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15,277 results for “GENETICS”
Data from: Propagule pressure and genetic diversity enhance colonization by a ruderal species: a multi-generation field experiment
Colonization is a critical filter, setting the stage for short-term and long-term population success. Increased propagule pressure (e.g., more founding individuals) usually enhances colonization; however, this pattern may be driven by purely numeric effects, population genetic diversity effects, or both. To determine the independent and interactive effects of propagule pressure and genetic diversity, we conducted a seed addition experiment in the field using the ruderal annual Arabidopsis thaliana. Propagule pressure treatments spanned five levels, from 32 to 960 seeds per 0.25-m2 plot. Founder populations were composed of one, four or eight genotypes and exposed to ambient or reduced levels of interspecific competition. Genotype monocultures were included to quantify additive versus non-additive effects. Populations were followed for three generations, with abundance, population persistence and genotype retention (the proportion of introduced genotypes persisting over time) as the major response variables. Increased propagule pressure enhanced abundance immediately following introduction, particularly where nutrient availability was high and competition reduced. Greater propagule pressure also increased the likelihood of population persistence and genotype retention through three generations. However, most populations experienced rapid abundance declines over time, yielding no relationship between propagule pressure and third-generation abundance across persisting populations. Under reduced competition, increased genetic diversity led to a marginal increase in persistence through the third generation that was more pronounced, and statistically significant, in low nutrient conditions. Genetic diversity did not affect persistence through the first generation, thus indicating that genetic diversity effects strengthened over time. Nevertheless, genotypic mixture populations fell short of expectations based on performance in monocultures (negative non-additive effects). Increased genetic diversity was also associated with abundance declines, largely due to one particularly high-performing genotype in the lowest diversity treatments (i.e, genotypic identity effects). Overall, our results indicate that increases in both propagule pressure and genetic diversity can enhance colonization success but are highly context-dependent. They also highlight novel ways in which both factors can impact the retention of introduced genetic diversity over time. Our findings pinpoint the determinants of a fundamental population process and have key implications for applications where enhanced or suppressed colonization is desired, including ecological restoration and invasive species management.
Data from: Inferring continuous and discrete population genetic structure across space
A classic problem in population genetics is the characterization of discrete population structure in the presence of continuous patterns of genetic differentiation. Especially when sampling is discontinuous, the use of clustering or assignment methods may incorrectly ascribe differentiation due to continuous processes (e.g., geographic isolation by distance) to discrete processes, such as geographic, ecological, or reproductive barriers between populations. This reflects a shortcoming of current methods for inferring and visualizing population structure when applied to genetic data deriving from geographically distributed populations. Here, we present a statistical framework for the simultaneous inference of continuous and discrete patterns of population structure. The method estimates ancestry proportions for each sample from a set of two-dimensional population layers, and, within each layer, estimates a rate at which relatedness decays with distance. This thereby explicitly addresses the "clines versus clusters" problem in modeling population genetic variation, and remedies some of the overfitting to which nonspatial models are prone. The method produces useful descriptions of structure in genetic relatedness in situations where separated, geographically distributed populations interact, as after a range expansion or secondary contact. We demonstrate the utility of this approach using simulations and by applying it to empirical datasets of poplars and black bears in North America.
