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55 results for “supergenes”
Data from: The fire ant social supergene is characterized by extensive gene and transposable element copy number variation
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Data from: Continuous variation in the shell colour of the snail <em>Cepaea nemoralis</em> is associated with the colour locus of the supergene
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Data from: Unexpected patterns of segregation distortion at a selfish supergene in the fire ant Solenopsis invicta
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Fine-scale habitat heterogeneity favours the coexistence of supergene-controlled social forms in Formica selysi
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Vasoactive intestinal peptide as a mediator of the effects of a supergene on social behavior
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Data from: Stepwise evolution of a butterfly supergene via duplication and inversion
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Data from: A socially polymorphic Formica ant species exhibits a novel distribution of social supergene genotypes
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Data from: The fire ant social chromosome supergene variant Sb shows low diversity but high divergence from SB
Variation in social behavior is common yet little is known about the genetic architectures underpinning its evolution. A rare exception is in the fire ant Solenopsis invicta: Alternative variants of a supergene region determine whether a colony will have exactly one or up to dozens of queens. The two variants of this region are carried by a pair of "social chromosomes", SB and Sb, which resemble a pair of sex chromosomes. Recombination is suppressed between the two chromosomes in the supergene region. While the X-like SB can recombine with itself in SB/SB queens, recombination is effectively absent in the Y-like Sb because Sb/Sb queens die before reproducing. Here, we analyze whole genome sequences of eight haploid SB males and eight haploid Sb males. We find extensive SB-Sb di↵erentiation throughout the >19Mb long supergene region. We find no evidence of "evolutionary strata" with different levels of divergence comparable to those reported in several sex chromosomes. A high proportion of substitutions between the SB and Sb haplotypes are nonsynonymous, suggesting inefficacy of purifying selection in Sb sequences, similar to that for Y-linked sequences in XY systems. Finally, we show that the Sb haplotype of the supergene region has 635-fold less nucleotide diversity than the rest of the genome. We discuss how this reduction could be due to a recent selective sweep affecting Sb specifically or associated with a population bottleneck during the invasion of North America by the sampled population.
Data from: An inversion supergene in Drosophila underpins latitudinal clines in survival traits
Chromosomal inversions often contribute to local adaptation across latitudinal clines, but the underlying selective mechanisms remain poorly understood. We and others have previously shown that a clinal inversion polymorphism in Drosophila melanogaster, In(3R)Payne, underpins body size clines along the North American and Australian east coasts. Here we ask whether this polymorphism also contributes to clinal variation in other fitness-related traits, namely survival traits (lifespan, survival upon starvation, and survival upon cold shock). We generated homokaryon lines, either carrying the inverted or standard chromosomal arrangement, isolated from populations approximating the endpoints of the North American cline (Florida, Maine), and phenotyped the flies at two growth temperatures (18°C, 25°C). Across both temperatures, high-latitude flies from Maine lived longer and were more stress resistant than low-latitude flies from Florida, as previously observed. Interestingly, we find that this latitudinal pattern is partly explained by the clinal distribution of the In(3R)P polymorphism, which is at ~50% frequency in Florida but absent in Maine: inverted karyotypes tended to be shorter-lived and less stress resistant than uninverted karyotypes. We also detected an interaction between karyotype and temperature on survival traits. Since In(3R)P influences body size and multiple survival traits, it can be viewed as a 'supergene', a cluster of tightly linked loci affecting multiple complex phenotypes. We conjecture that the inversion cline is maintained by fitness trade-offs and balancing selection across geography; elucidating the mechanisms whereby this inversion affects alternative, locally adapted phenotypes across the cline is an important task for future work.
