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788 results for “genotypic data”
Data from: Interactions among bacterial strains and fluke genotypes shape virulence of co-infection
Most studies of virulence of infection focus on pairwise host-parasite interactions. However, hosts are almost universally co-infected by several parasite strains and/or genotypes of the same or different species. While theory predicts that co infection favours more virulent parasite genotypes through intensified competition for host resources, knowledge of effects of genotype by genotype (G×G) interactions between unrelated parasite species on virulence of co infection is limited. Here we tested such relationship by challenging rainbow trout with replicated bacterial strains and fluke genotypes both singly and in all possible pairwise combinations. We found that virulence (host mortality) was higher in co infections compared to single-infections. Importantly, we also found that the overall virulence was dependent on the genetic identity of the co-infecting partners so that the outcome of co infection could not be predicted from the respective virulence of single infections. Our results imply that G×G interactions among co infecting parasites may significantly affect host health, add to variance in parasite fitness and thus influence evolutionary dynamics and ecology of disease in unexpected ways.
Data from: Dietary choices are influenced by genotype, mating status, and sex in Drosophila melanogaster
Mating causes many changes in physiology, behaviour and gene expression in a wide range of organisms. These changes are predicted to be sex-specific, influenced by the divergent reproductive roles of the sexes. In female insects, mating is associated with an increase in egg production which requires high levels of nutritional input with direct consequences for the physiological needs of individual females. Consequently, females alter their nutritional acquisition in line with the physiological demands imposed by mating. Although much is known about the female mating-induced nutritional response, far less is known about changes in males. In addition, it is unknown whether variation between genotypes translates into variation in dietary behavioral responses. Here we examine mating-induced shifts in male and female dietary preferences across genotypes of Drosophila melanogaster. We find sex- and genotype-specific effects on both the quantity and quality of the chosen diet. These results contribute to our understanding of sex-specific metabolism and reveal genotypic variation that influences responses to physiological demands.
Data from: Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae)
Background: The majority of the subspecies of Daucus carota have not yet been discriminated clearly by various molecular or morphological methods and hence their phylogeny and classification remains unresolved. Recent studies using 94 nuclear orthologs and morphological characters, and studies employing other molecular approaches were unable to distinguish clearly many of the subspecies. Fertile intercrosses among traditionally recognized subspecies are well documented. We here explore the utility of single nucleotide polymorphisms (SNPs) generated by genotyping-by-sequencing (GBS) to serve as an effective molecular method to discriminate the subspecies of the D. carota complex. Results: We used GBS to obtain SNPs covering all nine Daucus carota chromosomes from 162 accessions of Daucus and two related genera. To study Daucus phylogeny, we scored a total of 10,814 or 38,920 SNPs with a maximum of 10 or 30 % missing data, respectively. To investigate the subspecies of D. carota, we employed two data sets including 150 accessions: (i) rate of missing data 10 % with a total of 18,565 SNPs, and (ii) rate of missing data 30 %, totaling 43,713 SNPs. Consistent with prior results, the topology of both data sets separated species with 2n = 18 chromosome from all other species. Our results place all cultivated carrots (D. carota subsp. sativus) in a single clade. The wild members of D. carota from central Asia were on a clade with eastern members of subsp. sativus. The other subspecies of D. carota were in four clades associated with geographic groups: (1) the Balkan Peninsula and the Middle East, (2) North America and Europe, (3) North Africa exclusive of Morocco, and (4) the Iberian Peninsula and Morocco. Daucus carota subsp. maximus was discriminated, but neither it, nor subsp. gummifer (defined in a broad sense) are monophyletic. Conclusions: Our study suggests that (1) the morphotypes identified as D. carota subspecies gummifer (as currently broadly circumscribed), all confined to areas near the Atlantic Ocean and the western Mediterranean Sea, have separate origins from sympatric members of other subspecies of D. carota, (2) D. carota subsp. maximus, on two clades with some accessions of subsp. carota, can be distinguished from each other but only with poor morphological support, (3) D. carota subsp. capillifolius, well distinguished morphologically, is an apospecies relative to North African populations of D. carota subsp. carota, (4) the eastern cultivated carrots have origins closer to wild carrots from central Asia than to western cultivated carrots, and (5) large SNP data sets are suitable for species-level phylogenetic studies in Daucus.