Genetic variation and phenotypic plasticity in circadian rhythms of an armed beetle, Gnatocerus cornutus (Tenebrionidae)
<p>Circadian rhythms, their free-running periods and strength of the rhythm are often used as indicators of biological clocks, and there is evidence that the free-running periods of circadian rhythm are not affected by environmental factors like temperature. However, there are few studies of environmental effects on the power of rhythms and it is not clear if temperature compensation is universal. Additionally, genetic variation and phenotypic plasticity in biological clocks are important for understanding the evolution of biological rhythm, but genetic and plastic effects are rarely investigated. Here, we used 18 isofemale lines (genotypes) of <i>Gnatocerus cornutus</i> to assess rhythms of locomotor activity, while also testing for temperature effects. We found that total activity and power of circadian rhythm were affected by interactions between sex and genotype or sex, genotype and temperature, so that while males tended to be more active and showed greater increases in activity, this effect varied across both genotypes and temperatures. The period of activity only varied by genotype and was thus independent of temperature. The complicated genotype-sex-environment interactions we recorded stress the importance of investigating circadian activity in more integrated ways.</p>
Data from: Genetic structure of the Painted Bunting and its implications for conservation of migratory populations
The Painted Bunting Passerina ciris is a Neotropical songbird which breeds primarily in the United States during the summer and migrates to Mexico, Central America, southern Florida, and the Caribbean over the winter. Male Painted Buntings are brightly coloured, which makes them highly sought after as pets, particularly in Mexico, Central America and Europe. We used short sequence repeats (microsatellite DNA) to investigate the population genetic structure of the Painted Bunting and its implications in conservation management of migratory populations. We found a detectable level of population differentiation as revealed by pairwise FST and RST comparisons and Bayesian clustering analyses, with strong support for differentiation between eastern and western Painted Buntings (e.g. Oklahoma and Georgia FST = 0.1; P = 0.005; RST = 0.18; P = 0.04) in accordance with previous mitochondrial DNA analysis. We recovered additional support for two sub‐groups within the western clade. While linking migrant songbirds captured outside of the United States to their breeding populations remains a challenge, we show that natural levels of population genetic differentiation can be detected via microsatellite DNA markers and exploited in migratory connectivity studies. We also demonstrate the potential utility of our low‐cost markers for population identification of birds recovered from the pet trade by screening a small subset of samples (n = 5) collected as part of wildlife tracking. We discuss the implications of our results for future efforts to understand patterns of population decline in Painted Buntings more generally, as well as how we might expand this methodology to combat illegal pet‐trade activity in this and other songbird species.
Data from: Deciphering genetic mate choice: not so simple in group-housed conservation breeding programs
Incorporating mate choice into conservation breeding programs can improve reproduction and the retention of natural behaviours. However, different types of genetic-based mate choice can have varied consequences for genetic diversity management. As a result, it is important to examine mechanisms of mate choice in captivity to assess its costs and benefits. Most research in this area has focused on experimental pairing trials, however this resource-intensive approach is not always feasible in captive settings and can interfere with other management constraints. We used generalised linear mixed models and permutation approaches to investigate overall breeding success in group-housed Tasmanian devils at three non-mutually exclusive mate choice hypotheses: (i) advantage of heterozygous individuals, (ii) advantage of dissimilar mates, and (iii) optimum genetic distance, using both 1,948 genome-wide SNPs and 12 MHC-linked microsatellites. The managed devil insurance population is the largest such breeding program in Australia and is known to have high variance in reproductive success. We found that non-genetic factors such as age were the best predictors of breeding success in a competitive breeding scenario, with younger females and older males being more successful. We found no evidence of mate choice under the hypotheses tested. Mate choice varies among species and across environments, so we advocate for more studies in realistic captive management contexts as experimental or wild studies may not apply. Conservation managers must weigh up the need to wait for adequate sample sizes to detect mate choice with the risk that genetic changes may occur during this time in captivity. Our study shows that examining and integrating mate choice into the captive management of species housed in realistic, semi-natural group-based contexts may be more difficult than previously considered.
Data from: Selection on a genetic polymorphism counteracts ecological speciation in a stick insect
The interplay between selection and aspects of the genetic architecture of traits (such as linkage, dominance, and epistasis) can either drive or constrain speciation. Despite accumulating evidence that speciation can progress to "intermediate" stages—with populations evolving only partial reproductive isolation—studies describing selective mechanisms that impose constraints on speciation are more rare than those describing drivers. The stick insect Timema cristinae provides an example of a system in which partial reproductive isolation has evolved between populations adapted to different host plant environments, in part due to divergent selection acting on a pattern polymorphism. Here, we demonstrate how selection on a green/melanistic color polymorphism counteracts speciation in this system. Specifically, divergent selection between hosts does not occur on color phenotypes because melanistic T. cristinae are cryptic on the stems of both host species, are resistant to a fungal pathogen, and have a mating advantage. Using genetic crosses and genome-wide association mapping, we quantify the genetic architecture of both the pattern and color polymorphism, illustrating their simple genetic control. We use these empirical results to develop an individual-based model that shows how the melanistic phenotype acts as a "genetic bridge" that increases gene flow between populations living on different hosts. Our results demonstrate how variation in the nature of selection acting on traits, and aspects of trait genetic architecture, can impose constraints on both local adaptation and speciation.