Scores from S.invicta queen supergene pheromone discrimination assays
<p>Ants use chemical signals to communicate for various purposes related to colony function. Social organization in the red imported fire ant, <i>Solenopsis invicta</i>, is determined by the <i>Sb</i> supergene, with colonies of the monogyne (single-queen) form lacking the element and colonies of the polygyne (multiple-queen) form possessing it. Polygyne workers accept new reproductive queens in their nest, but only those carrying <i>Sb</i>; young winged queens lacking this genetic element are executed as they mature sexually in their natal nest or as they attempt to enter a foreign nest to initiate reproduction after mating and shedding their wings. It has been suggested that queen supergene genotype status is signaled to workers by unsaturated cuticular hydrocarbons, while queen reproductive status is signaled by piperidines (venom alkaloids). We used high-throughput behavioral assays to study worker acceptance of paper dummies dosed with fractions of extracts of polygyne queens, or blends of synthetic counterparts of queen cuticular compounds. We show that the queen supergene pheromone comprises a blend of monoene and diene unsaturated hydrocarbons. Our assays also reveal that unsaturated hydrocarbons elicit discrimination by polygyne workers only when associated with additional compounds that signal queen fertility. This synergistic effect was obtained with a polar fraction of queen extracts, but not by the piperidine alkaloids, suggesting that the chemical(s) indicating queen reproductive status are compounds more polar than cuticular hydrocarbons but are not the piperidine alkaloids. Our results advance understanding of the role of chemical signaling that is central to the regulation of social organization in an important invasive pest and model ant species.</p>
Data from: Multiple large inversions and breakpoint rewiring of gene expression in the evolution of the fire ant social supergene
Supergenes consist of co-adapted loci that segregate together and are associated with adaptive traits. In the fire ant Solenopsis invicta, two 'social' supergene variants regulate differences in colony queen number and other traits. Suppressed recombination in this system is maintained, in part, by a >9 Mb inversion, but the supergene is larger. Has the supergene in S. invicta undergone multiple large inversions? The initial gene content of the inverted allele of a supergene would be the same as that of the wild-type allele. So, how did the inversion increase in frequency? To address these questions, we cloned one extreme breakpoint in the fire ant supergene. In doing so, we found a second large (>800 Kb) rearrangement. Furthermore, we determined the temporal order of the two big inversions based on the translocation pattern of a third small fragment. Because the S. invicta supergene lacks evolutionary strata, our finding of multiple inversions may support an introgression model of the supergene. Finally, we showed that one of the inversions swapped the promoter of a breakpoint-adjacent gene, which might have conferred a selective advantage relative to the non-inverted allele. Our findings provide a rare example of gene alterations arising directly from an inversion event.
Life‐stage‐dependent supergene haplotype frequencies and metapopulation neutral genetic patterns of Atlantic cod, Gadus morhua, from Canada's Northern cod stock region and adjacent areas
<p class="BodyA">Among highly migratory fish species, nursery areas occupied by juveniles often differ from adult habitats. To better understand the spatial dynamics of Canada's Northern cod stock, juveniles caught off the east coast of Newfoundland and Labrador were compared to adults from the same region as well as individuals from other areas in Atlantic Canada using ddRAD-derived SNPs. A reduced proportion of homozygotes with a chromosomal inversion located in LG1 was detected between juvenile and adult samples in the Northern cod stock region, potentially indicating age-dependent habitat use or ontogenetic selection for attributes associated with the many genes located in LG1. No neutral genetic differences were found between samples from the Northern cod stock; however, significant differences were found between some of these samples and cod collected from St. Pierre Bank, Bay of Fundy, Browns Bank and the southern Scotian Shelf. Clustering analysis of variants at neutral loci provided evidence for three major genetic units: 1) the Newfoundland Atlantic Coast, 2) eastern and southern Gulf of St. Lawrence and Burgeo Bank, and 3) the Bay of Fundy, Browns Bank and southern Scotian Shelf. Both adaptive and neutral population structure within the Northern cod stock should be considered by managers to promote rebuilding.</p>