Data from: Degenerate adaptor sequences for detecting PCR duplicates in reduced representation sequencing data improve genotype calling accuracy
RAD-tag is a powerful tool for high-throughput genotyping. It relies on PCR amplification of the starting material, following enzymatic digestion and sequencing adaptor ligation. Amplification introduces duplicate reads into the data, which arise from the same template molecule and are statistically nonindependent, potentially introducing errors into genotype calling. In shotgun sequencing, data duplicates are removed by filtering reads starting at the same position in the alignment. However, restriction enzymes target specific locations within the genome, causing reads to start in the same place, and making it difficult to estimate the extent of PCR duplication. Here, we introduce a slight change to the Illumina sequencing adaptor chemistry, appending a unique four-base tag to the first index read, which allows duplicate discrimination in aligned data. This approach was validated on the Illumina MiSeq platform, using double-digest libraries of ants (Wasmannia auropunctata) and yeast (Saccharomyces cerevisiae) with known genotypes, producing modest though statistically significant gains in the odds of calling a genotype accurately. More importantly, removing duplicates also corrected for strong sample-to-sample variability of genotype calling accuracy seen in the ant samples. For libraries prepared from low-input degraded museum bird samples (Mixornis gularis), which had low complexity, having been generated from relatively few starting molecules, adaptor tags show that virtually all of the genotypes were called with inflated confidence as a result of PCR duplicates. Quantification of library complexity by adaptor tagging does not significantly increase the difficulty of the overall workflow or its cost, but corrects for differences in quality between samples and permits analysis of low-input material.
Data from: Leaf photosynthetic, economics and hydraulic traits are decoupled among genotypes of a widespread species of eucalypt grown under ambient and elevated CO2
Leaf economics and hydraulic traits strongly influence photosynthesis. While the level of coordination among these traits can differ between sets of species, leaf functional trait coordination within species remains poorly understood. Furthermore, elevated concentrations of atmospheric CO2 commonly influence the expression of leaf photosynthetic, economics and hydraulic traits in contrasting ways, yet the effect of variable concentrations of atmospheric CO2 on patterns of trait coordination within species remains largely untested. We examined the relationships among key leaf photosynthetic (e.g. net photosynthesis and photosynthetic biochemistry), economics and water-use (e.g. leaf mass per unit area and stomatal conductance) and hydraulic traits (e.g. vein density) in 14 genotypes of Eucalyptus camaldulensis grown in ambient (aCO2) and elevated (eCO2) [CO2]. We examined the level of coordination among leaf traits in aCO2 and then assessed whether growth in eCO2 altered that coordination. We found that leaf traits related to photosynthetic capacity, economics and water-use, and hydraulics were decoupled among genotypes grown in aCO2, yet strong relationships were generally observed among suites of traits within each 'functional group'. Significant responses to growth in eCO2 were observed for most leaf photosynthetic and economics and water-use traits, with the magnitude and direction of the response varying among traits. In contrast, leaf hydraulics traits were unaffected by variable growth CO2. Despite this, growth in eCO2 did not substantially alter patterns of leaf trait coordination observed in aCO2. These results suggest suites of leaf traits associated with photosynthetic capacity, economics and water-use and hydraulics, respectively, can form independent axes of variation among genotypes of a single species, regardless of growth CO2. Although growth in eCO2 did not substantially alter patterns of trait coordination, decoupling of leaf functional traits among genotypes may allow genetically distinct populations to produce novel combinations of traits that may be adaptive in response to changes in their local environment.
Data from: Gene flow between nascent species: geographic, genotypic and phenotypic differentiation within and between Aquilegia formosa and A. pubescens.
