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247 results for “relatedness”
Data from: Population structure, relatedness and ploidy levels in an apple gene bank revealed through genotyping-by-sequencing
In recent years, new genome-wide marker systems have provided highly informative alternatives to low density marker systems for evaluating plant populations. To date, most apple germplasm collections have been genotyped using low-density markers such as simple sequence repeats (SSRs), whereas only a few have been explored using high-density genome-wide marker information. We explored the genetic diversity of the Pometum gene bank collection (University of Copenhagen, Denmark) of 349 apple accessions using over 15,000 genome-wide single nucleotide polymorphisms (SNPs) and 15 SSR markers, in order to compare the strength of the two approaches for describing population structure. We found that 119 accessions shared a clonal relationship with at least one other accession in the collection, resulting in the identification of 272 (78%) unique accessions. Of these unique accessions, over half (52%) share a first-degree relationship with at least one other accession. There is therefore a high degree of clonal and family relatedness in the Danish apple gene bank. We find significant genetic differentiation between Malus domestica and its supposed primary wild ancestor, M. sieversii, as well as between accessions of Danish origin and all others. Overall, we found strong concordance between analyses based on the genome-wide SNPs and the 15 SSR loci. However, we argue that GBS is superior to traditional SSR approaches because it allowed the estimation of ploidy levels that were in accordance with flow cytometry results, and can be further exploited in genome-wide association studies (GWAS). Finally, we compare GBS with SSR for the purposes of characterizing a diverse apple gene bank and discuss the advantages and constraints of the two approaches.
Data from: Genotyping-by-sequencing for estimating relatedness in non-model organisms: avoiding the trap of precise bias
There has been remarkably little attention to using the high resolution provided by genotyping-by-sequencing (i.e. RADseq and similar methods) datasets for assessing relatedness in wildlife populations. A major hurdle is the genotyping error, especially allelic dropout, often found in this type of dataset that could lead to downward-biased, yet precise, estimates of relatedness. Here we assess the applicability of genotyping-by-sequencing datasets for relatedness inferences given their relatively high genotyping error rates. Individuals of known relatedness were simulated under genotyping error, allelic dropout, and missing data scenarios based on an empirical ddRAD dataset, and their true relatedness was compared to that estimated by seven relatedness estimators. We found that an estimator chosen through such analyses can circumvent the influence of genotyping error, with the estimator of Ritland (1996) shown to be unaffected by allelic dropout and to be the most accurate when there is genotyping error. We also found that the choice of estimator should not rely solely on the strength of correlation between estimated and true relatedness as a strong correlation does not necessarily mean estimates are close to true relatedness. We also demonstrated how even a large SNP dataset with genotyping error (allelic dropout or otherwise) or missing data still performs better than a perfectly genotyped microsatellite dataset of tens of markers. The simulation-based approach used here can be easily implemented by others on their own genotyping-by-sequencing datasets to confirm the most appropriate and powerful estimator for their dataset.
Data from: Genetic relatedness does not retain spatial pattern across multiple spatial scales: dispersal and colonization in the coral, Pocillopora damicornis
Patterns of isolation-by-distance are uncommon in coral populations. Here, we depart from historical trends of large-scale, geographic genetic analyses by scaling down to a single patch reef in Kāne'ohe Bay, Hawai'i, and map and genotype all colonies of the coral, Pocillopora damicornis. Six polymorphic microsatellite loci were used to assess population genetic and clonal structure and to calculate individual colony pairwise relatedness values. Our results point to an inbred, highly clonal reef (between 53 and 116 clonal lineages out of 2352 genotyped colonies) with a very skewed genet frequency distribution (over 70% of the reef was composed of just seven genotypes). Spatial autocorrelation analyses revealed that corals found close together on the reef were more genetically related than corals further apart. Spatial genetic structure disappears, however, as spatial scale increases and then becomes negative at the largest distances. Stratified, random sampling of three neighbouring reefs confirms that reefs are demographically open and inter-reef genetic structuring was not detected. Attributing process to pattern in corals is complicated by their mixed reproductive strategies. Separate autocorrelation analyses, however, show that the spatial distribution of both clones and non-clones contribute to spatial genetic structure. Overall, we demonstrate genetic structure on an intra-reef scale and genetic panmixia on an inter-reef scale indicating that, for P. damicornis, small- and large-scale dispersal processes are likely not the same. By starting from an inter-individual, intra-reef level before scaling up to an inter-reef level, this study demonstrates that isolation-by-distance patterns for the coral P. damicornis are limited to small scales and highlights the importance of investigating genetic patterns and ecological processes at multiple scales.
