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50 results for “evolution of mimicry”
Data from: The genomics and evolution of inter-sexual mimicry and female-limited polymorphisms in damselflies
<p>The dataset contains intermediate output files required to reproduce the figures in the main text and Supporting Material of Willink <em>et al</em>. 2023. The genomics and evolution of inter-sexual mimicry and female-limited polymorphisms in damselflies.</p> <p>FILE OVERVIEW:</p> <p>1. Morph-specific assemblies<br> A. File names: Afem_1354_ragtag.fasta.gz, Ifem_1049_ragtag.fa.gz, Ofem_0081_ragtag.fa.gz, O054_Shasta_run2.PMDV.HAP1.purged.fasta.gz, A059_Shasta_run1.PMDV.HAP1.purged.fa.gz<br> B. Description: genome assemblies for different morphs of <em>Ischnura elegans</em> (Afem_1354, Ifem_1049, and Ofem_0081) and <em>Ischnura senegalensis</em> (A059 and O054), generated in this study from long-read Nanopore data using Shasta v 0.7.0 (https://github.com/paoloshasta/shasta).</p> <p>2. Assembly statistics<br> A. File names: Assembly_statistics.csv, Assembly_statistics_sen.csv<br> B. Description: Completeness and quality metrics for <em>de novo</em> genome assemblies of <em>I. elegans</em> and <em>I. senegalensis</em> female morphs. See Fig. S1-S2.</p> <p>3. Repetitive content annotation<br> A. File names: A1354_ragtag_RED.bed.repeats.bed.gz, Afem_Shasta1_polished_ragtag_UPPER.fa.out.gz, Ifem_Shasta2_polished_ragtag_UPPER.fa.out.gz, ioIscEleg1.1.primary_UPPER.fa.out.gz, ToL_RED.repeats.bed.gz<br> B. Description: Annotation of repetitive sequences in morph-specific assemblies. All morph assemblies (A, I and Darwin Tree of Life assemblies) were annotated using RepeatModeler v 2.0.1 and RepeatMasker v 1.0.93 (http://www.repeatmasker.org). The A morph and DToL assemblies were additionally annotated using Red v 0.0.1 (https://github.com/BioinformaticsToolsmith/Red). RepeatMasker annotations were then used to estimate TE coverage. See Extended Data Fig. 4 and Fig. S7.</p> <p>4. GWAS output<br> A. File names: A1354_ragtag_AvI.assoc_filtered.txt.gz, A1354_ragtag_AvO.assoc_filtered.txt.gz, A1354_ragtag_IvO.assoc_filtered.txt.gz, ToL_AvI.assoc_filtered.txt.gz, ToL_AvO.assoc_filtered.txt.gz, ToL_IvO.assoc_filtered.txt.gz<br> B. Description: filtered SNPs in pairwise association tests between morphs (n = 19 resequencing samples per morph) of<em> I. elegans</em>. Analyses were conducted in PLINK v 1.9 (http://pngu.mgh.harvard.edu/purcell/plink/), using either the A morph assembly (Fig. 2a-b), or the Darwin Tree of Life (DToL) reference assembly (Extended Data Figure 8a-b) as mapping reference.</p> <p>5. Population statistics<br> A. File names: Afem_pixy_30K_fst.txt.gz, A1354_30kb.Tajima.D.gz, Afem_pi_30K_pi.txt.gz, ToL_30K_fst.txt.gz, ToL_30kb.Tajima.D.gz, ToL_30K_onepop_pi.txt.gz<br> B. Description: Genetic differentiation (fst) between morphs, Tajima's D statistics, and nucleotide diversity across 30 kb windows of the<em> I. elegans</em> genome. Population statistics were computed using either the A morph assembly (Fig. 2c-e), or the DToL reference assembly (Extended Data Figure 8c-e) as mapping reference.</p> <p>6. k-mer based GWAS<br> A. File names: AvI_kmers.fa.gz, AvO_kmers.fa.gz, OvAI_kmers.fa.gz, AvI_kmers.fa_v_A1354_Shasta_run1_table.tsv.gz, AvO_kmers.fa_v_A1354_Shasta_run1_table.tsv.gz, OvAI_kmers.fa_v_A1354_Shasta_run1_table.tsv.gz, OvAI_kmers.fa_v_Ifem_1049_ragtag_table.tsv.gz<br> B. Description: List of significant k-mers (in fasta format) in three k-mer based association analyses (n = 19 resequencing samples per morph) between morphs of<em> I. elegans</em>. Significant k-mers were then mapped to morph-specific assemblies using Blast v 2.22.28 (https://blast.ncbi.nlm.nih.gov/Blast.cgi) for short sequences. We include mapping results shown in Fig. 3a-b.