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53 results for “convergent patterns”
Convergent approaches to AI Explainability for HEP muonic particles pattern recognition Dataset
<p>Dataset associated to the publication "Convergent approaches to AI Explainability for HEP muonic particles pattern recognition", Leandro Maglianella, Lorenzo Nicoletti, Stefano Giagu*, Christian Napoli, and Simone Scardapane, submitted to Computing and Software for Big Science.</p> <p>*corresponding author: stefano.giagu [AT] uniroma1.it</p> <p>Description:</p> <p>provided as a compressed zip file. Contains 7 numpy .npy files:</p> <ul> <li>train_images_with_noise.npy: numpy array containing 850003 "images" of muonic tracks with detector noise (shape (850003, 9, 384)). Each image contains 1 muonic track.</li> <li>train_images_without_noise.npy: numpy array containing 850003 "images" of muonic tracks w/o detector noise (shape (850003, 9, 384)). Each image contains 1 muonic track.</li> <li>train_labels.npy: labels associated to each image (shape (850003, 5)), corresponding to (pT, eta, phi, 0, nhits) of the muonic track, with pT: transverse momentum, eta: pseudo-rapidity, phi: azimuthal angle, and nhits: the number of pixels turned on by the muon</li> <li>test_images_with_noise.npy: same as above for a 94445 images test set</li> <li>test_images_without_noise.npy: same as above for a 94445 images test set</li> <li>test_labels.npy: same as above for a 94445 images test set</li> <li>images_only_noise.npy: numpy array containing 944448 "images" w/o muons, containing detector noise only (shape (944448, 9, 384))</li> </ul>
Convergent geographic patterns between grizzly bear population genetic structure and Indigenous language groups in coastal British Columbia
<p>Microsatellite loci calls, sex, and mean centre detection per individual (GrizzlyMicroLociMeanXY.csv) and code associated with the paper: "Convergent geographic patterns between grizzly bear population genetic structure and Indigenous language groups in coastal British Columbia". All code is from published R packages or GitHub repositories not created by the author. Code used is best described in these alternate resources. </p>
Replication Data For: Spiking patterns in the globus pallidus highlight convergent neural dynamics across diverse genetic dystonia syndromes
<div><strong>Human Globus Pallidum Single-Unit Activity Dataset in Genetic Dystonia Patients</strong></div> <div> </div> <div>This dataset consists of tabular data encompassing diverse neural features extracted from spiking trains of stable single-unit activity. These units were isolated from raw microelectrode recordings obtained from the globus pallidum of genetic dystonia patients who underwent globus pallidus internal (GPi) deep brain stimulation (DBS) surgery. The dataset includes anonymized patient IDs, details about the patient's genetic dystonia mutation, as well as information on the hemisphere and depth of microelectrode recordings (MER). Additionally, it features neural properties such as firing rate, spiking regularity, neural bursts, oscillations, and pause characteristics of isolated single-unit activities (SUAs).</div> <div> </div> <div>To process the raw MER, we applied a semi-parametric offline spike sorting algorithm to isolate SUAs. The SUAs were analyzed both in the temporal and frequency domains to derive a comprehensive set of features related to spiking patterns.</div> <div> </div> <div>For those interested in replicating or understanding the feature extraction process, the MATLAB source code is available in the <a href="github.com/ahmetofficial/Spike-Feature-Generator">Github repository</a>.</div>
Data from: Complex dynamics underlie the evolution of imperfect wing pattern convergence in butterflies
Adaptive radiation is characterized by rapid diversification that is strongly associated with ecological specialization. However, understanding the evolutionary mechanisms fueling adaptive diversification requires a detailed knowledge of how natural selection acts at multiple life-history stages. Butterflies within the genus Adelpha represent one of the largest and most diverse butterfly lineages in the Neotropics. Although Adelpha species feed on an extraordinary diversity of larval hosts, convergent evolution is widespread in this group suggesting that selection for mimicry may contribute to adaptive divergence among species. To investigate this hypothesis, we conducted predation studies in Costa Rica using artificial butterfly facsimiles. Specifically, we predicted that non-toxic, palatable Adelpha species that do not feed on host plants in the family Rubiaceae would benefit from sharing a locally convergent wing pattern with the presumably toxic Rubiaceae-feeding species via reduced predation. Contrary to expectations, we found that the presumed mimic was attacked significantly more than its locally convergent model, at a frequency paralleling attack rates on both novel and palatable prey. Although these data reveal the first evidence for protection from avian predators by the supposed toxic, Rubiaceae-feeding Adelpha species, we conclude that imprecise mimetic patterns have high costs for Batesian mimics in the tropics.