Data from: A coalescent-based estimator of genetic drift, and acoustic divergence in the Pteronotus parnellii species complex
Determining the processes responsible for phenotypic variation is one of the central tasks of evolutionary biology. While the importance of acoustic traits for foraging and communication in echolocating mammals suggests adaptation, the seldom-tested null hypothesis to explain trait divergence is genetic drift. Here we derive FST values from multi-locus coalescent isolation-with-migration models, and couple them with estimates of quantitative trait divergence, or PST, to test drift as the evolutionary process responsible for phenotypic divergence in island populations of the Pteronotus parnellii species complex. Compared to traditional comparisons of PST to FST, the migration-based estimates of FST are unidirectional instead of bidirectional, simultaneously integrate variation among loci and individuals, and posterior densities of PST and FST can be compared directly. We found the evolution of higher call frequencies is inconsistent with genetic drift for the Hispaniolan population, despite many generations of isolation from its Puerto Rican counterpart. While the Hispaniolan population displays dimorphism in call frequencies, the higher frequency of the females is incompatible with sexual selection. Instead, cultural drift toward higher frequencies among Hispaniolan females might explain the divergence. By integrating Bayesian coalescent and trait analyses, this study demonstrates a powerful approach to testing genetic drift as the default evolutionary mechanism of trait differentiation between populations.
Genetic associations of the non-MHC region with systemic sclerosis in a Han Chinese population
<p>Systemic sclerosis (SSc) is a complex autoimmune disease with unknown etiology and genetic factors contribute significantly to its pathogenesis. Several studies have identified multiple SSc-susceptible genes while the majority of them were discovered mainly in Caucasians. Recent studies have revealed significant genetic differences between different ethnicities, illustrating the importance of cross-ethnicity validation of candidate SNPs in SSc patients other than Caucasians. In this study, we recruited 1,059 SSc patients and 1,951 matched controls to validate the associations of those reported non-MHC polymorphisms in a Han Chinese population. We searched for the SNPs associated with SSc in the studies published from 2004 to 2019 through Google Scholar and PubMed with the keywords “systemic sclerosis” and “genetics”. In total, 101 SNPs were remained for validation. </p>
Climate associated genetic variation in Fagus sylvatica and potential responses to climate change in the French Alps
<p><span><span><span><span><span><span><span><span><span><span><span>Local adaptation patterns have been found in many plants and animals, highlighting the genetic heterogeneity of species along their range of distribution. In the next decades, global warming is predicted to induce a change in the selective pressures that drive this adaptive variation, forcing a reshuffling of the underlying adaptive allele distributions. For species with low dispersion capacity and long generation time such as trees, the rapidity of the change could imped the migration of beneficial alleles and lower their capacity to track the changing environment. Identifying the main selective pressures driving the adaptive genetic variation is thus necessary when investigating species capacity to respond to global warming. In this study, we investigate the adaptive landscape of <i>Fagus sylvatica</i> along a gradient of populations in the French Alps. Using a double digest restriction-site associated DNA (ddRAD) sequencing approach, we identified 7,000 SNPs from 570 individuals across 36 different sites. A redundancy analysis (RDA)-derived method allowed us to identify several SNPs that were strongly associated with climatic gradients; moreover, we defined the primary selective gradients along the natural populations of <i>F. sylvatica</i> in the Alps. Strong effects of elevation and humidity, which contrast north-western and south-eastern site, were found and were believed to be important drivers of genetic adaptation. Finally, simulations of future genetic landscapes that used these findings allowed identifying populations at risk for <i>F. sylvatica </i>in the Alps, which could be helpful for future management plans. </span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Agonistic character displacement of genetically based male colour patterns across darters
Agonistic character displacement (ACD) occurs when selection to avoid maladaptive interspecific aggression leads to the evolution of agonistic signals and/or associated behavioural biases in sympatry. Here we test for a pattern consistent with ACD in male colour pattern in darters (Percidae: Etheostoma). Male colour pattern has been shown to function in male-male competition rather than female mating preferences in several darter species. Additionally, males bias their aggression towards conspecific over heterospecific males in sympatry but not in allopatry, consistent with divergent ACD in male behavioural biases. We use a common garden approach to show that differences in male colour pattern among four closely related darter species are genetically based. Additionally, we demonstrate that some aspects of male colour pattern exhibit enhanced differences in sympatric compared to allopatric populations of two darter species, consistent with ACD. However, other male colour traits are more similar between species in sympatry compared to allopatry, indicating that not all signal components are under strong divergent selection in sympatry. This study provides evidence that interspecific male-male aggressive interactions alone can promote elaborate male signal evolution both between and within species. We discuss the implications this has for male-driven ACD and cascade ACD.