Speciation can be described as a reduction, and the eventual cessation, in the ability to interbreed. Thus, determining how gene flow differs within and between nascent species can illuminate the relative stage the taxa have attained in the speciation process. Aquilegia formosa and A. pubescens are fully intercompatible yet occur in different habitats and have flowers specialized for pollination by hummingbirds and hawkmoths respectively. Using 79 SNP loci we genotyped nearly 1,000 individuals from populations of both species in close proximity to each other and from putative hybrid zones. The species shared all but one SNP polymorphism and on average, allele frequencies differed by only 0.14. However, the species were clearly differentiated using Structure and admixed individuals were primarily identified at putative hybrid zones. PopGraph identified a highly integrated network among all populations but populations of each species and hybrid zones occupied distinct regions in the network. Using either conditional graph distance (cGD) or Fst/(1-Fst) we found significant isolation by distance (IBD) among populations. Within species, IBD was strong, indicating high historic gene flow. IBD extended approximately 100 km in A. pubescens and 30 km in A. formosa. However, IBD between the species was very weak and extended only a few km beyond hybrid zones, suggesting little recent gene flow. The extensive sharing of SNP polymorphisms between these species suggests that they are very early in the speciation process while the low signal of IBD suggests that they have largely ceased gene exchange.
Genotyping by sequencing data of five legume tree species widespread in the rainforests of West and Central Africa
<p>Although today the forest cover is continuous in Central Africa this may have not always been the case, as the scarce fossil record in this region suggests that arid conditions might have significantly reduced tree density during the Ice Ages. Our aim was to investigate whether the dry ice-age periods left a genetic signature on tree species that can be used to infer the date of the past fragmentation of the rainforest. We sequenced reduced representation libraries of 182 samples representing five widespread Legume trees and seven outgroups. Phylogenetic analyses identified an early divergent lineage for all species in West Africa (Upper Guinea), and two clades in Central Africa: Lower Guinea-North and Lower Guinea-South. As the structure separating the Northern and Southern clades -congruent across species- cannot be explained by geographic barriers, we tested other hypotheses with demographic model testing using ∂a∂I. The best estimates indicate that the two clades split between the Upper Pliocene and the Pleistocene, a date compatible with forest fragmentation driven by ice-age climatic oscillations. Furthermore, we found remarkably older split dates for the shade-tolerant tree species with non-assisted seed dispersal than for light-demanding species with long-distance wind dispersal. Different recolonisation abilities after recurrent cycles of forest fragmentation seem to explain why species with long-distance dispersal show more recent genetic admixture between the two clades than species with limited seed dispersal. Despite their old history, our results depict the African rainforests as a dynamic biome where tree species have expanded relatively recently after the last glaciation.</p>
Data from: Genotype-free estimation of allele frequencies reduces bias and improves demographic inference from RADSeq data
Restriction-site associated sequencing (RADSeq) facilitates rapid generation of thousands of genetic markers at relatively low cost; however, several sources of error specific to RADSeq methods often lead to biased estimates of allele frequencies and thereby to erroneous population genetic inference. Estimating the distribution of sample allele frequencies without calling genotypes was shown to improve population inference from whole genome sequencing data, but the ability of this approach to account for RADSeq-specific biases remains unexplored. Here we assess in how far genotype-free methods of allele frequency estimation affect demographic inference from empirical RADSeq data. Using the well-studied pied flycatcher (Ficedula hypoleuca) as a study system, we compare allele frequency estimation and demographic inference from whole genome sequencing data with that from RADSeq data matched for samples using both genotype-based and genotype free methods. The demographic history of pied flycatchers as inferred from RADSeq data was highly congruent with that inferred from WGS data when allele frequencies were estimated directly from the read data. In contrast, when allele frequencies were derived from called genotypes, RADSeq-based estimates of most model parameters fell outside the 95% confidence interval (CI) of estimates derived from WGS data. Notably, more stringent filtering of genotypes tended to increase the discrepancy between parameter estimates from WGS and RADSeq data, respectively. The results from this study demonstrate the ability of genotype-free methods to improve AFS-based demographic inference from RADSeq data and highlight the need to account for uncertainty in NGS data regardless of sequencing method.