Data from: Complex dynamics underlie the evolution of imperfect wing pattern convergence in butterflies
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FIGURE 1 in A new species of Hemiphyllodactylus Bleeker (Squamata; Gekkonidae) from Peninsular Thailand that converges in morphology and color pattern on Pseudogekko smaragdinus (Taylor) from the Philippines
FIGURE 1. Confirmed localities of Hemiphyllodactylus pardalis sp. nov. and other species of Hemiphyllodactylus known from Thailand. The type locality of H. pardalis sp. nov. is indicated with a square; other localities are indicated with circles. Data for H. chiangmaiensis come from Grismer et al. (2014), data for H. flaviventris and H. khlonglanensis come from Sukprasert et al. (2018), data for H. cf. yunnanensis come from Zug (2010 and pers. comm, 2020), and data for H. typus come from voucher photos from Khao Luang, Nakkon Si Thammarat (LSUDPC 11147–50) in the south and Khao Yai, Nakkon Ratchasima (LSUDPC 11151–54) in the north. Photo thumbnail illustrates the paratype of Hemiphyllodactylus pardalis sp. nov. (AUP-00766, adult female), photo by Parinya Pawangkhanant.
Data from: Evaluating patterns of convergent evolution and trans-species polymorphism at MHC immunogenes in two sympatric stickleback species
The immunologically important major histocompatibility complex (MHC) harbors some of the most polymorphic genes in vertebrates. These genes presumably evolve under parasite-mediated selection and frequently show inconsistent allelic genealogies, where some alleles are more similar between species than within species. This phenomenon is thought to arise either from convergent evolution under parallel selection or from the preservation of ancient allelic lineages beyond speciation events (trans-species polymorphism, TSP). Here we examine natural populations of two sympatric stickleback species (Gasterosteus aculeatus and Pungitius pungitius) to investigate the contribution of these two mechanisms to the evolution of inconsistent allelic genealogies at the MHC. Overlapping parasite taxa between the two host species in three different habitats suggest contemporary parallel selection on the MHC genes. Accordingly, we detected a lack of species-specific phylogenetic clustering in the immunologically relevant antigen-binding residues of the MHC IIB genes which contrasted with the rest of the coding and non-coding sequence. However, clustering was not habitat-specific and a codon-usage analysis revealed patterns of similarity by descent. In this light, common descent via TSP, in combination with intra-species gene conversion, rather than convergent evolution is the more strongly supported scenario for the inconsistent genealogy at the MHC.
Data from: Phylo-allometric analyses showcase the interplay between life history patterns and phenotypic convergence in cleaner wrasses
Phenotypic convergence is a macroevolutionary pattern that need not be consistent across life history. Ontogenetic transitions in dietary specialization clearly illustrate the dynamics of ecological selection as organisms grow. The extent of phenotypic convergence among taxa that share a similar ecological niche may therefore vary ontogenetically. Because ontogenetic processes have been shown to evolve, phylogenetic comparative methods can be useful in examining how the scaling of traits relates to ecology. Cleaning, a behavior in which taxa consume ectoparasites off clientele, is well-represented among wrasses (Labridae). Nearly three-fourths of labrids that clean do so predominately as juveniles, transitioning away as adults. We examine the scaling patterns of 33 labrid species to understand how life history patterns of cleaning relate to ontogenetic patterns of phenotypic convergence. We find that as juveniles, cleaners exhibit convergence in body and cranial traits that enhance ectoparasitivory. We then find that taxa that transition away from cleaning exhibit ontogenetic trajectories that are distinct from those of other wrasses. Obligate and facultative species that continue to clean over ontogeny, however, maintain characteristics that are conducive to cleaning. Collectively, we find that life history patterns of cleaning behavior are concordant with ontogenetic patterns in phenotype in wrasses.