Data from: Competition decreases with relatedness and lek size in mole crickets: a role for kin selection?
Twenty years ago, Kokko & Lindstrom (1996) introduced the hypothesis that kin selection may drive the evolution of leks, shifting the lek-paradigm away from a competitive framework and spurring research on the relatedness of males on leks. However, support for Kokko & Lindstrom's kin selection hypothesis has been sparse; most studies have shown related males to occur on leks no more than expected by chance. Additionally, evidence supporting the proposed mechanism is mixed; by joining a lek males do not always increase the female visitation rate on a per-capita basis. The prairie mole cricket Gryllotalpa major is a lekking cricket in which male relatives advertise in close proximity. We reject the Kokko-Lindstrom hypothesis for this species because G. major females do not preferentially visit larger leks. Interestingly, more females visited smaller leks, where the presence of larger, more highly related males suggest reduced levels of local competition. Although the mechanism continues to be explored, these results provide an alternative inclusive fitness scenario to consider for lekking species – the existence of kin benefits between related neighbors rather than spread across the lek as a whole.
Data from: Relatedness severely impacts accuracy of marker- assisted selection for disease resistance in hybrid wheat
The accuracy of genomic selection depends on the relatedness between the members of the set in which marker effects are estimated based on evaluation data and the types for which performance is predicted. Here, we investigate the impact of relatedness on the performance of marker-assisted selection for fungal disease resistance in hybrid wheat. A large and diverse mapping population of 1,739 elite European winter wheat inbred lines and hybrids was evaluated for powdery mildew, leaf rust, and stripe rust resistance in multi-location field trials and fingerprinted with 9k and 90k SNP arrays. Comparison of the accuracies of prediction achieved with data sets from the two marker arrays revealed a crucial role for a sufficiently high marker density in genome-wide association mapping. Cross- validation studies using test sets with varying degrees of relationship to the corresponding estimation sets unraveled that close relatedness leads to a substantial increase in the proportion of total genotypic variance explained by the identified QTL and, consequently, to an overoptimistic judgment of the prospected precision of marker-assisted selection.
Genomic relatedness and diversity of Swedish native cattle breeds
<p><b>Background</b></p> <p>Native cattle breeds are important genetic resources given their adaptation to the local environment in which they are bred. However, the widespread use of commercial cattle breeds has resulted in a marked reduction in population size of several native cattle breeds worldwide. Therefore, conservation management of native cattle breeds requires urgent attention to avoid their extinction. To this end, we genotyped nine Swedish native cattle breeds with genome-wide 150K single nucleotide polymorphisms (SNPs) to investigate the level of genetic diversity and relatedness between these breeds.</p> <p><b>Results</b></p> <p>We used various SNP-based approaches on this dataset to connect the demographic history with the genetic diversity and population structure of these Swedish cattle breeds. Our results suggest that the Väne and Ringamåla breeds originating from southern Sweden have experienced population isolation and have a low genetic diversity, whereas the Fjäll breed has a large founder population and a relatively high genetic diversity. Based on the shared ancestry and the constructed phylogenetic trees, we identified two major clusters in Swedish native cattle. In the first cluster, which includes Swedish mountain cattle breeds, there was little differentiation among the Fjäll, Fjällnära, Swedish Polled, and Bohus Polled breeds. The second cluster consists of breeds from southern Sweden: Väne, Ringamåla and Swedish Red. Interestingly, we also identified sub-structuring in the Fjällnära breed, which indicates different breeding practices on the farms that maintain this breed.</p> <p><b>Conclusions</b></p> <p>This study represents the first comprehensive genome-wide analysis of the genetic relatedness and diversity in Swedish native cattle breeds. Our results show that different demographic patterns such as genetic isolation and cross-breeding have shaped the genomic diversity of Swedish native cattle breeds and that the Swedish mountain breeds have retained their authentic distinct gene pool without significant contribution from any of the other European cattle breeds that were included in this study.</p>
Data from: Egg morphology fails to identify nests parasitized by conspecifics in common pochard: a test based on protein fingerprinting and including female relatedness
Conspecific brood parasites lay eggs in nests of other females of the same species. A variety of methods have been developed and used to detect conspecific brood parasitism (CBP). Traditional methods may be inaccurate in detecting CBP and in revealing its true frequency. On the other hand more accurate molecular methods are expensive and time consuming. Eadie developed a method for revealing CBP based on differences in egg morphology. That method is based on Euclidean distances calculated for pairs of eggs within a clutch using standardized egg measurements (length, width and weight). We tested the applicability of this method in the common pochard Aythya ferina using nests that were identified as parasitized (39 nests) or non-parasitized (16 nests) based on protein fingerprinting of eggs. We also analyzed whether we can distinguish between parasitic and host eggs in the nest. We found that variation in MED can be explained by parasitism but there was a huge overlap in MED between parasitized and non-parasitized nests. MED also increased with clutch size. Using discriminant function analysis (DFA) we found that only 76.4% of nests were correctly assigned as parasitized or nonparasitized and only 68.3% of eggs as parasitic or host eggs. Moreover we found that MED in parasitized nests increased with relatedness of the females that laid eggs in the nest. This finding was supported by positive correlation between MED and estimated relatedness in female–female pairs. Although variation in egg morphology is associated with CBP, it does not provide a reliable clue for distinguishing parasitized nests from non-parasitized nests in common pochard.