Data from: Genetic sampling for estimating density of common species
Understanding population dynamics requires reliable estimates of population density, yet this basic information is often surprisingly difficult to obtain. With rare or difficult-to-capture species, genetic surveys from noninvasive collection of hair or scat has proved cost-efficient for estimating densities. Here, we explored whether noninvasive genetic sampling (NGS) also offers promise for sampling a relatively common species, the snowshoe hare (Lepus americanus Erxleben, 1777), in comparison with traditional live trapping. We optimized a protocol for single-session NGS sampling of hares. We compared spatial capture–recapture population estimates from live trapping to estimates derived from NGS, and assessed NGS costs. NGS provided population estimates similar to those derived from live trapping, but a higher density of sampling plots was required for NGS. The optimal NGS protocol for our study entailed deploying 160 sampling plots for 4 days and genotyping one pellet per plot. NGS laboratory costs ranged from approximately $670 to $3000 USD per field site. While live trapping does not incur laboratory costs, its field costs can be considerably higher than for NGS, especially when study sites are difficult to access. We conclude that NGS can work for common species, but that it will require field and laboratory pilot testing to develop cost-effective sampling protocols.
A genetic mechanism for sexual dichromatism in birds
<p>Sexual dichromatism — a difference in coloration between males and females — is central to the study of ornamentation, mate choice, and sexual selection. Here, we show that carotenoid-based dichromatism in mosaic canaries, a hybrid product between the sexually dichromatic red siskin and monochromatic canaries, is controlled by the carotenoid-cleaving enzyme Beta-Carotene Oxygenase 2 (<i>BCO2</i>). Dichromatism in mosaic canaries is explained by differential carotenoid degradation in the integument of each sex, rather than sex-specific variation in physiological functions such as pigment uptake or transport. Transcriptome analyses suggest that carotenoid degradation in the integument might be a common mechanism contributing to sexual dichromatism in other finches. Our findings demonstrate how differences in ornamental coloration between sexes can evolve through simple molecular mechanisms controlled by genes of major effect.</p>
Data from: Evaluation of a single nucleotide polymorphism baseline for genetic stock identification of Chinook Salmon (Oncorhynchus tshawytscha) in the California Current Large Marine Ecosystem
Chinook Salmon is an economically and ecologically important species, and populations from the west coast of North America are a major component of fisheries in the North Pacific Ocean. The anadromous life history strategy of this species generates populations (or stocks) that typically are differentiated from neighboring populations. In many cases, it is desirable to discern the stock of origin of an individual fish or the stock composition of a mixed sample to monitor the stock-specific effects of anthropogenic impacts and alter management strategies accordingly. Genetic stock identification (GSI) provides such discrimination, and we describe here a novel GSI baseline composed of genotypes from more than 8000 individual fish from 69 distinct populations at 96 single nucleotide polymorphism (SNP) loci. The populations included in this baseline represent the likely sources for more than 99% of the salmon encountered in ocean fisheries of California and Oregon. This new genetic baseline permits GSI with the use of rapid and cost-effective SNP genotyping, and power analyses indicate that it provides very accurate identification of important stocks of Chinook Salmon. In an ocean fishery sample, GSI assignments of more than 1000 fish, with our baseline, were highly concordant (98.95%) at the reporting unit level with information from the physical tags recovered from the same fish. This SNP baseline represents an important advance in the technologies available to managers and researchers of this species.