</p> <p>7. Read-depth coverage<br> A. File names: reseq_coverage_norepeat_500_window.bed.gz, nano_coverage_norepeat_500_window.bed.gz, Ifem_nano_coverage_norepeat_500_window.bed.gz, Ifem_reseq_coverage_norepeat_500_window_15Mb.bed.gz, poolseq_coverage_norepeat_500_window.bed.gz, morph_coverage_norepeat_diff_500.tsv.gz, SwD_popmap<br> B. Description: Read depth coverage of the morph locus and a 15 mb region used to estimate baseline read depths. 19 Illumina resequencing samples, and one long-read Nanopore sample of each morph of <em>I. elegans</em> were mapped to both the A and I assemblies to estimate read depth. Two poolseq samples (each pool consisting of 30 females of each morph) of<em> I. senegalensis</em> were mapped to the A assembly of<em> I. elegans</em> to estimate read depth. Read depth was estimated in mosdepth v 0.2.8 (https://github.com/brentp/mosdepth) across 500 bp windows after filtering windows with more than 10% repetitive content. For poolseq samples, the difference in coverage values between the A and O pools was computed across the entire genome. Sample information for resequencing samples is recorded in the file SwD_popmap. See Fig. 3c-d, 5b, and S8.</p> <p>8. Assembly alignment<br> A. File names: nucmer_aln_Ifem_1049_ragtag_Afem_1354_ragtag.qr1_filter.reformat.coords.gz, nucmer_aln_Ofem_0081_ragtag_Afem_1354_ragtag.qr1_filter.reformat.coords.gz, nucmer_aln_Afem_Isen_Afem_Iele.qr1_filter.reformat.coords.gz, nucmer_aln_Ofem_Isen_Afem_Iele.qr1_filter.reformat.coords.gz, karyotype_AI_RagTag.csv, karyotype_AO_RagTag.csv, karyotype_AIsen_AIele.cs, karyotype_OIsen_AIele.csv<br> B. Description: Assembly alignments using nucmer v 4.0.0 (https://github.com/mummer4/mummer) and contig synteny for plotting using RIdeogram v 0.2.2 (https://cran.r-project.org/web/packages/RIdeogram/vignettes/RIdeogram.html) in R v 4.2.2 (https://www.r-project.org/). The A morph assembly of <em>I. elegans</em> was aligned to the I and O morph assemblies of<em> I. elegans</em> and to the A and O-like assemblies of <em>I. senegalensis</em>. See Fig. 4a, 5c.</p> <p>9. Genotyping the Darwin Tree of Life assembly<br> A. File names: nucmer_aln_Afem_ragtag_ToL-haplotigs.qr1_filter.reformat.coords.gz, nucmer_aln_Afem_ragtag_ToL-primary.qr1_filter.reformat.coords.gz, ToL_500_norepeat.regions.bed.gz, karyotype_AToL_13_unloc_RagTag.csv, karyotype_AToL_RagTag_haplotigs.csv<br> B. Description: To genotype the DToL reference assembly of<em> I. elegans</em>, we estimated read-depth coverage of the DToL long-read Pacbio data mapped to the A morph assembly of <em>I. elegans</em> generated in this study, and aligned the A morph assembly to both the primary DToL assembly and to the purged haplotigs. Read depth was estimated in mosdepth v 0.2.8 (https://github.com/brentp/mosdepth) and assembly alignments were conducted using nucmer v 4.0.0 (https://github.com/mummer4/mummer). See Fig. S3.</p> <p>10. SV calling<br> A. File names: A_to_A.bam, A_to_A.bam.bai, A_to_I.bam, A_to_I.bam.bai, A_to_O.bam, A_to_O.bam.bai, A_to_ToL_2mb.bam, A_to_ToL_2mb.bam.bai, I_to_A.bam, I_to_A.bam.bai, I_to_I.bam, I_to_I.bam.bai, I_to_O.bam, I_to_O.bam.bai, I_to_ToL_2mb.bam, I_to_ToL_2mb.bam.bai, O_to_A.bam, O_to_A.bam.bai, O_to_I.bam, O_to_I.bam.bai, O_to_O.bam, O_to_O.bam.bai, O_to_ToL_2mb.bam, O_to_ToL_2mb.bam.bai<br> B. Description: mergede alignements of resequencing samples (n = 19 per morph) to alternative reference assemblies (A, I, O, and DToL) for<em> I. elegans</em>. The alignments have been filtered by quality and to contain only the unlocalized scaffold 2 of chromosome 13, which includes the morph locus. These files were used to call morph-specific structural variants using samplot v 1.3.0 (https://github.com/ryanlayer/samplot). See Extended Data Figs 2, 7, and Fig. S5-S6.