Data from: Contrasting effects of phylogenetic relatedness on plant invader success in experimental grassland communities
1. Identifying the factors determining the success of invasive species is critical for management of biological invasions. Darwin's naturalization conundrum states that exotic species closely related to natives should be successful because of a shared affinity for local environmental conditions, but at the same time close relatives often compete more intensively, limiting 'niche' opportunities for the invaders. Previous studies have generally considered these two 'opposing' hypotheses as mutually exclusive, yet evidence for both of them abounds, indicating a practical dilemma for management of biological invasions. 2. In this study, we sowed the seeds of the invasive exotic Ambrosia artemisiifolia L. into 369 experimental plant communities to mimic an introduction of the exotics into a series of new habitats. We further linked the establishment and growth performance of the invader in these experimental communities to the phylogenetic relatedness between the invader and the community residents where it was introduced. 3. We found that the probability of invader establishment declined with increasing phylogenetic distance between the invader and residents, whereas the average size of surviving invader individuals increased with the phylogenetic distance. 4. These results can be at least partly explained by the observations that close relatives tend to create similar soil microhabitat through harboring similar soil enzymes (e.g. alkaline and acid phosphatases) benefiting invader establishment, and that intense competitive interactions between the invader and its close relatives suppressed exotic growth. 5. Synthesis and applications. This study presents the first experimental evidence that phylogenetic relatedness has contrasting effects on different aspects of invader success, thus shedding light on the long-standing Darwin's naturalization conundrum. Moreover, our findings also have important implications for management of plant invasions: for controlling invasive species characterized by high establishment probability, native species distantly related to the invasive species can be planted in sites surrounding the invasion foci; whereas, the opposite seems to be true for controlling those characterized by large individual size.
Data from: Relatedness within and between leks of golden-collared manakin differ between sexes and age classes
Several hypotheses have been advanced to explain the evolution of leks, a mating system in which males aggregate at display sites where females choose their mates. Only a small proportion of males obtain copulations, and why other males join the lek remains unexplained. One hypothesis has called kin selection into play: if juvenile males join leks where their relatives display and contribute to attract females to the lek, they can gain indirect fitness benefits. We investigated the genetic structure of eight leks of golden-collared manakin, a tropical Passerine. Adult court-holder males, females, and immature males were caught within lek boundaries and the geographical location of the courts was recorded. For court-holding males, within-lek relatedness among four leks was significantly higher than average across-lek relatedness. Courts of more closely related males were not spatially associated within leks. Relatedness among immature males was relatively lower, yet higher within than between leks. Values of relatedness and genetic differentiation among leks were even lower for females. Thus, leks were composed of males that were more related to each other than to other males of the population, and the degree of relatedness decreased from court holding males to immature males to females. This suggests that immature males explore several leks and eventually join those where their relatives display, whereas females appear to visit leks randomly with respect to relatedness. Our results provide support for the hypothesis that kin selection influences the evolution of lekking behavior in this species.