Krieg et al. (2024) Fern gametophytes exhibit distinct patterns of niche exploration and global convergence in ecophysiological functioning
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Fig. 7 in Camel spider trait evolution demonstrates repeated patterns of convergence (Arachnida: Solifugae: Eremobatidae)
Fig. 7. Ancestral state estimation and mapping of binary states of male A) male flagellar groove and B) fondal notch. Absent = no flagellar groove/no fondal notch, present = flagellar groove/fondal notch.
Fig. 4 in Camel spider trait evolution demonstrates repeated patterns of convergence (Arachnida: Solifugae: Eremobatidae)
Fig. 4. Maximum likelihood topology of Eremobatidae inferred using IQ-TREE 2 and the 75% occupancy concatenated UCE matrix with taxa that rendered>10 UCE loci with outgroups removed. Nodal support for major clades refer to maximum likelihood bootstrap values (ML) on the left and local posterior probabilities estimated based on gene tree quartet frequencies in ASTRAL (MSC) on the right.Tip colors illustrate generic designations as per current eremobatid taxonomy. Male (left column) and female (right column) structures of eremobatid species are shown on the right of the topology. Images are ordered phylogenetically. A) Eremochelis andreasana (♂, DMNS ZA.41919; ♀, DMNS ZA.40822). B) Hemerotrecha marathoni (♂, CNAN loan; ♀, CNAN loan). C) Hemerotrecha xena (♂, DMNS ZA.16469; ♀, DMNS ZA.42101). D) Eremochelis bilobatus (♂, DMNS ZA.17629; ♀, DMNS ZA.17359). E) Horribates spinigerus (♂, DMNS ZA.40086; ♀, AMNH_ Holotype). F) Chanbria regalis (♂, DMNS ZA.25443; ♀, DMNS ZA.25442). G) Hemerotrecha serrata (♂, DMNS ZA.16059; ♀, DMNS ZA.22169). H) Eremochelis flexacus (♂, DMNS ZA.16134; ♀, DMNS ZA.23593). I) Hemerotrecha parva (♂, DMNS ZA.42131; ♀, DMNS ZA.42131). J) Eremochelis larreae (♂, CASENT9033550; ♀, DMNS ZA.33721). K) Eremochelis insignatus (♂, DMNS ZA.28260; ♀, DMNS ZA.26390). L) Eremochelis striodorsalis (♂, DMNS ZA.31773; ♀, DMNS ZA.23593). M) Hemerotrecha californica (♂, DMNS ZA.18288; ♀, DMNS ZA.32217). All scale bars represent 1 mm.
Fig. 8 in Camel spider trait evolution demonstrates repeated patterns of convergence (Arachnida: Solifugae: Eremobatidae)
Fig. 8. Ancestral state estimation and mapping of Gaussian mixture modeling (GMM) cluster membership onto our phylogram for ingroup male eremobatid species inferred from Elliptical Fourier coefficients for chelicerae. Character states 1−4 refer to the 4 distinct clusters in morphospace (Fig. 5B).
Fig. 1. Male chelicera variation from the family Eremobatidae. A in Camel spider trait evolution demonstrates repeated patterns of convergence (Arachnida: Solifugae: Eremobatidae)
Fig. 1. Male chelicera variation from the family Eremobatidae. A) Hemerotrecha parva (DMNS ZA.42131), B) Hemerotrecha macra (DMNS ZA.35652), C) Eremochelis branchi (DMNS ZA.38315), D) Eremochelis flexacus (DMNS ZA.16134), E) Chanbria regalis (DMNS ZA.25444), F) Eremorhax magnus (DMNS ZA.42055. Photograph credit: Cole Logan), G) Hemerotrecha hanfordana (DMNS ZA.37358), H) Horribates spinigerus (DMNS ZA.40086), I) Eremobates leechi (DMNS ZA.37070. Photograph credit: Quincy Hansen). All scale bars refer to 1 mm, except F, which refers to 2.5 mm.