</p> <p>11. Mapping of inversion breakpoint reads<br> A. File names: AvO_3K.tsv.gz, AvO_22K.tsv.gz, AvO_sen_3K.tsv.gz, AvO_sen_22K.tsv.gz, IvO_3K.tsv.gz<br> B. Description: Signatures of an inversion with breakpoints at ~ 3 kb and ~ 22 kb of the unlocalized scaffold 2 of chromosome 13 on the O assembly were found in A and I resequencing samples of <em>I. elegans</em> and in poolseq samples of A females of <em>I. senegalensis</em>. We queried the reads mapping to the inversion breakpoints and then tabulated their mapping locations of the A morph assembly of<em> I. elegans</em> (Fig. 6 and Extended Data Fig. 3, 7b-c). For the first inversion breakpoint, we also mapped reads on the I morph assembly of <em>I.</em> elegans (Fig. S12).</p> <p>12. Evidence of translocation in I<br> A. File names: Ifem_nano_SUPER_13_unloc_2.bam, Ifem_nano_SUPER_13_unloc_2.bam.bai<br> B. Description: Long-read Nanopore data of a I morph female of <em>I. elegans</em> mapped to the A morph of <em>I. elegans</em> and filtered to contain the entire unlocalized scaffold 2 of chromosome 13. Read mapping was conducted in minimap2 v 2.22-r1110 (https://github.com/lh3/minimap2) and used to identify a translocation signature in the I morph, relative to the A morph of <em>I. elegans</em>. See Extended Data Fig. 6.</p> <p>13. PCA output<br> A. File names: A1354_all.eigenval, A1354_all.eigenvec, I1049_all.eigenval, I1049_all.eigenvec<br> B. Description: Eigenvectors and eigenvalues of PCA analyses of population structure between morphs of <em>I. elegans</em>. PCA analysis were conducted on morph locus, using either the A morph or the I morph assembly as mapping reference in PLINK v 1.9 (http://pngu.mgh.harvard.edu/purcell/plink/). See Fig. S4.</p> <p>14. Linkage disequilibrium<br> A. File names: A1354_SUPER_1_allr.ld.gz, A1354_SUPER_2_allr.ld.gz, A1354_SUPER_3_allr.ld.gz, A1354_SUPER_4_allr.ld.gz, A1354_SUPER_5_allr.ld.gz, A1354_SUPER_6_allr.ld.gz, A1354_SUPER_7_allr.ld.gz, A1354_SUPER_8_allr.ld.gz, A1354_SUPER_9_allr.ld.gz, A1354_SUPER_10_allr.ld.gz, A1354_SUPER_11_allr.ld.gz, A1354_SUPER_12_allr.ld.gz, A1354_SUPER_13_allr.ld.gz, A1354_SUPER_13_unloc_1_allr.ld.gz, A1354_SUPER_13_unloc_2_allr.ld.gz, A1354_SUPER_13_unloc_3_allr.ld.gz, A1354_SUPER_13_unloc_4_allr.ld.gz, A1354_SUPER_X_allr.ld.gz<br> B. Description: Estimates of recombination rate (R2) between SNPs across the first 15 mb of each chromosome and unlocalized segments of chromosome 13 of <em>I. elegans</em>. Recombination rates were estimated based on 57 resequencing samples and using the A morph assembly as mapping reference in PLINK v 1.9 (http://pngu.mgh.harvard.edu/purcell/plink/). See Extended Data Fig. 5.</p> <p>15. Gene annotations<br> A. File names: Afem_all_ragtag.gtf.gz, Afem_all_transcripts.transdecoder.genome.gff3.gz, Isen.gtf.gz<br> B. Description: Annotation of the A morph assembly of <em>I. elegans</em> using RNAseq data to assemble transcripts <em>de novo </em>for <em>I. elengans</em> and <em>I. senegalensis</em> in Stringtie v 2.1.4 (https://ccb.jhu.edu/software/stringtie/). Peptide sequences for the <em>I. elegans</em> transcripts were then predicted using Transdecoder v 5.5.0 (https://github.com/TransDecoder/TransDecoder).</p> <p>16. Gene annotations in the morph locus<br> A. File names: gene_models_shared_trancripts_simple.csv, gene_models_shared_trancripts_simple_I.csv<br> B. Description: locations of exon features for genes in the morphs locus and expressed in at least one adult sample of both<em> I. elegans</em> and <em>I. senegalensis</em>. Locations are given for the A and I assemblies. See Fig. 6 and S12.