Data from: SIDER: an R package for predicting trophic discrimination factors of consumers based on their ecology and phylogenetic relatedness
Stable isotope mixing models (SIMMs) are an important tool used to study species' trophic ecology. These models are dependent on, and sensitive to, the choice of trophic discrimination factors (TDF) representing the offset in stable isotope delta values between a consumer and their food source when they are at equilibrium. Ideally, controlled feeding trials should be conducted to determine the appropriate TDF for each consumer, tissue type, food source, and isotope combination used in a study. In reality however, this is often not feasible nor practical. In the absence of species-specific information, many researchers either default to an average TDF value for the major taxonomic group of their consumer, or they choose the nearest phylogenetic neighbour for which a TDF is available. Here, we present the SIDER package for R, which uses a phylogenetic regression model based on a compiled dataset to impute (estimate) a TDF of a consumer. We apply information on the tissue type and feeding ecology of the consumer, all of which are known to affect TDFs, using Bayesian inference. Presently, our approach can estimate TDFs for two commonly used isotopes (nitrogen and carbon), for species of mammals and birds with or without previous TDF information. The estimated posterior probability provides both a mean and variance, reflecting the uncertainty of the estimate, and can be subsequently used in the current suite of SIMM software. SIDER allows users to place a greater degree of confidence on their choice of TDF and its associated uncertainty, thereby leading to more robust predictions about trophic relationships in cases where study-specific data from feeding trials is unavailable. The underlying database can be updated readily to incorporate more stable isotope tracers, replicates and taxonomic groups to further increase the confidence in dietary estimates from stable isotope mixing models, as this information becomes available.
FIGURE 1 in Morphological similarities between Amphisbaena mitchelli Procter, 1923 and A. miringoera Vanzolini, 1971 (Squamata: Amphisbaenidae): phylogenetic relatedness or morphological convergence?
FIGURE 1. Phylogram of amphisbaenians recovered by a Bayesian inference using 1,068 base pairs of the genes16S rRNA and C- MOS. The clade formed by Amphisbaena mitchelli and Amphisbaena miringoera is highlighted in a gray background. Accession numbers are provided next to the species names for 16S rRNA and C-MOS, respectively. Asterisks indicate specimens included in the matrix as missing data for C-MOS. Amphisbaenids with two pre-cloacal pores are in bold. Posterior probabilities and bootstrap values are provided next to the nodes.
Data from: Exploring trophic role similarity and phylogenetic relatedness between species in food webs
<p>Understanding the mechanism shaping species assemblage is a fundamental goal in ecology. In the past two hypotheses have been suggested. One is the filtering hypothesis where environmental factors select for species of similar traits such that they co-occurring in similar niches. The other is the competitive exclusion hypothesis where related species are driven far apart by competition such that they over-disperse across different niches. Here, we investigate the relationship between species assemblage and their phylogenetic relatedness from the network perspective by using five different ecosystems ranging from oceans to an inland lake. We quantified the similarity in species'network positions in a food web and cluster them into different trophic role groups; and from an on-line database we quantified their phylogenetic distances. We then investigated whether related species tend to under or overdisperse across different trophic role groups. In general, our result suggests the environmental filtering process is the dominant force shaping the species assemblage of those ecosystems. However, there are some possible cases where related species are driven by competition such that they evolve to adopt different trophic roles in relatively closed ecosystems.</p>
Impacts of growth form and phylogenetic relatedness on seed germination: a large-scale analysis of a subtropical regional flora
<p>Plant regeneration strategy plays a critical role in species survival and can be used as a proxy for the evolutionary response of species to climate change. However, information on the effects of key plant traits and phylogenetic relatedness on seed germination is limited at large regional scales that vary in climate. To test the hypotheses that phylogenetic niche conservatism plays a critical force in shaping seed ecophysiological traits across species, and also drives their response to climatic fluctuation, we conducted a controlled experiment on seed germination and determined the percentage and rate of germination for 249 species in subtropical China under two temperature regimes (i.e., daily 25ºC; daily alternating 25/15ºC for each 12 h). Germination was low with a skewed distribution (mean = 38.9% at 25ºC, and 43.3% at 25/15ºC). One fifth of the species had low (<10%) and slow (4–30d) germination, and only a few (8%) species had a high (>80%) and rapid (1.2–6.6d) germination. All studied plant traits (including germination responses) showed a significant phylogenetic signal, with an exception of seed germination percentage under the alternating temperature scenario. Generalized linear models (GLMs) and phylogenetic generalized estimation equations (GEEs) demonstrated that growth form and seed dispersal mode were strong drivers of germination. Our experimental study highlights that integrating plant key traits and phylogeny is critical to predicting seed germination response to future climate change.</p>
Kin recognition in Drosophila: Rearing environment and relatedness can modulate gut microbiota and cuticular hydrocarbon odour profiles