Data from: Cryptic recessive lethality of a supergene controlling social organization in ants
<p>Supergenes are clusters of linked loci that control complex phenotypes, such as alternate forms of social organization in ants. Explaining the long-term maintenance of supergenes is challenging, particularly when the derived haplotype lacks homozygous lethality and causes gene drive. In the Alpine silver ant, <em>Formica selysi</em>, a large and ancient social supergene with two haplotypes, <em>M</em> and <em>P</em>, controls colony social organization. Single-queen colonies only contain <em>MM </em>females, while multi-queen colonies contain <em>MP</em> and <em>PP</em> females. The derived <em>P</em> haplotype, found only in multi-queen colonies, selfishly enhances its transmission through maternal effect killing, which could have led to its fixation. A population genetic model showed that a stable social polymorphism can only be maintained under a narrow set of conditions, which includes partial assortative mating by social form (which is known to occur in the wild), and low fitness of <em>PP</em> queens. With a combination of field and laboratory experiments, we show that the <em>P</em> haplotype has deleterious effects on female fitness. The survival rate of <em>PP</em> queens and workers was around half the one of other genotypes. Moreover, <em>P</em>-carrying queens had lower fertility and fecundity compared to other queens. We discuss how cryptic lethal effects of the P haplotype help stabilize this ancient polymorphism.</p>
Supergenes and maintenance of alternative reproductive tacitcs
<p># Archived outputs from models of alternative reproductive tactics</p> <p>This repository contains outputs from models of the evolution of alternative reproductive tactics, with accompanying code available on github (https://github.com/spflanagan/ARTs).<br> The repository supports a manuscript submitted to Proceedings of the Royal Society B, which is investigating the effects of explicit genetic architecture on evolutionary dynamics of alternative reproductive tactics. </p> <p>The analysis used two separate programs: a baseline analytical model (written in R) and a simulation-based model (written in C++). Outputs from both of these models are archived here.</p> <p>## Baseline model</p> <p>- `morph_results_Ns.RDS`: An R data file containing a data.frame with the results of the baseline analytical model. It contains 11 columns:<br> - initial_CP = frequency of the courter/parent morph in the initial generation of the model<br> - initial_CN = frequency of the courter/non-parent morph in the initial generation of the model<br> - initial_NP = frequency of the non-courter/parent morph in the initial generation of the model<br> - initial_NN = frequency of the non-courter/non-parent morph in the initial generation of the model<br> - CP = frequency of the courter/parent morph in the final generation of the model<br> - CN = frequency of the courter/non-parent morph in the final generation of the model<br> - NP = frequency of the non-courter/parent morph in the final generation of the model<br> - NN = frequency of the non-courter/non-parent morph in the final generation of the model<br> - r = the relative reproductive investment parameter<br> - c = the sperm competition coefficient<br> - num_sneak = the number of males allowed to sneak fertilisations within a single clutch<br> - `morph_results_10000_equalStart.RDS`: An R data file containing a data.frame with the results of the baseline analytical model after it had been run for 10,000 generations. It contains the same 11 columns as `morph_results_Ns.RDS`.</p> <p>## Simulation model</p> <p>The simulation model was run with a variety of parameter combinations, which have been summarised in various files and the archived files are provided.</p> <p>### Raw outputs</p> <p>These results were generated by running the scripts `scripts/101_model-informed-single-locus.sh`, `101_model-informed-single-locus-tradeoffs.sh`, and `102_model-informed-genetics.sh`. Each parameter combination was run multiple times and generated the same sets of files:</p> <p>- `*_parameters.txt`: Outputs the parameter settings for that run in a text file with each parameter on its own line<br> - `*_log.txt`: A text file with the log outputs from the model - will note whether any errors occurred in that run.<br> - `*_traits.txt`: A tab-delimited file containing the trait data for every individual in generation 0 and generation 12000. The columns are:<br> - Gen: generation<br> - Pop: population ID within simulations that started with identical starting conditions<br> - Individual: A numerical index for the individual whose information is output.