Data from: Tapeworm manipulation of copepod behaviour: parasite genotype has a larger effect than host genotype
Compared to uninfected individuals, infected animals can exhibit altered phenotypes. The changes often appear beneficial to parasites, leading to the notion that modified host phenotypes are extended parasite phenotypes, shaped by parasite genes. However, the phenotype of a parasitized individual may reflect parasitic manipulation, host responses to infection, or both, and disentangling the contribution of parasite genes versus host genes to these altered phenotypes is challenging. Using a tapeworm (Schistocephalus solidus) infecting its copepod first intermediate host, I performed a full-factorial, cross-infection experiment with five host and five parasite genotypes. I found that a behavioural trait modified by infection, copepod activity, was affected by both host and parasite genotype. There was not clear evidence for host genotype by parasite genotype interactions. Several observations indicated that host behaviour was chiefly determined by parasite genes: 1) all infected copepods, regardless of host or parasite genotype, exhibited behavioural changes, 2) parasitism reduced the differences among copepod genotypes, and 3) within infected copepods, parasite genotype had twice as large an effect on behaviour as host genotype. I conclude that the altered behaviour of infected copepods primarily represents an extended parasite phenotype, and I discuss how genetic variation in parasitic host manipulation could be maintained.
Data from: Evolution of increased intraspecific competitive ability following introduction: the importance of relatedness among genotypes.
1.A long‐standing explanation for invasion success is that invasive plants could evolve to be more competitive following introduction. This evolution of increased competitive ability (EICA) hypothesis, however, has seldom been tested with regard to intraspecific competition. Given that plants can display different responses to related and unrelated conspecifics, the evolution of intraspecific competitive ability might be specific to genotypes of different relatedness. 2.Here, we grew five native (South American) and five introduced (North American) genotypes of the clonal herbaceous invasive plant Alternanthera philoxeroides alone, with aboveground competition from kin (the same genotype) or from one of two types of strangers (another genotype from the same range or another genotype from the other range). 3.When grown alone, introduced and native genotypes produced similar total biomass and storage‐root biomass. However, in response to intraspecific competition, introduced genotypes showed increases in total biomass and stem length, and a decrease in specific stem length, whereas native genotypes showed the opposite pattern. When grown with kin instead of strangers, introduced genotypes showed an increase in branch number, whereas native genotypes showed the opposite. 4.Synthesis. Our study provided evidence for evolution of increased intraspecific competitive responses in an invasive plant. We also found, for the first time, that the interactions among kin were likely to shift from competition towards facilitation following introduction.
Data from: Linking genotype, ecotype, and phenotype in an intensively managed large carnivore
Numerous factors influence fitness of free-ranging animals, yet often these are uncharacterized. We integrated GPS habitat use data and genetic profiling to determine their influence on fitness proxies (mass, length, and body condition) in a threatened population of grizzly bears (Ursus arctos) in Alberta, Canada. We detected distinct genetic and habitat use (ecotype) clusters, with individual cluster assignments, or genotype/ecotype, being correlated (Pearson r = 0.34, P < 0.01). Related individuals showed evidence of similar habitat use patterns, irrespective of geographic distance and sex. Fitness proxies were influenced by sex, age, and habitat use, and homozygosity had a positive effect on these proxies that could be indicative of outbreeding depression. We further documented over 300 translocations occurring in the province since the 1970s, often to areas with significantly different habitat. We argue this could be unintentionally causing the pattern of outbreeding, although the heterozygosity correlation may instead be explained by the energetic costs associated with larger body size. The observed patterns, together with the unprecedented human-mediated migrations, make understanding the link between genotype, ecotype, and phenotype and mechanisms behind the negative heterozygosity-fitness correlations critical for management and conservation of this species.