<p>From inbreeding avoidance to kin-selected cooperation, social behaviours are frequently reliant on kin recognition. However, kin recognition mechanisms are costly to evolve and currently not very well understood. Recent evidence suggests that, by altering their host's odour, gut and other host-associated microorganisms may provide a promising avenue for understanding kin recognition. In Drosophila melanogaster, kin recognition can mediate mate choice, sexual conflict and larval competition/cooperation, underscoring its important functional role. As is commonly the case, kin recognition in this species depends on both familiarity (i.e. shared rearing environment) and relatedness, and seems to rely mainly on body odours determined by cuticular hydrocarbons. Here, we investigated the degree to which larval rearing environment and relatedness (full-sibs vs. unrelated) determine co-variation between gut microbiota and cuticular hydrocarbons in D. melanogaster. We found that rearing environment strongly determined both microbiota and cuticular hydrocarbon composition, but that these effects were independent from each other. In contrast, relatedness did not influence microbiota composition, but had a strong influence on microbiota diversity, which in turn covaried significantly with cuticular hydrocarbon composition. Our results show that, in D. melanogaster, odours may convey information about both familiarity and relatedness via an interaction between: a) direct effects of the rearing environment on cuticular hydrocarbons and b) indirect effects of relatedness on cuticular hydrocarbons via gut microbiota diversity.</p>
Genetic diversity and relatedness among African Painted dogs in North America
<p>African painted dogs (<em>Lycaon pictus, </em>APD) are highly endangered, with fewer than 7,000 remaining in nature. Captive breeding programs can preserve a genetically diverse population and provide a source of individuals for re-introductions. However, most programs are initiated from few founders and suffer from low genetic diversity and inbreeding. The aims of this study were to use molecular markers to assess genetic variation, inbreeding, and relatedness among APDs in the North American captive population, to use these data to realign studbook records, and to compare these data to wild populations and to the European captive population to facilitate development of a global management plan. We sequenced mitochondrial and major histocompatibility (MHC) class II loci, and genotyped 14 microsatellite loci from 109 APDs from 34 institutions in North America. We identified three likely studbook errors and resolved ten cases of uncertain paternity. Overall, microsatellite heterozygosity was higher than reported in Europe, but effective population size estimates were lower. Mitochondrial sequence variation was extremely limited, and there were fewer MHC haplotypes than in Europe or the wild. Although the population did not show evidence of significant inbreeding overall, several individuals shared high relatedness values, which should be incorporated into future breeding programs.</p>
Phylogenetic relatedness of food plants reveals highest insect herbivore specialization at intermediate temperatures along a broad climatic gradient
<p>Phytophagous insects differ in their degree of specialisation, biased by resource availability. The composition and richness of herbivore and plant assemblages change along climatic gradients, but knowledge about associated shifts in specialisation is scarce and lacks controlling for abundance and phylogeny of interaction partners. Thus, we aimed to test whether the specialisation of herbivores in insect- plant – interaction networks decreases towards cold habitats as predicted by the 'altitude niche-breadth hypothesis' to forecast possible consequences of interaction rewiring under climate change.</p> <p>We used a non-invasive, standardized metabarcoding approach to reconstruct dietary relationships of Orthoptera species as a major insect herbivore taxon along a broad temperature gradient (~12 °C) in southern Germany. Based on orthopteran surveys, direct feeding observations in field, collection of faecal pellets from > 3,000 individuals of 54 species, and parallel vegetation surveys on 41 grassland sites, we quantified plant resource availability and its use by herbivores. Faecal samples were pooled for each species per site.</p>
Association Rules and Semantic Relatedness (ARSR) - Evaluation Data
<p><em><strong>ARSR</strong></em> stands for "<strong><em>Association Rules and Semantic Relatedness</em></strong>",<br> a recommender system that combines association rule mining and semantic relatedness to create recommendations for form fields.</p> <p>ARSR was evaluated with focus on recommending values for fields of metadata forms.<br> The evaluation was performed with two sets of association rules (R1 and R2).<br> <strong>R1</strong> was primarily used to assess the recommendation performance.<br> <strong>R2</strong> served as an alternative and led to similar results.</p> <p>This dataset contains the raw data ("<strong>collected</strong>", JSON format), generated during the evaluation.<br> It includes i.a. input (populated fields and target field), expected output, and the top 40 generated recommendations for each test combination.</p> <p>In addition, the processed data ("<strong>analysed</strong>", CSV format) is provided.<br> It is based on the raw data and is used to calculate metrics and plot the results.</p> <p>The <strong>source code</strong> for ARSR and the evaluation is available on <a href="https://gitlab.com/dlr-dw/arsr">GitLab (gitlab.com)</a>.</p> <p> </p> <p><em>Note:</em><br> To perform the analysis on the raw data (collected) yourself, make sure to follow the setup instruction in the evaluation repository first.<br> More specifically, install dependencies and unzip "data/cedar/test-instances.zip" so that URI mappings can be accessed.<br> Then follow the instructions provided by the README file in the raw data archives (e.g. collected-R1.zip).</p>