<br> - Sex: whether the individual is MALE or FEMALE<br> - Courter: A boolean value for whether the individual has the courter trait (1) or the non-courter trait (0). Note that females can carry the courter trait (i.e., have a value of 1 in this column) but do not express the courter trait.<br> - CourtTrait: The actual trait value for the individual, which is the sum of allelic effects at courter QTLs. <br> - Parent: A boolean value for whether the individual has the parent trait (1) or the non-parent trait (0). Note that females can carry the parent trait (i.e., have a value of 1 in this column) but do not express the parent trait.<br> - ParentTrait: The actual trait value for the individual, which is the sum of allelic effects at parent QTLs.<br> - Preference: A boolean value for whether the individual prefers the courting male (1) or non-courting males (0). For the simulation runs here, all individuals have a preference for courters.<br> - PrefTrait: The trait value for the preference trait if the trait has a genetic basis. In all iterations of the model shared here, the preference trait was not genetically inherited.<br> - MateFound: A count of how many mates the individual was able to obtain.<br> - PotRS: The potential reproductive success of the individual, based on their fecundity (which is set by the parameter settings in the model).<br> - LifetimeRS: The realised reproductive success of the individual based on the number of matings and the number of offpsring produced.<br> - Alive: A boolean value tracking whether the individual died or survived to mate. <br> - `*_summary.txt`: A tab-delimited file summarising the final frequencies of various morphs and other demographic parameters for each generation of the model, and for each population (when populations were initiated with identical starting parameters). It contains the following columns:<br> - Generation: Generation number (an integer)<br> - Pop: Numerical population ID. All populations were initiatlised with identical conditions within a single file.<br> - PopSize: The population size (i.e., number of adults)<br> - NumMal: Number of adult males in the population<br> - NumFem: Number of adult females in the population<br> - NumProgeny: The number of progeny produced<br> - ParentThresh: The population-level threshold for the parent trait to switch from parent to non-parent (this is the mean allelic effects in Gen 0).<br> - ParentFreq: Frequency of the parent trait in the population<br> - ParentAEmean: Mean allelic effects of the Parent QTLs<br> - ParentAEsd: Standard deviation in allelic effects of the Parent QTLs<br> - ParentW: Relative fitness of parent males<br> - NonParentW: Relative fitness of non-parent males<br> - CourterThresh: The population-level threshold for the courter trait to switch from courter to non-courter (this is the mean allelic effects in Gen 0).<br> - CourterFreq: Frequency of the courter trait in the population<br> - CourterAEmean: Mean allelic effects of courter QTLs<br> - CourterAEsd: Standard deviation of allelic effects of courter QTLs<br> - CourterW: Relative fitness of courting males<br> - NonCourterW: Relative fitness of non-courting males<br> - FreqNcNp: Frequency of non-courting/non-parent (NN) morph<br> - FreqCNp: Frequency of courting/non-parent (CN) morph<br> - FreqNcP: Frequency of non-courting/parent (NP) morph<br> - Freq CP: Frequency of courting/parent (CP) morph<br> - PrefThresh: The population-level threshold for the preference trait to switch from preferring the courting to non-courting males (not relevant to these simulations)<br> - PrefFreq: Frequency of the preference for the courting male in th epopulation (not relevant to these simulations)<br> - NumRandMate: Number of females that randomly mated (i.e., did not find a partner with the preferred trait)</p> <p>The runs with explicit genetic architectures also have the following files:</p> <p>- `*_qtlinfo.txt`: A tab-delimited file summarising the location of each type of QTL. Each column is a different QTL and each row is a different population. If they are initialised to be identical, the QTL information will be the same for each population. The format of the QTL location information is a the chromosome number as an integer (starting at 0), followed by a decimal, and the following numbers are the location among the marker loci. So, 0.850 refers to a QTL on chromosome 0 at marker location 850 (out of 1000). <br> - `*_allelic-effects.txt`: A tab-delimited file containing the allelic effects for each QTL. These are the additive contributions each QTL makes towards the trait, and these mutate if a mutation occurs at the location of the QTL (which is recorded in the corresponding `*_qtlinfo.txt` file).