a Number of case studies (potentially several case studies per article) recorded for each category of organism: angiosperms (n =210), nonangiosperm terrestrial plants (n = 36), "algae", non-terrestrial chlorophyllian lineages (n = 9), tetrapods (n = 381), non-tetrapod vertebrates (n =121), hexapods (n =153), non-hexapod invertebrates (n = 90), fungi, Eumycetes (n =22), non-metazoan heterotrophic eukaryotes
Fig. 1 in The hypothesis of adaptive radiation in evolutionary biology: hard facts about a hazy concept
Fig. 1 Various metrics relative to the study of adaptive radiations over the 2003–2012 time period. a Number of articles extracted from the Web of Science™ database, after the third step of our search procedure (see the "Material and methods" section for details), for each journal and for each year. b Percentage of articles that examined the hypotheses of radiation
Fig. 5 in The hypothesis of adaptive radiation in evolutionary biology: hard facts about a hazy concept
Fig. 5 Features of the insular systems investigated in studies about radiations between 2003 and 2012. Numbers and percentages are relative to case studies (potentially several case studies per article). a Location of the possible radiation. b Percentage of case studies for each of the island types identified in the dataset. c The Suski Inselberg, Maripasoula, French Guiana (credit: Corinne Sarthou). d Number of
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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.