Data from: Indirect genetic effects and sexual conflicts: Partner genotype influences multiple morphological and behavioural reproductive traits in a flatworm
The expression of an individual's phenotypic traits can be influenced by genes expressed in its social partners. Theoretical models predict that such indirect genetic effects (IGEs) on reproductive traits should play an important role in determining the evolutionary outcome of sexual conflict. However, empirical tests of (i) whether reproductive IGEs exist, (ii) how they vary among genotypes, and (iii) whether they are uniform for different types of reproductive traits are largely lacking. We addressed this in a series of experiments in the simultaneously hermaphroditic flatworm Macrostomum lignano. We found strong evidence for IGEs on both morphological and behavioural reproductive traits. Partner genotype had a significant impact on the testis size of focal individuals—varying up to 2.4-fold—suggesting that IGEs could mediate sexual conflicts that target the male sex function. We also found that time to first copulation was affected by a genotype × genotype interaction between mating partners, and that partner genotype affected the propensity to copulate and perform the postcopulatory suck behaviour, which may mediate conflicts over the fate of received ejaculate components. These findings provide clear empirical evidence for IGEs on multiple behavioural and morphological reproductive traits, which suggests that the evolutionary dynamics of these traits could be altered by genes contained in the social environment.
Data from: Evolutionary rescue and local adaptation under different rates of temperature increase: a combined analysis of changes in phenotype expression and genotype frequency in Paramecium microcosms
Evolutionary Rescue (ER) occurs when populations, which have declined due to rapid environmental change, recover through genetic adaptation. The success of this process and the evolutionary trajectory of the population strongly depend on the rate of environmental change. Here we investigated how different rates of temperature increase (from 23°C to 32°C) affect population persistence and evolutionary change in experimental microcosms of the protozoan Paramecium caudatum. Consistent with theory on ER, we found that those populations experiencing the slowest rate of temperature increase were the least likely to become extinct and tended to be the best adapted to the new temperature environment. All high-temperature populations were more tolerant to severe heat stress (35°C, 37°C), indicating a common mechanism of heat protection. High-temperature populations also had superior growth rates at optimum temperatures, leading to the absence of a pattern of local adaptation to control (23°C) and high-temperature (32°C) environments. However, high-temperature populations had reduced growth at low temperatures (5-9°C), causing a shift in the temperature niche. In part, the observed evolutionary change can be explained by selection from standing variation. Using mitochondrial markers, we found complete divergence between control and high-temperature populations in the frequencies of six initial founder genotypes. Our results confirm basic predictions of ER and illustrate how adaptation to an extreme local environment can produce positive as well as negative correlated responses to selection over the entire range of the ecological niche.
Data from: Evaluation of two approaches to genotyping MHC class I in a passerine – CE-SSCP and 454 pyrosequencing
Genes of the highly dynamic major histocompatibility complex (MHC) are directly linked to individual fitness and are of high interest in evolutionary ecology and conservation genetics. Gene duplication and positive selection usually lead to high levels of polymorphism in the MHC region, making genotyping of MHC a challenging task. Here, we compare the performance of two methods for MHC class I genotyping in a passerine with highly duplicated MHC class I genes: capillary electrophoresis single strand conformation polymorphism (CE-SSCP) analysis and 454 GS FLX Titanium pyrosequencing. According to our findings, the number of MHC variants (called alleles for simplicity) detected by CE-SSCP is significantly lower than detected by 454. To resolve discrepancies between the two methods we cloned and Sanger sequenced a MHC class I amplicon for an individual with high number of alleles. We found a perfect congruence between cloning/Sanger sequencing results and 454. Thus, in case of multi-locus amplification, CE-SSCP considerably underestimates individual MHC diversity. However, numbers of alleles detected by both methods are significantly correlated, although the correlation is weak (r = 0.32). Thus, in systems with highly duplicated MHC, 454 provides more reliable information on individual diversity than CE-SSCP.