<br> - `*_markers.txt`: A tab-delimited file summarising the allele frequency at each marker locus.<br> - `*vcf`: A variant call format file for the population in the final generation of the simulations. See standard formats for this type of file online (e.g., https://samtools.github.io/hts-specs/VCFv4.2.pdf)<br> - `*Tajima.D`: The vcftools output format containing Tajima's D statistics, which was generated using the vcf file. See the vcftools manual for more details (https://vcftools.github.io/man_latest.html)<br> - `*LD.geno.ld`: The vcftools output format containing pairwise linkage disequilibrium statistics, which was generated using the vcf file. See the vcftools manual for more details (https://vcftools.github.io/man_latest.html)<br> - `*_gt.csv`: A comma-separated file summarising the genotype information for each individual at all marker loci. It is similar to vcf file format, with the following columns:<br> - Marker: marker ID<br> - Chrom: Chromosome ID or number (starting at 0)<br> - Position: Locaiton on the chromosome (starting at 0)<br> - REF: Reference allele<br> - ALT: Alternative allele<br> - The remaining columns are each individual's genotype <br> - `*_pheno.csv`: A comma-separated file summarising the phenotypes for a population with the following columns:<br> - ID: individual ID<br> - CourtTrait: Whether the individual is a courter (2) or a non-courter (1)<br> - ParentTrait: Whether the individual is a parent (2) or a non-parent (1)<br> - Sex: Whether the individual is a male (MAL) or a female (FEM)<br> - Morph: The morph of the individual (CP = courter/parent, C = courter, P = non-courter/parent, N = non-courter/non-parent; females can have preferences as well but this is not relevant to these datasets)</p> <p><br> These above outputs, run with various parameter settings, are found in the following `tar.gz` files:</p> <p>- `stochasticity.tar.gz`: Contains the output for the parameter combinations without explicit genetic architectures but including demographic stochasticity, recombination, and mutation. Their file names contain the following labels:<br> - lowDiversity, highDiversity, or highDiversityStrict: indicates the parameter settings used as described in the main text. The 'Strict' case is described in the supplement.<br> - polygyny or monogamy: Specifies if males were allowed to mate with multiple females.<br> - RM: if present, it means that females mated randomly if no suitable males were found<br> - nm: if present, it means that no random mating was permitted if a suitable male was not found<br> - v0: if present, no viability selection was imposed on males<br> - _\d: the final number in the name represents the replicate number that was run with the particular parameter combination<br> - `qtls.tar.gz`: Contains the output for parameter combinations run at high diversity, low diversity, various mating systems, and various genetic parameters. Their file names contain the following labels:<br> - highDiversity or lowDiversity: indicates the parameter settings used as described in the main text.<br> - polygyny or monogamy: Specifies if males were allowed to mate with multiple females. (if this is absent, polygyny is the default)<br> - nm: if present, it means that no random mating was permitted if a suitable male was not found<br> - q\d+: The number of QTLs underlying each trait<br> - c\d+: The number of chromosomes in the simulation<br> - _\d+: the final number in the name represents the replicate number that was run with the particular parameter combination<br> - pop_\d+: For some genomic analyses, the population number from within a replicate is also included. Within a replicate, all populations had identical starting conditions. <br> - `supergene.tar.gz`: Contains the output for parameter combinations run at high diversity, low diversity, various mating systems, and various supergene genetic parameters. Their file names contain the following labels:<br> - highDiversity or lowDiversity: indicates the parameter settings used as described in the main text.<br> - polygyny or monogamy: Specifies if males were allowed to mate with multiple females. (if this is absent, polygyny is the default)<br> - nm: if present, it means that no random mating was permitted if a suitable male was not found<br> - prop\d.