</p> <p>17. Gene expression<br> A. File names: DToL_gene_count_matrix.csv.gz, DToL_transcript_count_matrix.csv.gz, gene_count_matrix.csv.gz, transcript_count_matrix.csv.gz, Isen_gene_count_matrix.csv.gz, Isen_transcript_count_matrix.csv.gz, Iele_phenodata.csv, Isen_phenodata.csv<br> B. Description: Sample information (phenodata), gene and transcript count matrices for gene expression analysis. For <em>I. elegans</em>, gene expression was quantified on thoracic tissue of six adult females of each morph and six adult males (three sexually mature and three sexually immature in each group). Reads were mapped to both the A morph assembly and the DToL reference assembly. For <em>I. senegalensis</em>, we used previously published data (NCBI BioProject PRJDB11387) from different tissues of adult females of each morph and males (one upon emergence and one two days after emergence for each group) mapped to the A morph assembly. Gene and transcript counts were generated using Stringtie v 2.1.4 (https://ccb.jhu.edu/software/stringtie/). See Fig. 6, S9-S11, S13.</p> <p>18. SNPs in the morph locus<br> A. File names: A1354-ragtag-allsites-candidate_gene_cds.vcf.gz, A1354-ragtag-allsites-candidate_gene_cds.vcf.gz.tbi, vcf_popmap<br> B. Description: SNPs in 57 resequencing samples across coding sequences of the morph locus of <em>I. elegans</em>. The A morph assembly was used as mapping reference. Sample information for resequencing samples is recorded in the file vcf_popmap. See Fig. S14a.</p> <p>19. Domains and orthologues of Gastrula zinc-finger transcription factor in the morph locus<br> A. File names: GZnf_domain_annot.csv, GZnF_orthologue.tre, GZnf_orthologue_annot.txt<br> B. Description: Functional domains were annotated using InterProScan (https://www.ebi.ac.uk/interpro/). The gene orthologue tree was inferred using OrthoFinder v 2.5.2 (https://github.com/davidemms/OrthoFinder). See Fig. S14.</p>
Uncovering the effects of Müllerian mimicry on the evolution of conspicuousness in colour patterns
Variation in the conspicuousness of colour patterns is observed within and among defended prey species. The evolution of conspicuous colour pattern in defended species can be strongly impaired because of increased detectability by predators. Nevertheless, such evolution of the colour pattern can be favoured if changes in conspicuousness result in Müllerian mimicry with other defended prey. Here, we develop a model describing the population dynamics of a conspicuous defended prey species, and we assess the invasion conditions of derived phenotypes that differ from the ancestral phenotype by their conspicuousness. Such change in conspicuousness may then modify their level of mimicry with the local community of defended species. Derived colour pattern displayed in this focal population can therefore be either exactly similar, partially resembling or completely dissimilar to the local mimicry ring displaying the ancestral colour pattern. We assume that predation risk depends (1) on the number of individuals sharing a given colour pattern within the population, (2) on the occurrence of co-mimetic defended species, and (3) on the availability of alternative edible prey. Using a combination of analytical derivations and numerical simulations, we show that colour patterns that are less conspicuous than the ancestral one are generally favoured within mimicry rings, unless reduced conspicuousness impairs mimicry. By contrast, when a mutation affecting the colour pattern leads to a shift toward a better protected mimicry ring, a more conspicuous colour pattern can be favoured. The selected aposematic pattern then depends on the local communities of defended and edible prey, as well as on the detectability, memorability and level of mimicry of the colour patterns.
Fig. 2c. Tillomorphites otiliae n in Two new fossil species of Tillomorphites Vitali (Coleoptera: Cerambycidae) and remarks on the morphological evolution, mimicry, biogeography and phylogeny of the tribe Tillomorphini
Fig. 2c. Tillomorphites otiliae n. sp., habitus, Fig. 2 e. Tillomorphites otiliae n. sp., reconstruction. Paratype, colour reconstruction.