Data from: Influence of a climatic gradient on genetic exchange between two oak species
Premise of the study. In plant groups with limited intrinsic barriers to gene flow, it is thought that environmental conditions can modulate interspecific genetic exchange. Oaks are known for limited barriers to gene flow among closely related species. Here, we use Quercus as a living laboratory in which to pursue a fundamental question in plant evolution: do environmental gradients restrict or promote genetic exchange between species? Methods. We focused on two North American oaks, the rare Q. dumosa and the widespread Q. berberidifolia. We sampled intensively along a contact zone in California. We sequenced restriction site associated DNA markers and measured vegetative phenotype. We tested for genetic exchange, the association with climate, and the effect on phenotype. Key results. There is evidence for genetic exchange between the species. Admixed plants are found in areas of intermediate climate, while less admixed plants are found at the extremes of the climatic gradient. Genetic and phenotypic patterns are out of phase in the zone of contact; some plants display the phenotype of one species but are genetically associated with another. Conclusions. Our results support the hypothesis that a strong climatic gradient can promote genetic exchange between species. The overall weak correlation between genotype and phenotype in the contact zone between the species suggests that genetic exchange can lead to the breakdown of trait combinations used to define species. This incongruency predicts ongoing problems for conservation of Q. dumosa, with implications for conservation of other oaks. Please be aware that if you ask to have your user record removed, we will retain your name in the records concerning manuscripts for which you were an author, reviewer, or editor. In compliance with data protection regulations, you may request that we remove your personal registration details at any time. (Use the following URL: https://www.editorialmanager.com/ajb/login.asp?a=r) Please contact the publication office if you have any questions.
Supplementary Material for Frontiers Plant Genetics and Genomics 'Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality'
<p>Authors</p> <p>Zhian N. Kamvar, Jonah C. Brooks, and Niklaus J. Grünwald</p>
Supporting datasets PubFig05 for: "Heterogeneous Ensemble Combination Search using Genetic Algorithm for Class Imbalanced Data Classification"
<p><strong>Faces Dataset: PubFig05</strong></p> <p>This is a subset of the ''PubFig83'' dataset [1] which provides 100 images each of 5 most difficult celebrities to recognise (referred as class in the classification problem). For each celebrity persons, we took 100 images and separated them into training and testing sets of 90 and 10 images, respectively:</p> <p><strong>Person: </strong>Jenifer Lopez; Katherine Heigl; Scarlett Johansson; Mariah Carey; Jessica Alba</p> <p> </p> <p><strong>Feature Extraction</strong></p> <p>To extract features from images, we have applied the HT-L3-model as described in [2] and obtained 25600 features.</p> <p><strong>Feature Selection</strong></p> <p>Details about feature selection followed in brief as follows:</p> <ol> <li> <p><strong>Entropy Filtering:</strong> First we apply an implementation of Fayyad and Irani's [3] entropy base heuristic to discretise the dataset and discarded features using the minimum description length (MDL) principle and only 4878 passed this entropy based filtering method.</p> </li> <li> <p><strong>Class-Distribution Balancing:</strong> Next, we have converted the dataset to binary-class problem by separating into 5 binary-class datasets using one-vs-all setup. Hence, these datasets became <em>imbalanced</em> at a ratio of 1:4. Then we converted them into <em>balanced binary-class</em> datasets using random sub-sampled method. Further processing of the dataset has been described in the paper.</p> </li> <li> <p><strong>(alpha,beta)-k Feature selection:</strong> To get a good feature set for training the classifier, we select the features using the approach based on the (alpha,beta)-k feature selection [4] problem. It selects a minimum subset of features that maximise both within class similarity and dissimilarity in different classes. We applied the entropy filtering and (alpha,beta)-k feature subset selection methods in three ways and obtained different numbers of features (in the Table below) after consolidating them into binary class dataset.</p> </li> </ol> <ul> <li> <p><strong>UAB:</strong> We applied (alpha,beta)-k feature set method on each of the balanced binary-class datasets and we took the <em>union</em> of selected features for each binary-class datasets. Finally, we applied the (alpha,beta)-k feature set selection method on each of the binary-class datasets and get a set of features.