Fig. 3 in Camel spider trait evolution demonstrates repeated patterns of convergence (Arachnida: Solifugae: Eremobatidae)
Fig. 3. Summary of the quantitative and qualitative traits considered in this study for eremobatid males and females. A) Right, retrolateral view of male Eremochelis insignatus (DMNS ZA.33749) chelicera. Measurements considered in this study are illustrated. B) Scanning electron microscope (SEM) image of papillated texturing inside flagellar groove of Eremochelis branchi (DMNS ZA.37135). C) SEM image of prolateral view of male fixed finger and associated flagellar groove belonging to Eremochelis branchi (DMNS ZA.37135). D) Right, retrolateral view of female chelicera of Hemerotrecha delicatula (DMNS ZA.41812) depicting the fixed finger tooth pattern and tip (apex) of fixed finger to fixed finger distal tooth (FF-to-FD) measure. Coloration and abbreviations follow Bird et al. (2015).Terminology abbreviations are FD = fixed finger, distal teeth, FSD = fixed finger, subdistal teeth, FM = fixed finger, medial teeth, FSM = fixed finger, submedial teeth, FP = fixed finger, proximal teeth. E) Operculum length, width, and diagonal measures on female Eremochelis plicatus (DMNS ZA.41887).
Fig. 2 in Camel spider trait evolution demonstrates repeated patterns of convergence (Arachnida: Solifugae: Eremobatidae)
Fig. 2. Female cheliceral morphology from representatives of the family Eremobatidae. A) Hemerotrecha delicatula (DMNS ZA.41812), B) Eremochelis striodorsalis (DMNS ZA.18968), C) Horribates spinigerus (AMNH Holotype), D) Chanbria rectus (DMNS ZA.25456), E) Eremochelis andreasana (DMNS ZA.40822), F) Hemerotrecha serrata (DMNS ZA.25449), G) Hemerotrecha sp. (CIDA107821), H) Hemerotrecha prenticei (DMNS ZA.18169), I) Eremochelis bilobatus (DMNS ZA.17685). All scale bars refer to 1 mm.
Fig. 6 in Camel spider trait evolution demonstrates repeated patterns of convergence (Arachnida: Solifugae: Eremobatidae)
Fig. 6. Ancestral state reconstruction of EFA coefficients. A) PC1 from the PCA of male chelicera EF coefficients and B) PC1 from the PCA of female opercula EF coefficients.
Fig. 5 in Camel spider trait evolution demonstrates repeated patterns of convergence (Arachnida: Solifugae: Eremobatidae)
Fig. 5. Morphospace plots based on PCA analysis of EF coefficients and GMM cluster assignments recovered from the first 3 PCs as input. Individuals with uncertain cluster membership are displayed in gray.Top row pertains to male chelicera, central row depicts female chelicera, and bottom row refers to female opercula. All PCA plots summarize PC1 and PC2 and illustrate: A) male cheliceral shape by genus, B) male cheliceral shape by cluster membership with mean shapes of each cluster to the right (cluster 1 was not supported after implementing the 0.95 uncertainty threshold), C) female cheliceral shape by genus, D) female cheliceral shape by cluster membership with mean shapes of each cluster to the right, E) female opercula shape by genus, F) female opercula shape by cluster membership with reconstructed operculum from the single opercula median shape. All shapes are not to scale.