\d+: specifies the proportion of a chromosome the supergene stretched across. The options are 0.05,0.25,0.5<br> - q\d+: The number of QTLs underlying each trait<br> - c\d+: The number of chromosomes in the simulation<br> - _\d+: the final number in the name represents the replicate number that was run with the particular parameter combination<br> - pop_\d+: For some genomic analyses, the population number from within a replicate is also included. Within a replicate, all populations had identical starting conditions.</p> <p><br> ### Summaries</p> <p>The outputs in the zipped files listed above were analysed and summarised in a variety of ways, and those summaries were saved into files for ease of analysis and figure making. </p> <p>- `lowDiv.RDS`, `highDiv.RDS`, and `highDivStrict.RDS` are three R data files that summarise the final frequencies in the simulations witout explicit genetic archictecures (from the `stochastic.tar.gz` file). These files are produced in `docs/102_all-model-outcomes.Rmd`. All three are lists with names reflecting the replicate ID and population, and each list element contains three frequencies, in this order: <br> - frequency of the courter/parent morph in the final generation of the model<br> - frequency of the non-courter/parent morph in the final generation of the model <br> - frequency of the non-courter/non-parent morph in the final generation of the model <br> - `morph_freqs_summary.csv`: A comma-separated file containing the final frequencies of all four morphs for all analysed simulations with explicit genetic architectures (qtls vs supergenes). It contains a header row describing the five columns:<br> - CP = frequency of the courter/parent morph<br> - C = frequency of the courter/non-parent morph<br> - P = frequency of the non-courter/parent morph<br> - NON = frequency of the non-courter/non-parent morph<br> - file = the name and relative path (on my computer) where the results are stored<br> - `selection_gradients.RDS`: An R data file containing a list of data.frames. Each list item contains the name of the trait file it summarises, which captures details on the simulation settings and replicate number. The summary statistics were generated in `docs/101_explicit-genetics-outcomes.Rmd`. Each data.frame contains one row per population for each of generation 0 and generation 12000, with the following columns:<br> - court_cat_b0: intercept of the regression of courter trait values on lifetime reproductive success <br> - court_cat_b0_se: standard error of the intercept of the regression of courter trait values on lifetime reproductive success <br> - court_cat_b0_p: p-value associated with the intercept of the regression of courter trait values on lifetime reproductive success <br> - court_cat_b1: slope of the regression of courter trait values on lifetime reproductive success <br> - court_cat_b1_se: standard error of the slope of the regression of courter trait values on lifetime reproductive success <br> - court_cat_b1_p: p-value associated with the slope of the regression of courter trait values on lifetime reproductive success <br> - parent_cat_b0: intercept of the regression of parent trait values on lifetime reproductive success <br> - parent_cat_b0_se: standard error of the intercept of the regression of parent trait values on lifetime reproductive success <br> - parent_cat_b0_p: p-value associated with the intercept of the regression of parent trait values on lifetime reproductive success <br> - parent_cat_b1: slope of the regression of parent trait values on lifetime reproductive success <br> - parent_cat_b1_se: standard error of the slope of the regression of parent trait values on lifetime reproductive success <br> - parent_cat_b1_p: p-value associated with the slope of the regression of parent trait values on lifetime reproductive success <br> - cp_freq: frequency of the courter/parent morph in the final generation of the model<br> - np_freq: frequency of the non-courter/parent morph in the final generation of the model <br> - cn_freq: frequency of the courter/non-parent morph in the final generation of the model<br> - nn_freq: frequency of the non-courter/non-parent morph in the final generation of the model <br> - gen: which generation the results come from<br> - pop: which identically-initialised population doe the results come from<br> - supergene: A boolean value representing whether the replicate had a supergene (1) or did not (0)<br> - highDiv: Whether the replicate used high-diversity parameter settings (1) or low diversity parameter settings (0)<br> - `fitness_dat.RDS`: An R data file containing a list of data.frames. Each list item is named as the trait file it summarises, which captures the details of the replicate settings. Each data.frame contains one row per population for generation 0 and generation 12000, with the following columns:<br> - cp_muRS: Mean lifetime reproductive success for males of the courter/parent