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296 results for “evolution pattern”
Data from: Natural selection and repeated patterns of molecular evolution following allopatric divergence
Background: Geographic speciation is a major force in generating biodiversity. However, how genomes diverge over time after geographic isolation has halted gene flow has remained unclear. We examine genome-wide divergence of putatively single-copy orthologous genes (POGs) from transcriptomes in 20 allopatric species/variety pairs from diverse angiosperm clades. Sixteen of these pairs reflect the well-known eastern Asia – eastern North America floristic disjunction; these species have been isolated for different lengths of time, from the Miocene to Pleistocene. Results: Molecular evolutionary analyses revealed that >90% of the genes examined are under purifying selection and <10% are under positive selection, and this pattern was observed for all taxon pairs, despite differences in divergence time. The divergence level at synonymous sites shared by most POGs in each taxon pair predicts the divergence time between the species/varieties. Divergence time estimates were positively correlated with abundance of genes under moderate purifying selection, but negatively correlated with abundance of genes under strong purifying selection. We identified 200 genes under strong positive selection across the species pairs, with 14 shared by 10-15 pairs and one shared by all taxon pairs. An additional 15 loci annotated to biological processes responding to various stimuli were present in 1-3 pairs.Conclusions: Our results suggest a common "most genes conserved–few genes adaptive" genomic architecture for the taxon pairs, which may be a key for maintaining a balance between the ability to conserve ancestral functions and the ability to evolve new features beneficial for new adaptations. As geographic isolation proceeds through time, the evolutionary trajectory of some genes changed from strong purifying selection to more relaxed selection. The allopatric divergence of these taxon pairs involved both neutral and adaptive evolution of functional genes.
Novelty and emergent patterns in sperm: morphological diversity and evolution of spermatozoa and sperm conjugation in ground beetles (Coleoptera: Carabidae)
<p>The beetle family Carabidae, with about 40,000 species, exhibits enough diversity in sperm structure and behavior to be an excellent model system for studying patterns and processes of sperm evolution. We explore their potential, documenting<b> </b>sperm form in 177 species of ground beetles using light microscopy and collecting data on 1 qualitative and 7 quantitative sperm phenotypic traits. Our sampling captures 61% of the tribal-level diversity of ground beetles. These data highlight the notable morphological diversity of sperm in ground beetles and suggest that sperm in the group have dynamic evolutionary histories with much morphological innovation and convergence. Sperm vary among species in total length (48–3,400mm), head length (0.5–270mm), and head width (0.2–6.3mm). Most ground beetles make sperm with heads that are indistinct from the flagella at the gross morphological level. However, some or all <i>Omophron</i>,<i>Trachypachus</i>, and Dyschiriini make broad-headed sperm that show morphological differences between species. Most ground beetles package their sperm into groups of sperm, termed conjugates, and ground beetles show variation in conjugate form and in the number and arrangement of sperm in a conjugate. Most ground beetles make sperm conjugates by embedding their sperm in a hyaline rod or spermatostyle. The spermatostyle is remarkably variable among species and varies in length from 17–41,000mm. Several unrelated groups of ground beetles make only singleton sperm, including Nebriinae, Cicindelinae, many Trechinae, and the tribe Paussini. In order to study patterns in sperm evolution, we combine these data with a low-resolution phylogeny of ground beetles. Results from modern comparative analyses suggest the following: sperm differ from conjugates in some aspect of their underlying evolutionary process, sperm have influenced conjugate evolution and vice versa, and conjugation with a spermatostyle likely evolved early within the history of Carabidae and it has been lost independently at least three times.</p>
Supplementary Data for: A time-calibrated 'Tree of Life' of aquatic insects for knitting historical patterns of evolution and measuring extant phylogenetic biodiversity across the world