Data from 'Convergent patterns of body size variation in distinct parasite taxa with convergent life cycles'
<p><b>Aim:</b> Interspecific variation among metazoans often follows a latitudinal pattern, with species at higher latitudes being larger-bodied than related species from lower latitudes (Bergmann's rule). For parasitic species, body sizes within any higher taxon often correlate with the body sizes of their hosts (Harrison's rule). Whether temperature-driven latitudinal effects or host-driven resource constraints act independently or additively to shape interspecific variation in parasite body sizes remains unknown. We use a comparative approach to test the effects of latitude and host body size on parasite body sizes in two taxa of parasitic worms showing convergent life cycles.</p> <p><b>Location:</b> Global.</p> <p><b>Time period:</b> Contemporary.</p> <p><b>Major taxa studied:</b> Hairworms (Nematomorpha) and mermithids (Nematoda) parasitic in arthropods.</p> <p><b>Methods:</b> With 223 records for mermithids and 258 for nematomorphs worldwide, we used linear mixed effects models to test the effects of latitude and host body size on parasite length, intraspecific length variation, parasite egg diameter, and variation in egg diameter. Further, we modelled parasite length with local mean annual temperature as predictor instead of latitude, as a direct test of underlying mechanisms. All models took into account host and parasite taxonomic structure within the datasets.</p> <p><b>Results:</b> For both taxa, host body size was clearly the main determinant of parasite body length, with neither latitude nor local temperature (annual mean or range) having an effect. No predictor affected intraspecific length variation, whereas egg diameter was positively associated with parasite length and variation in egg diameter was negatively associated with latitude.</p> <p><b>Main conclusions:</b> Our results support a strong role for host traits in shaping the evolution of parasite body sizes (Harrison's rule), but no role for latitude (Bergmann's rule), even though these parasites infect ectothermic hosts.<span> At a mechanistic level, the evolutionary driving force of external temperature on parasite physiology seems to be eclipsed by the availability of resources from the host.</span></p>
Script and data used in: A lot of convergence, a bit of divergence: environment and interspecific interactions shape body color patterns in Lissotriton newts
<p>Coexistence with related species poses evolutionary challenges to which populations may react in diverse ways. When exposed to similar environments, sympatric populations of two species may adopt similar phenotypic trait values. However, selection may also favor trait divergence as a way to reduce competition for resources or mates. The characteristics of external body parts, such as coloration and external morphology, are involved to varying degrees in intraspecific signaling as well as in the adaptation to the environment, and consequently may be diversely affected by interspecific interactions in sympatry. Here, we studied the effect of sympatry on various color and morphological traits in males and females of two related newt species <i>Lissotriton helveticus</i> and <i>L. vulgaris</i>. Importantly, we did not only estimate how raw trait differences between species respond to sympatry, but also the marginal responses after controlling for environmental variation. We found that dorsal and caudal coloration converged in sympatry, likely reflecting their role in adaptation to local environments, especially concealment from predators. In contrast, aspects of male and female ventral coloration, which harbours sexual signals in both species, diverged in sympatry. This divergence may reduce opportunities for interspecific sexual interactions and the associated loss of energy, suggesting reproductive character displacement (RCD). Our study emphasizes the contrasting patterns of traits involved in different functions and calls for the need to consider this diversity in evolutionary studies.</p>
Figure 6 in Morphology, morphogenesis, and molecular phylogeny of a new marine urostylid ciliate (Ciliophora, Stichotrichia) from the South China Sea, and a brief overview of the convergent evolution of the midventral pattern within the Spirotrichea
Figure 6. The maximum-likelihood (ML) tree inferred from the small subunit ribosomal RNA (SSU rRNA) gene sequences of 63 spirotrichous taxa, showing the position of Bergeriella ovata gen. et sp. nov. (boxed), and the phylogenetic relationships among the taxa possessing midventral cirral rows (i.e. urostylids s.l.; branches are depicted by thick lines, and species names are highlighted in bold text). Nodal support for branches in the ML, Bayesian inference (BI), and neighbour-joining (NJ) trees are marked in order. Bootstrap values lower than 50% and Bayesian posterior probabilities lower than 0.70 are replaced with hyphens. Clades with different topologies in the NJ tree relative to the ML and BI trees are indicated with asterisks. All branches are drawn to scale. The scale bar corresponds to five substitutions per 100 nucleotide positions. Phacodinium and Protocruzia were taken as out-group taxa.
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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.