morph<br> - np_muRS: Mean lifetime reproductive success for males of the non-courter/parent morph <br> - cn_muRS: Mean lifetime reproductive success for males of the courter/non-parent morph <br> - nn_muRS: Mean lifetime reproductive success for males of the non-courter/non-parent morph <br> - cp_semRS: standard error of the mean lifetime reproductive success for males of the courter/parent morph <br> - np_semRS: standard error of the mean lifetime reproductive success for males of the non-courter/parent morph <br> - cn_semRS: standard error of the mean lifetime reproductive success for males of the courter/non-parent morph <br> - nn_semRS: standard error of the mean lifetime reproductive success for males of the non-courter/non-parent morph <br> - cp_freq: frequency of the courter/parent morph in the final generation of the model<br> - np_freq: frequency of the non-courter/parent morph in the final generation of the model <br> - cn_freq: frequency of the courter/non-parent morph in the final generation of the model<br> - nn_freq: frequency of the non-courter/non-parent morph in the final generation of the model <br> - gen: which generation the results come from<br> - pop: which identically-initialised population doe the results come from<br> - supergene: A boolean value representing whether the replicate had a supergene (1) or did not (0)<br> - highDiv: Whether the replicate used high-diversity parameter settings (1) or low diversity parameter settings (0)<br> - `GWAS_summary.csv`: A comma-separated file containing the genome-wide association study summary outputs as generated by `R/103_run_gwas.R`. It contains 9 columns and no header row:<br> - Marker ID<br> - Chromosome number<br> - position on chromosome<br> - which GWAS model it was an outlier in<br> - The estimated $R^2$<br> - the p-value for the GWAS test<br> - A boolean value identifying whether the outlier is near a QTL (in a QTL peak, see `docs/103_genomics-ARTs.Rmd`)<br> - Which trait was used in the association (Courter or Parent)<br> - filename for the vcf file used in the analysis<br> - `ld_summary_all.csv`: A comma-separated file containing linkage disequilibrium summary statistics. It does not contain a header row or rownames, and has the following columns:<br> - Chromosome Id<br> - position on the chromosome<br> - average $R^2$ value for that locus<br> - average $R^2$ value for that locus but only when compared to QTLs<br> - average $R^2$ value for that locus but only when compared to non-QTLs<br> - filename of LD results (which inludes replicate and population IDs)<br> - `ld_summary_resampled.csv`: A comma-separated file containing rownames (first column) and 10 additional columns, as well as a header row. The file contains average linkage disequilibrium coefficients and averages from resampling. Thos resampled values were generated using `ld_summary_all.csv` and the analysis is detailed in `docs/103_genomics-ARTs.Rmd`. The rownames are the name of the file analysed (i.e., replicate and population IDs), and the subsequent rows are:<br> - nqtl: number of QTL parameterised in the simulation<br> - nqtl_actual: the actual number of QTLs in the simulations. This number sometimes differed if the same marker locus was randomly chosen more than once in the initialisation of the simulations (especially in supergene scenarios)<br> - nchrom: number of chromosomes<br> - prop: the proportion of a chromosome with a supergene (NA if supergenes were not modelled)<br> - avgQ: Average pairwise linkage disequilibrium (LD) for QTLs<br> - semQ: standard error of the mean pairwise LD for QTLs<br> - avgNQ: Average pairwise LD for non-QTLs<br> - semNQ: standard error of the mean pairwise LD for non-QTLs<br> - avgResampled: average pairwise LD for $n$ randomly chosen loci, where $n$ is the number of QTLs in the simulation, averaged over 999 iterations of random re-sampling<br> - semResampled: standard error of the mean pairwise LD for $n$ randomly chosen loci, where $n$ is the number of QTLs in the simulation, averaged over 999 iterations of random re-sampling<br> - `td_freqs.csv`: A comma-separated file containing summary statistics about Tajima's D values for each population and each replicate. Tajima's D values were estimated by vcftools and the processing of those outputs is recorded in `docs/103_ARTs-genomics`. Note that all items are quoted. The file contains a header row and 10 columns:<br> - unnamed (i.e., rownames): Filename and relative path of the replicate and population<br> - avgTD: average Tajima's D genome-wide<br> - semTD: Standard error of the mean Tajima's D genome-wide<br> - avgTD_qtls: average Tajima's D of only the true QTLs<br> - semTD_qtls: Standard error