Data from: A genotypic trade-off between constitutive resistance to viral infection and host growth rate
Genotypic trade-offs are fundamental to the understanding of the evolution of life-history traits. In particular, the evolution of optimal host defence and the maintenance of variation in defence against infectious disease is thought to be underpinned by such evolutionary trade-offs. However, empirical demonstrations of these trade-offs that satisfy the strict assumptions made by theoretical models are rare. Additionally, none of these trade-offs have yet been shown to be robustly replicable using a variety of different experimental approaches to rule out confounding issues with particular experimental designs. Here, we use inbred isolines as a novel experimental approach to test whether a trade-off between viral resistance and growth rate in Plodia interpunctella, previously demonstrated by multiple selection experiments, is robust and meets the strict criteria required to underpin theoretical work in this field. Critically, we demonstrate that this trade-off is both genetic and constitutive. This finding helps support the large body of theory which relies on these assumptions, and makes this trade-off for resistance unique in being replicated through multiple experimental approaches and definitively shown to be genetic and constitutive.
Data from: MHC genotype predicts mate choice in the ring-necked pheasant Phasianus colchicus
Females of several vertebrate species selectively mate with males on the basis of the major histocompatibility complex (MHC) genes. As androgen-mediated maternal effects have long-lasting consequences for the adult phenotype, both mating and reproductive success may depend on the combined effect of MHC genotype and exposure to androgens during early ontogeny. We studied how MHC-based mate choice in ring-necked pheasants (Phasianus colchicus) was influenced by an experimental in ovo testosterone (T) increase. There was no conclusive evidence of in ovo T treatment differentially affecting mate choice in relation to MHC genotype. However, females avoided mating with males with a wholly different MHC genotype compared with males sharing at least one MHC allele. Females also tended to avoid mating with MHC-identical males, though not significantly so. These findings suggest that female pheasants preferred males with intermediate MHC dissimilarity. Male MHC heterozygosity or diversity did not predict the expression of ornaments or male dominance rank. Thus, MHC-based mating preferences in the ring-necked pheasant do not seem to be mediated by ornaments' expression and may have evolved mainly to reduce the costs of high heterozygosity at MHC loci for the progeny, such as increased risk of autoimmune diseases or disruption of coadapted gene pools.
Data from: GIbPSs: a toolkit for fast and accurate analyses of genotyping-by-sequencing data without a reference genome
Genotyping-by-sequencing (GBS) and related methods are increasingly used for studies of non-model organisms from population genetic to phylogenetic scales. We present GIbPSs, a new genotyping toolkit for the analysis of data from various protocols such as RAD, double-digest RAD, GBS, and two-enzyme GBS without a reference genome. GIbPSs can handle paired-end GBS data and is able to assign reads from both strands of a restriction fragment to the same locus. GIbPSs is most suitable for population genetic and phylogeographic analyses. It avoids genotyping errors due to indel variation by identifying and discarding affected loci. GIbPSs creates a genotype database that offers rich functionality for data filtering and export in numerous formats. We performed comparative analyses of simulated and real GBS data with GIbPSs and another program, pyRAD. This program accounts for indel variation by aligning homologous sequences. GIbPSs performed better than pyRAD in several aspects. It required much less computation time and displayed higher genotyping accuracy. GIbPSs retained smaller numbers of loci overall in analyses of real GBS data. It nevertheless delivered more complete genotype matrices with greater locus overlap between individuals and greater numbers of loci sampled in all individuals.
Data from: How to measure maturation: a comparison of probabilistic methods used to test for genotypic variation and plasticity in the decision to mature
Maturation is a developmental trait that plays a key role in shaping organisms' life-history. However, progress in understanding how maturation phenotypes evolve has been held back by confusion over how best to model maturation decisions and a lack of studies comparing genotypic variation in maturation. Here, we fitted probabilistic maturation reaction norms (PMRNs) to data collected from five clones of Daphnia magna and five of Daphnia pulex collected from within and between different populations. We directly compared the utility of modeling approaches that assume maturation to be a process with an instantaneous rate with those that do not by fitting maturation rate and logistic regression models, and emphasize similarities and differences between them. Our results demonstrate that in Daphnia, PMRNs using a logistic regression approach were simpler to use and provided a better fit to the data. The decision to mature was plastic across a range of growth trajectories and dependent upon both body size and age. However, the age effect was stronger in D. magna than D. pulex and varied considerably between clones. Our results support the idea that maturation thresholds can evolve but also suggest that the notion of a threshold based on a single fixed state is an oversimplification that underestimates the adaptability of these important traits.