Phylogeny, systematics and evolution of mimicry patterns in Neotropical limenitidine butterflies
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Uncovering the effects of Müllerian mimicry on the evolution of conspicuousness in colour patterns
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Chase-away evolution maintains imperfect mimicry despite rapid evolution of mimics
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Data from: Foraging predicts the evolution of warning coloration and mimicry in snakes
<p><span>Warning coloration and Batesian mimicry are classic examples of Darwinian evolution, but empirical evolutionary patterns are often paradoxical. We test whether a new factor, trade-offs with foraging, influences the evolution of striking coloration by integrating genetic and ecological data for aposematic and mimetic snakes (Elapidae and Dipsadidae). Our phylogenetic comparison of a total of 432 species demonstrated that dramatic changes in coloration were well-predicted by the foraging strategy. Multiple tests consistently indicated that warning coloration and conspicuous mimicry were more likely to evolve in species where foraging costs of conspicuous appearance were relaxed by the poor vision of their prey or concealed habitat. Reversion to crypsis was also well-predicted by ecology for elapids, but not for dipsadids. In contrast to a theoretical prediction and general trends, snakes' conspicuous coloration was correlated with secretive ecology, suggesting that a selection regime underlies evolutionary patterns. We also found evidence that mimicry of inconspicuous models (pitvipers) may have evolved in association with foraging demand for crypsis. These findings demonstrate that foraging is an important factor necessary to understand the evolution, persistence, and diversity of warning coloration and mimicry of snakes, highlighting the significance of additional selective factors in solving the warning coloration paradox.</span></p>
Fig. 4b in Two new fossil species of Tillomorphites Vitali (Coleoptera: Cerambycidae) and remarks on the morphological evolution, mimicry, biogeography and phylogeny of the tribe Tillomorphini
Fig. 4b. Tillomorphites elachys (Martins & Galileo, 2013) n. comb., Paratype.
Fig. 3c Tillomorphites spinipes n in Two new fossil species of Tillomorphites Vitali (Coleoptera: Cerambycidae) and remarks on the morphological evolution, mimicry, biogeography and phylogeny of the tribe Tillomorphini
Fig. 3c Tillomorphites spinipes n. sp., Holotype, particular.
Fig. 3b Tillomorphites spinipes n in Two new fossil species of Tillomorphites Vitali (Coleoptera: Cerambycidae) and remarks on the morphological evolution, mimicry, biogeography and phylogeny of the tribe Tillomorphini
Fig. 3b Tillomorphites spinipes n. sp., Holotype, ventral view.
Fig. 3a Tillomorphites spinipes n in Two new fossil species of Tillomorphites Vitali (Coleoptera: Cerambycidae) and remarks on the morphological evolution, mimicry, biogeography and phylogeny of the tribe Tillomorphini
Fig. 3a Tillomorphites spinipes n. sp., Holotype, dorsal view.
Fig. 2 d. Tillomorphites otiliae n in Two new fossil species of Tillomorphites Vitali (Coleoptera: Cerambycidae) and remarks on the morphological evolution, mimicry, biogeography and phylogeny of the tribe Tillomorphini
Fig. 2 d. Tillomorphites otiliae n. sp., Holotype, colour reconstruction.
Fig. 2b. Tillomorphites otiliae n in Two new fossil species of Tillomorphites Vitali (Coleoptera: Cerambycidae) and remarks on the morphological evolution, mimicry, biogeography and phylogeny of the tribe Tillomorphini
Fig. 2b. Tillomorphites otiliae n. sp., Paratype.
Fig. 2a. Tillomorphites otiliae n in Two new fossil species of Tillomorphites Vitali (Coleoptera: Cerambycidae) and remarks on the morphological evolution, mimicry, biogeography and phylogeny of the tribe Tillomorphini
Fig. 2a. Tillomorphites otiliae n. sp., Holotype.
Fig. 1a. Tillomorphites robustus Vitali, 2011 in Two new fossil species of Tillomorphites Vitali (Coleoptera: Cerambycidae) and remarks on the morphological evolution, mimicry, biogeography and phylogeny of the tribe Tillomorphini
Fig. 1a. Tillomorphites robustus Vitali, 2011, Holotype.
Fig. 4a in Two new fossil species of Tillomorphites Vitali (Coleoptera: Cerambycidae) and remarks on the morphological evolution, mimicry, biogeography and phylogeny of the tribe Tillomorphini
Fig. 4a. Tillomorphites elachys (Martins & Galileo, 2013) n. comb., Holotype.
Fig1b. Tillomorphites robustus Vitali, 2011 in Two new fossil species of Tillomorphites Vitali (Coleoptera: Cerambycidae) and remarks on the morphological evolution, mimicry, biogeography and phylogeny of the tribe Tillomorphini
Fig1b. Tillomorphites robustus Vitali, 2011, habitus, new reconstruction.
Data from: Non-adaptive radiation promotes phenotypic diversification and convergent evolution of aposematic mimicry in a highly diverse genus of Megaloptera
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Data from: Foraging predicts the evolution of warning coloration and mimicry in snakes
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Evolution of novel mimicry polymorphisms through Haldane’s sieve and rare recombination
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