<p>This compendium of files includes the dated phylogenetic tree in Newick format (<strong>Data S1</strong>), the list of statistical routines used for the three empirical case studies (<strong>Data S2</strong>), and the high-resolution version of the figures in the supplementary materials and main text (<strong>Data S3</strong>) for the <em>Earth-Science Reviews</em> paper "A time-calibrated ‘Tree of Life’ of aquatic insects for knitting historical patterns of evolution and measuring extant phylogenetic biodiversity across the world", which is under consideration. The best-scoring molecular tree (<strong>Data S1</strong>) can be opened using freely available programs like R (R Development Core Team, 2021), Dendroscope (Huson and Scornavacca, 2012), and FigTree (Rambaut, 2018).</p> <p>Please, feel free to send an email to the maintainer Dr. Jorge García Girón (jogarg@unileon.es OR Jorge.Garcia-Giron@oulu.fi) if you face any trouble downloading, opening, or using these files.</p> <ul> <li>Huson, D. H., & Scornavacca, C. (2012). Dendroscope 3: An interactive tool for rooted phylogenetic trees and networks. <em>Systematic Biology</em>, <em>61(6)</em>, 1061–1067.</li> <li>R Development Core Team (2021). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/</li> <li>Rambaut, A. (2018). FigTree. Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK. http://tree.bio.ed.ac.uk/software/figtree/</li> </ul>
Uncovering the effects of Müllerian mimicry on the evolution of conspicuousness in colour patterns
Variation in the conspicuousness of colour patterns is observed within and among defended prey species. The evolution of conspicuous colour pattern in defended species can be strongly impaired because of increased detectability by predators. Nevertheless, such evolution of the colour pattern can be favoured if changes in conspicuousness result in Müllerian mimicry with other defended prey. Here, we develop a model describing the population dynamics of a conspicuous defended prey species, and we assess the invasion conditions of derived phenotypes that differ from the ancestral phenotype by their conspicuousness. Such change in conspicuousness may then modify their level of mimicry with the local community of defended species. Derived colour pattern displayed in this focal population can therefore be either exactly similar, partially resembling or completely dissimilar to the local mimicry ring displaying the ancestral colour pattern. We assume that predation risk depends (1) on the number of individuals sharing a given colour pattern within the population, (2) on the occurrence of co-mimetic defended species, and (3) on the availability of alternative edible prey. Using a combination of analytical derivations and numerical simulations, we show that colour patterns that are less conspicuous than the ancestral one are generally favoured within mimicry rings, unless reduced conspicuousness impairs mimicry. By contrast, when a mutation affecting the colour pattern leads to a shift toward a better protected mimicry ring, a more conspicuous colour pattern can be favoured. The selected aposematic pattern then depends on the local communities of defended and edible prey, as well as on the detectability, memorability and level of mimicry of the colour patterns.
Temperature-dependent evolutionary speed shapes the evolution of biodiversity patterns across tetrapod radiations
<p>Biodiversity varies predictably with environmental energy around the globe, but the underlying mechanisms remain incompletely understood. The evolutionary speed hypothesis predicts that environmental energy shapes variation in speciation rates through temperature- or life history-dependent rates of evolution. To test whether variation in evolutionary speed can explain the relationship between energy and biodiversity in birds, mammals, amphibians, and reptiles, we simulated diversification over 65 million years of geological and climatic change with a spatially explicit eco-evolutionary simulation model. We modeled four distinct evolutionary scenarios in which speciation-completion rates were dependent on temperature (M1), life history (M2), temperature and life history (M3), or were independent of temperature and life-history (M0). To assess the agreement between simulated and empirical data, we performed model selection by fitting supervised machine learning models to multidimensional biodiversity patterns. We show that a model with temperature-dependent rates of speciation (M1) consistently had the strongest support. In contrast to statistical inferences, which showed no general relationships between temperature and speciation rates in tetrapods, we demonstrate how process-based modeling can disentangle the causes behind empirical biodiversity patterns. Our study highlights how environmental energy has played a fundamental role in the evolution of biodiversity over deep time.</p>
Fuel Consumption Patterns linked to Evolution of India's PM2.5 Pollution Between 1998 and 2020