</p> </li> <li> <p><strong>IAB:</strong> We applied (alpha,beta)-k feature set method on each of the balanced binary-class datasets and we took the <em>intersection</em> of selected features for each binary-class datasets. Finally, we applied the (alpha,beta)-k feature set selection method on each of the binary-class datasets and get a set of features.</p> </li> <li> <p><strong>UEAB:</strong> We applied (alpha,beta)-k feature set method on each of the balanced binary-class datasets. Then, we applied the entropy filtering and (alpha,beta)-k feature set selection method on each of the balanced binary-class datasets. Finally, we took the <em>union</em> of selected features for each <em>balanced binary-class</em> datasets and get a set of features.</p> </li> </ul> <p>All of these datasets are inside the compressed folder. It also contains the document describing the process detail.</p> <p> </p> <p><strong>References</strong></p> <p>[1] Pinto, N., Stone, Z., Zickler, T., & Cox, D. (2011). Scaling up biologically-inspired computer vision: A case study in unconstrained face recognition on facebook. In Computer Vision and Pattern Recognition Workshops (CVPRW), 2011 IEEE Computer Society Conference on (pp. 35–42).</p> <p>[2] Cox, D., & Pinto, N. (2011). Beyond simple features: A large-scale feature search approach to unconstrained face recognition. In Automatic Face Gesture Recognition and Workshops (FG 2011), 2011 IEEE International Conference on (pp. 8–15).</p> <p>[3] Fayyad, U. M., & Irani, K. B. (1993). Multi-Interval Discretization of Continuous-Valued Attributes for Classification Learning. In International Joint Conference on Artificial Intelligence (pp. 1022–1029).</p> <p>[4] Berretta, R., Mendes, A., & Moscato, P. (2005). Integer programming models and algorithms for molecular classification of cancer from microarray data. In Proceedings of the Twenty-eighth Australasian conference on Computer Science - Volume 38 (pp. 361–370). 1082201: Australian Computer Society, Inc.</p> <p> </p>
Ultra-deep sequencing of HIV-1 near full-length and partial proviral genomes reveals high genetic diversity among Brazilian blood donors
<p>Here, we aimed to gain a comprehensive picture of the HIV-1 diversity in the northeast and southeast part of Brazil. To this end, a high-throughput sequencing-by-synthesis protocol and instrument were used to characterize the near full length (NFLG) and partial HIV-1 proviral genome in 259 HIV-1 infected blood donors at four major blood centers in Brazil: Pro-Sangue foundation (São Paulo state (SP), n 51), Hemominas foundation (Minas Gerais state (MG), n 41), Hemope foundation (Recife state (PE), n 96) and Hemorio blood bank (Rio de Janeiro (RJ), n 70).</p>
Parallel reverse genetic screening in mutant human cells using transcriptomics - Data and analyses
<p>This dataset contains data files and analysis code associated with manuscript entitled "Parallel reverse genetic screening in mutant human cells using transcriptomics".</p> <p>Data files include expression profiles for over 1800 RNA-seq samples and annotations.</p> <p>Analysis files include R scripts to generate summary figures.</p>
QTL script and VCF files - GENETIC ARCHITECTURE OF FLOWERING-TIME VARIATION IN BRACHYPODIUM DISTACHYON
<p>Supplemental data for the article:</p> <p>GENETIC ARCHITECTURE OF FLOWERING-TIME VARIATION IN BRACHYPODIUM DISTACHYON (Woods et al., 2016).</p> <p>Supplemental data includes:</p> <ul> <li> <p>A folder named “Data”, which contains:</p> <ol> <li> <p><strong>Raw genotypic data</strong>. Data showing the parental genotype in a RIL population (F7; Bd21 X Bd1-1)</p> </li> <li> <p><strong>Raw phenotypic data</strong>. Flowering time (leaves and days to flowering) of the RIL population in different growth environments.</p> </li> <li> <p><strong>The genetic map </strong>(see material and methods section of Woods et al., 2016 for additional information).</p> </li> <li> <p><strong>Gene positions.</strong> A file containing the position of annotated genes on the Brachypodium distachyon genome V2.1. Data from Phytozome (https://phytozome.jgi.doe.gov/pz/portal.html).</p> </li> </ol> </li> <li> <p>The<strong> R script</strong> used for the QTL analysis (Final_script.R).</p> </li> <li> <p><strong>VCF files of the loci of interest</strong>. A folder called “VCF” includes the VCF files of the genes presented in Fig. 6 (VRN1, PHYC, VRN2, and FD). </p> </li> </ul> <p> </p>
Figure 4. - Intralineage and interlineage uncorrected genetic distance values for the "ivonicus/yuna" and "carteri" lineages.
Figure 4. - Intralineage and interlineage uncorrected genetic distance values for the "ivonicus/yuna" and "carteri" lineages.
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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.