Data from: Estimating relatedness and inbreeding using molecular markers and pedigrees: the effect of demographic history
Estimates of inbreeding and relatedness are commonly calculated using molecular markers, although the accuracy of such estimates has been questioned. As a further complication, in many situations, such estimates are required in populations with reduced genetic diversity, which is likely to affect their accuracy. We investigated the correlation between microsatellite- and pedigree-based coefficients of inbreeding and relatedness in laboratory populations of Drosophila melanogaster that had passed through bottlenecks to manipulate their genetic diversity. We also used simulations to predict expected correlations between marker- and pedigree-based estimates and to investigate the influence of linkage between loci and null alleles. Our empirical data showed lower correlations between marker- and pedigree-based estimates in our control (nonbottleneck) population than were predicted by our simulations or those found in similar studies. Correlations were weaker in bottleneck populations, confirming that extreme reductions in diversity can compromise the ability of molecular estimates to detect recent inbreeding events. However, this result was highly dependent on the strength of the bottleneck and we did not observe or predict any reduction in correlations in our population that went through a relatively severe bottleneck of N = 10 for one generation. Our results are therefore encouraging, as molecular estimates appeared robust to quite severe reductions in genetic diversity. It should also be remembered that pedigree-based estimates may not capture realized identity-by-decent and that marker-based estimates may actually be more useful in certain situations.
Stegodyphus africanus group feeding performance depending on relatedness
<p>Cooperation involving shared-resource systems is prone to 'the tragedy of the commons', where individuals act in their own self-interest to exploit the resource in a manner that is detrimental to the common good of all group members. Directing cooperation towards kin provides a solution to this problem, and predicts the differential performance depending on relatedness of group members. In subsocial spiders, juveniles live in transient groups that cooperate in hunting and communal feeding. Prey capture is costly in terms of risk of injury and investment of venom and digestive enzymes, and therefore presents a situation where individuals may attempt to avoid costly interactions and exploit the resource acquired by other group members. We tested the prediction that individuals differentiate participation and/or investment in cooperative prey capture and extra-oral digestion (injection of digestive enzymes into prey prior to the initiation of extraction of nutrients) in response to relatedness of group members with whom they interact, in the subsocial spider <i>Stegodyphus africanus</i>. The performance of groups and interactions over prey attack in groups of either related or mixed kin spiderlings were determined over a period of four weeks. We show that kin groups attack the prey significantly faster, recruit individuals to form feeding groups faster, extract prey body mass more efficiently, and experience less antagonistic interactions than groups of mixed relatedness, which ultimately translates into an elevated growth rate. These results indicate that related individuals are more willing to take risks and invest in communal digestion when foraging with kin, as predicted by inclusive fitness theory as a solution to the tragedy of the commons.</p>
Plant growth over one growing season of Medicago truncatula in competition with conspecifics of different genetic relatedness
<p><span>Kin recognition and kin selection have long been known to occur in animals where it shapes altruistic behavior towards relatives. More recently, studies have found that kin recognition and altered behavior towards kin can also occur in plants. However, inferring the underlying mechanism responsible for variation in plant performance in experimental studies is challenging as often, results can be explained by alternative and non-exclusive mechanisms such as niche differences, kin competition avoidance, and genetic variation in growth rate and competitive ability. Plant-plant interactions may change with the life stage of plants, and competition is often most intense towards the end of plants growing season. However, changes in plant-plant interaction intensity across plants life cycle are rarely considered in kin interaction studies. Here, we adapt a model of plant growth over time modified to specifically include effects of kin and non-kin competition. The model decompose competitive interactions at different stages during plant growth from initial growth to the end of the growing season. It estimates genotype specific variation in growth rate, and how sensitive individual genotypes are to competition neighbors. Furthermore, it estimates size asymmetry among plants accounting for both variation in growth rate, neighbor relatedness, and resource variation (here water availability). We use this model to analyze the results from a competition experiment where plants grew in mini-communities with neighbor plants that were either kin or non-kin. We find that when applied to our experiments, this approach can disentangle kin effects from other effects caused by genotypic variation in growth rate and competitive response to neighbors, and thus significantly help to detect whether plants exhibit kin-cooperative behavior</span></p>
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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.