<p>These datasets are part of Supplementary information for the journal article<br> "<a href="https://doi.org/10.1039/D2EA00027J">Evolution of India’s PM2.5 Pollution Between 1998 and 2020 Using Global Reanalysis Fields Coupled with Satellite Observations and Fuel Consumption Patterns</a>"</p> <p>Pollution data summaries are listed <a href="https://doi.org/10.5281/zenodo.7115052">here</a>.<br> <a href="https://doi.org/10.5281/zenodo.7115052">https://doi.org/10.5281/zenodo.7115052</a></p> <p>Fuel consumption and activity data over the years is collected from indiastats.<br> Excel files include absolute activity data.<br> Figures are showing the ratio to year 2000 for each of the categories<br> Individual figures are included in the power point for reference and use.<br> Individual figures are also included in the respective excel files</p> <p>Files listed below</p> <ol> <li>coal.consumption.total.xlsx (total coal)</li> <li>electricity.consumption.xlsx (industry, domestic, railways, agriculture, commercial, and total)</li> <li>fuel.consumption.xlsx (LPG, petrol, diesel, kerosene, ATF, others, and petcoke)</li> <li>pass.freight.movement.xlsx (freight as tonne/km and passenger as pass/km)</li> <li>vehicle.registrations.xlsx (2-wheelers+4-wheelers, buses, freight, and all vehicles)</li> </ol>
Frontiers in Ecology and Evolution 01 frontiersin.org Why grazing and soil matter for dry grassland diversity: New insights from multigroup structural equation modeling of micro-patterns
<p>Grazing is recognized as a major process driving the composition of plant<br> communities in grasslands, mostly due to the heterogeneous removal of<br> plant species and soil compaction that results in a mosaic of small patches<br> called micro-patterns. To date, no study has investigated the differences in<br> composition and functioning among these micro-patterns in grasslands in<br> relation to grazing and soil environmental variables at the micro-local scale.<br> In this study, we ask (1) To what extent are micro-patterns different from each<br> other in terms of species composition, species richness, vegetation volume,<br> evenness, and functioning? and (2) based on multigroup structural equation<br> modeling, are those differences directly or indirectly driven by grazing and soil<br> characteristics? We focused on three micro-patterns of the Mediterranean dry<br> grassland of the Crau area, a protected area traditionally grazed in the South-<br> East of France. From 70 plant community relevés carried out in three micro-<br> patterns located in four sites with different soil and grazing characteristics,<br> we performed univariate, multivariate analyses and applied structural equation<br> modeling for the first time to this type of data. Our results show evidence<br> of clear differences among micro-pattern patches in terms of species<br> composition, vegetation volume, species richness, evenness, and functioning<br> at the micro-local scale. These differences are maintained not only by direct<br> and indirect effects of grazing but also by several soil variables such as fine<br> granulometry. Biological crusts appeared mostly driven by these soil variables,<br> whereas reference and edge communities are mostly the result of different<br> levels of grazing pressure revealing three distinct functioning specific to each<br> micro-pattern, all of them coexisting at the micro-local scale in the studied<br> Mediterranean dry grassland. This first overview of the multiple effects of<br> grazing and soil characteristics on communities in micro-patterns is discussed<br> within the scope of the conservation of dry grasslands plant diversity.</p>
Fig. 24. A in Phylogeny of Eulithis Hübner and Related Genera (Lepidoptera: Geometridae), with an Implication of Wing Pattern Evolution
Fig. 24. A reconstruction of wing pattern element. White branches: bandshaped; black branches: lines.
Fig. 16 in Phylogeny of Eulithis Hübner and Related Genera (Lepidoptera: Geometridae), with an Implication of Wing Pattern Evolution
Fig. 16. Female genitalia. Scale bar = 1 mm. A. Chartographa (= Callabraxas) ludovicaria; B. C. (= Callabraxas) fabiolaria; C. Callabraxas (= Gandaritis) maculata; D. Gandaritis fixseni; E. Chartographa (= Callabraxas) compositata.
Fig. 21 in Phylogeny of Eulithis Hübner and Related Genera (Lepidoptera: Geometridae), with an Implication of Wing Pattern Evolution
Fig. 21. Character reconstruction over the preferred cladogram of Eulithis and related genera (continued). Presence of marking on the tornus of hindwing (character 14). White branches: without marking; hatched branches: tinged with blackish waved lines; black branches: yellowish marking. See fig. 19 for abbreviations.
Fig. 17 in Phylogeny of Eulithis Hübner and Related Genera (Lepidoptera: Geometridae), with an Implication of Wing Pattern Evolution
Fig. 17. Strict consensus of 38 equally most parsimonious trees with length of 353, derived from the data matrix shown in Table 2. Abbreviations for genera, see Table 2.
Fig. 3 in Phylogeny of Eulithis Hübner and Related Genera (Lepidoptera: Geometridae), with an Implication of Wing Pattern Evolution
Fig. 3. Adults of ingroup taxa. A. Eulithis diversilineata; B. E. testata; C. E. propulsata; D. E. populata; E. E. luteolata; F. E. destinata; G. E. xylina; H. E. (= Gandaritis) pyraliata; I. E. mellinata; J. E. (= Gandaritis) powellata.