of the mean Tajima's D at true QTLs<br> - avgTD_neutral: average Tajima's D of only neutral markers<br> - semTD_neutral: Standard error of the mean Tajima's D at neutral markers<br> - t.t: test statistic from a Welch's corrected t-test comparing average Tajima's D at QTLs vs neutral markers<br> - df.df: degrees of freedom from a Welch's corrected t-test comparing average Tajima's D at QTLs vs neutral markers<br> - p: p-value from a Welch's corrected t-test comparing average Tajima's D at QTLs vs neutral markers<br> - architecture: The genetic architecture in the simulation (QTLs vs supergene)<br> - diversity: Whether the simulation was run with high diversity parameters or low diversity parameters<br> - CP = frequency of the courter/parent morph in the final generation of the model<br> - C = frequency of the courter/non-parent morph in the final generation of the model<br> - P = frequency of the non-courter/parent morph in the final generation of the model<br> - NON = frequency of the non-courter/non-parent morph in the final generation of the model<br> - file = the name and relative path (on my computer) where the results are stored <br> - `popgen_summary.csv`: A comma-separated file containing summary statistics from the population genomics analyses for each simulation. The file was generated in `docs/103_genomics-ARTs.Rmd`. It has the following columns:<br> - sim: The name of the simulation <br> - nChrom: Number of chromosomes in the simulation<br> - nQTLS: Number of QTLs in the simulation<br> - propMale: The proportion of individuals in the population that were male<br> - propP: Proportion of males in the population that were non-courter/parents<br> - propCP: Proportion of males in the population that were courter/parents<br> - propC: Proportion of males in the population that were courter/non-parents<br> - propN: Proportion of males in the population that were non-courter/non-parents<br> - propPref0: Proportion of individuals the preferred the non-courters (not relevant to this study)<br> - gHtMean: Mean $H_t$ for all genomic markers<br> - gHtMedian: Median $H_t$ for all genomic markers<br> - gHtVar: Variance in $H_t$ for all genomic markers<br> - qHtMean: Mean $H_t$ for QTLs only <br> - qHtMedian: Median $H_t$ for QTLs only <br> - qHtVar: Variance in $H_t$ for QTLs only <br> - gGpMeanMM: Mean $G'$ for the male-male comparison for all genomic markers<br> - gGpMedianMM: Median $G'$ for the male-male comparison for all genomic markers<br> - gGpVarMM: Variance in $G'$ for the male-male comparison for all genomic markers<br> - qGpMeanMM: Mean $G'$ for the male-male comparison for QTLs only<br> - qGpMedianMM: Median $G'$ for the male-male comparison for QTLs only<br> - qGpVarMM: Variance in $G'$ for the male-male comparison for QTLs only<br> - nPeaksMM: The number of $G'$ peaks identified for the male-male comparison<br> - nSigPeaksMM: The number of significant $G'$ peaks in the male-male comparison<br> - propQTLsInPeaksMM: Proportion of QTLs that were in $G'$ peaks for the male-male comparison<br> - gGpMeanMF: Mean $G'$ for the male-female comparison for all genomic markers<br> - gGpMedianMF: Median $G'$ for the male-female comparison for all genomic markers<br> - gGpVarMF: Variance in $G'$ for the male-female comparison for all genomic markers<br> - qGpMeanMF: Mean $G'$ for the male-female comparison for QTLs only<br> - qGpMedianMF: Median $G'$ for the male-female comparison for QTLs only<br> - qGpVarMF: Variance in $G'$ for the male-female comparison for QTLs only<br> - nPeaksMF: The number of $G'$ peaks identified for the male-female comparison<br> - nSigPeaksMF: The number of significant $G'$ peaks in the male-female comparison<br> - propQTLsInPeaksMM: Proportion of QTLs that were in $G'$ peaks for the male-male comparison - Architecture<br> - Architecture: The genetic architecture in the simulation (QTLs vs supergene)<br> - HetP: The p-value comparing mean heterozygosity between QTLs and genome-wide markers<br> - Diversity: Whether the simulation was run with high diversity parameters or low diversity parameters</p> <p>## Reproducing main figures</p> <p>To reproduce **Figure 1** in the main text, the following files are required:</p> <p>- `morph_results_Ns.RDS`<br> - `lowDiv.RDS`<br> - `highDiv.RDS`<br> - `morph_freqs_summary.csv`</p> <p>These files are converted into appropriate formats for ternary plots and compared to each other in `docs/102_all-model-outcomes.Rmd`.</p> <p>To reproduce **Figure 2** in the main text, the following files are required:</p> <p>- `popgen_summary.csv`<br> - `td_freqs.csv`</p> <p>The figure is produced in `docs/103_genomics-ARTs`.</p>
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