Data from: Characterization of the gray whale Eschrichtius robustus genome and a genotyping array based on single-nucleotide polymorphisms in candidate genes
Genetic and genomic approaches have much to offer in terms of ecology, evolution, and conservation. To better understand the biology of the gray whale Eschrichtius robustus (Lilljeborg, 1861), we sequenced the genome and produced an assembly that contains ∼95% of the genes known to be highly conserved among eukaryotes. From this assembly, we annotated 22,711 genes and identified 2,057,254 single-nucleotide polymorphisms (SNPs). Using this assembly, we generated a curated list of candidate genes potentially subject to strong natural selection, including genes associated with osmoregulation, oxygen binding and delivery, and other aspects of marine life. From these candidate genes, we queried 92 autosomal protein-coding markers with a panel of 96 SNPs that also included 2 sexing and 2 mitochondrial markers. Genotyping error rates, calculated across loci and across 69 intentional replicate samples, were low (0.021%), and observed heterozygosity was 0.33 averaged over all autosomal markers. This level of variability provides substantial discriminatory power across loci (mean probability of identity of 1.6 × 10−25 and mean probability of exclusion >0.999 with neither parent known), indicating that these markers provide a powerful means to assess parentage and relatedness in gray whales. We found 29 unique multilocus genotypes represented among our 36 biopsies (indicating that we inadvertently sampled 7 whales twice). In total, we compiled an individual data set of 28 western gray whales (WGSs) and 1 presumptive eastern gray whale (EGW). The lone EGW we sampled was no more or less related to the WGWs than expected by chance alone. The gray whale genomes reported here will enable comparative studies of natural selection in cetaceans, and the SNP markers should be highly informative for future studies of gray whale evolution, population structure, demography, and relatedness.
Data from: Vitis phylogenomics: hybridization intensities from a SNP array outperform genotype calls
Understanding relationships among species is a fundamental goal of evolutionary biology. Single nucleotide polymorphisms (SNPs) identified through next generation sequencing and related technologies enable phylogeny reconstruction by providing unprecedented numbers of characters for analysis. One approach to SNP-based phylogeny reconstruction is to identify SNPs in a subset of individuals, and then to compile SNPs on an array that can be used to genotype additional samples at hundreds or thousands of sites simultaneously. Although powerful and efficient, this method is subject to ascertainment bias because applying variation discovered in a representative subset to a larger sample favors identification of SNPs with high minor allele frequencies and introduces bias against rare alleles. Here, we demonstrate that the use of hybridization intensity data, rather than genotype calls, reduces the effects of ascertainment bias. Whereas traditional SNP calls assess known variants based on diversity housed in the discovery panel, hybridization intensity data survey variation in the broader sample pool, regardless of whether those variants are present in the initial SNP discovery process. We apply SNP genotype and hybridization intensity data derived from the Vitis9kSNP array developed for grape to show the effects of ascertainment bias and to reconstruct evolutionary relationships among Vitis species. We demonstrate that phylogenies constructed using hybridization intensities suffer less from the distorting effects of ascertainment bias, and are thus more accurate than phylogenies based on genotype calls. Moreover, we reconstruct the phylogeny of the genus Vitis using hybridization data, show that North American subgenus Vitis species are monophyletic, and resolve several previously poorly known relationships among North American species. This study builds on earlier work that applied the Vitis9kSNP array to evolutionary questions within Vitis vinifera and has general implications for addressing ascertainment bias in array-enabled phylogeny reconstruction.
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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.