Fig. 1 in Phylogeny of Eulithis Hübner and Related Genera (Lepidoptera: Geometridae), with an Implication of Wing Pattern Evolution
Fig. 1. Adults of Abraxas Leach and its larentiine mimics. 1st row (from left to right). Abraxas sylvata (Ennominae); Xanthorhoe abraxina; Eucosmabraxas (= Gandaritis) placida; Calleulype (= Gandaritis) whitelyi. 2nd row. Callabraxas (= Gandaritis) maculata; Eucosmabraxas (= Gandaritis) evanescens; E. (= Gandaritis) pseudolargetaui; E. (= Gandaritis) octoscripta. 3rd row. Gandaritis agnes; G. subalba; G. fixseni. 4th row. Chartographa (= Callabraxas) fabiolaria; C. (= Callabraxas) trigoniplaga; C. (= Callabraxas) intersectaria; C. (= Callabraxas) plurilineata. 5th row. Eulithis convergenata; Chartographa (= Callabraxas) compositata; C. (= Callabraxas) ludovicaria; C. (= Callabraxas) convexa (Larentiinae).
Fig. 8 in Phylogeny of Eulithis Hübner and Related Genera (Lepidoptera: Geometridae), with an Implication of Wing Pattern Evolution
Fig. 8. Wing pattern elements of ingroup. The drawings are not to scale. Numbers indicate character and character state. A. Eustroma melancholicum; B. Chartographa (= Callabraxas) compositata; C. Gandaritis fixseni; D. Eustroma reticulatum.
Fig. 12 in Phylogeny of Eulithis Hübner and Related Genera (Lepidoptera: Geometridae), with an Implication of Wing Pattern Evolution
Fig. 12. Male genital capsule. Scale bar = 1 mm. A. Lobogonodes multistriata; B. Eulithis (= Gandaritis) pyraliata; C. E. (= Gandaritis) powellata; D. E. luteolata; E. E. propulsata.
Fig. 4 in Phylogeny of Eulithis Hübner and Related Genera (Lepidoptera: Geometridae), with an Implication of Wing Pattern Evolution
Fig. 4. Scanning electron micrographs of male antennae, ventral surface (character 0). AB. Eulithis diversilineata; CD. E. xylina; EF. E. populata.
Fig. 23 in Phylogeny of Eulithis Hübner and Related Genera (Lepidoptera: Geometridae), with an Implication of Wing Pattern Evolution
Fig. 23. Character reconstruction over the preferred cladogram of Eulithis and related genera (continued). Presence of black dots on abdomen (character 18). White branches: absent; black branches: present. See fig. 19 for abbreviations.
Fig. 15 in Phylogeny of Eulithis Hübner and Related Genera (Lepidoptera: Geometridae), with an Implication of Wing Pattern Evolution
Fig. 15. Female genitalia. Scale bar = 1 mm. A. Eustroma (= Antepirrhoe) semiatratum; B. Evecliptopera illitata; C. Eulithis luteolata; D. E. explanata; E. E. (= Gandaritis) powellata.
Fig. 2 in Phylogeny of Eulithis Hübner and Related Genera (Lepidoptera: Geometridae), with an Implication of Wing Pattern Evolution
Fig. 2. Adults of ingroup taxa. A. Ecliptopera (= Gandaritis) atricolorata; B. Lobogonodes multistriata; C. Eustroma (= Antepirrhoe) fasciatum; D. Eustroma (= Antepirrhoe) atrifasciatum; E. Evecliptopera illitata; F. Eustroma reticulatum; G. Eustroma aerosum; H. Eustroma melancholicum; I. Eulithis ledereri; J. Eulithis explanata.
Fig. 14 in Phylogeny of Eulithis Hübner and Related Genera (Lepidoptera: Geometridae), with an Implication of Wing Pattern Evolution
Fig. 14. Female genitalia. Scale bar = 1 mm. A. Eustroma aerosum; B. Eucosmabraxas (= Gandaritis) evanescens; C. Calleulype (= Gandaritis) whitelyi; D. Ecliptopera (= Gandaritis) atricolorata.
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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.