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25 results for “Danaus plexippus”
Data from: Genome assembly of Danaus chrysippus and comparison with the Monarch Danaus plexippus
<p><strong>GENOME ASSEMBLY DATA</strong></p> <p><strong>Dchry2_unaltered.fa.gz</strong><br> Unaltered version of Dchry2 before manual edits</p> <p><strong>Dchry2.haplotigs.fasta.gz</strong><br> Haplotypic contigs removed in the Purge_haplotigs step</p> <p><strong>Dchry2_to_Dchry2.2_transfers.txt</strong><br> Edits of the Dchry2 assembly to produce Dchry2.2 (contig breaks, reverse complements and name changes). Columns are: new contig name, new contig start, new contig end, original contig name, original contig start, original contig end, orientation. New contig numbers indicate the chromosome they correspond to.</p> <p><strong>mxv1.200520.ragoo.rnm.fa.gz</strong><br> Fasta file from of MEX_DaPlex assembly with mxdp_ fasta headers</p> <p><br> <strong>GENE AND REPEAT ANNOTATION</strong></p> <p><strong>danaus_plex_mex_braker_a002.sequences.tidy.gff3.gz</strong><br> Sorted and tidied gff3 from MEX_DaPlex re-annotation </p> <p><strong>danaus_plexv4_braker_a006.sequences.tidy.gff3.gz</strong><br> Sorted and tidied gff3 from Dplex_v4 re-annotation </p> <p><strong>mxv1.200520.ragoo.rnm.wDpv3.gff3.gz</strong><br> gff3 file from Cei of MEX_DaPlex annotation</p> <p><strong>dplex2_uniprot-proteome_UP000596680_and_dplex_mex.fasta.gz</strong><br> Protein set used for annotation of all three assemblies</p> <p><strong>functional_annotation_output.tar.gz</strong><br> all output from pannzer2 regarding functinal annotation of the Dchry2.2 genome</p> <p><strong>Lepidoptera_and_danaus_chrysippus2.2.repeatmasker.gz</strong><br> Custom repeat library (combination of lepidoptera and specific dchry2.2 library)</p>
Figura 1 in Primer reporte de infección causada por el protozoario Ophryocystis elektroscirrha McLaughlin y Myers (Neogregarinida: Ophryocystidae) en la mariposa monarca Danaus plexippus megalippe f. portoricensis A. Clark (Lepidoptera: Nymphalidae) en Puerto Rico
Figura 1. Imágenes de microscopÍa electrónica de barrido correspondientes a esporas de OE en escamas abdominales de especÍmenes adultos de Danaus plexippus megalippe f. portoricensis.
Data from: Intra-population variation in the natal origins and wing morphology of overwintering western monarch butterflies Danaus plexippus
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Host plant specificity of the monarch butterfly Danaus plexippus: A systematic review and meta-analysis
<p>The preference-performance hypothesis explains host specificity in phytophagous insects, positing that host plants chosen by adults confer the greatest larval fitness. However, adults sometimes oviposit on plants supporting low larval success because the components of host specificity (adult preference, plant palatability, and larval survival) are non-binary and not necessarily correlated. Palatability (willingness to eat) is governed by chemical cues and physical barriers such as trichomes, while survival (ability to complete development) depends upon nutrition and toxicity. Absence of a correlation between the components of host specificity results in low-performance hosts supporting limited larval development. Most studies of specificity focus on oviposition behavior leaving the importance and basis of palatability and survival under-explored. We conducted a comprehensive review of 127 plant species that have been claimed or tested to be hosts for the monarch butterfly Danaus plexippus to classify them as non-hosts, low performance, or high performance. We performed a meta-analysis to test if performance status could be explained by the properties of neurotoxic cardenolides or trichome density. We also conducted a no-choice larval feeding experiment to identify the causes of low performance. We identified 34 high performance, 42 low performance, 33 non-hosts, and 18 species with unsubstantiated claims. Mean cardenolide concentration was greater in high- than low-performance hosts and a significant predictor of host status, suggesting possible evolutionary trade-offs in monarch specialization. Other cardenolide properties and trichome density were not significant predictors of host status. In the experiment, we found, of the 62% of larvae that attempted to eat low-performance hosts, only 3.5% survived to adult compared to 85% of those on the high-performance host, demonstrating that multiple factors affect larval host plant specificity. Our study is the first to classify all known host plants for monarchs and has conservation implications for this threatened species.</p>
Plant water limitation and its impact on the oviposition preferences of the monarch butterfly, Danaus plexippus (Lepidoptera: Nymphalidae)
<p>Intensifying drought conditions across the western United States due to global climate change are altering plant-insect interactions. Specialist herbivores must find their host plants within a matrix of nonhosts, and thus often rely upon specific plant secondary chemistry for host location and oviposition cues. Climate-induced alterations to plant chemistry could thus affect female selection of larval food-plants. Here, we investigated whether host-plant water limitation influenced oviposition preference in a threatened invertebrate: the monarch butterfly (<em>Danaus plexippus</em>). We found that females deposited more eggs on reduced-water than on well-watered narrowleaf milkweed plants (<em>Asclepias fascicularis</em>), but we could not attribute this change to any specific change in plant chemistry. Specialist herbivores, such as the monarch butterfly, which are tightly linked to specific plant cues, may experience a shift in preferences under global-change conditions. Understanding oviposition preferences will be important to directing ongoing habitat restoration activities for this declining insect.</p>
Danaus plexippus genome annotation and orthofinder results
<p>Funannotate v1.5.3 docker image was used to train Augustus v3.2.3, predict gene models, and perform functional annotation. As input for optimizing the performance of Augustus v3.2.3, funannotate used 2,404 PASA v2.3.3 gene models. To obtain this training gene model set, transcripts were de novo assembled with Trinity v2018-2.8.3 under settings --SS_lib_type RF, using all poly(A) RNA-seq paired reads after adapter removal with Trimmomatic v0.32. These transcripts were aligned to the genome under PASA using BLAT v36, obtaining a first set of gene models. The 500 longest non-redundant ORFs associated with the PASA gene models were used to train TransDecoder v5.2.0. Then the gene models were selected according to their abundance as estimated by Kallisto v0.44.0 under settings --rf-stranded using the Trinity normalized reads. Ultimately, BRAKER v2.0.3b trained Augustus with the retained gene models.<br>For gene prediction, funannotate aligned mRNAs and proteins from the previous annotation (official gene set 2, OGS2) with minimap v2.14-r883 under settings -ax splice --cs -u b -G 3000, and Diamond blastx v0.8.22, respectively. Protein alignments were further refined by funannotate, including 3 kb upstream and downstream of the region of alignment, and subsequently executing Exonerate v2.4.0. Additionally, funannotate parsed the introns supported by alignments of poly(A) RNA-seq reads generated with HISAT v2.1 under settings --rna-strandness RF --max-intronlen 10,000. This combination of hints (protein alignments, transcript alignments, and intron locations) was used by Augustus to predict a second set of 16,756 gene models. Of them, 9,695 were dubbed as highly supported, i.e. had more than 90% of their model supported either by intron hints, transcript alignments, or protein alignments. GeneMark-ET v4.35, under settings --max_intron 3,000 --soft_mask 2,000, was also run independently to predict a third set of gene models but only relying on intron hints.<br>The PASA, Augustus highly supported, Augustus not highly supported, and GeneMark prediction sets were combined by EVidenceModeler, assigning them 10, 5, 1, and 1 relative weights, respectively. The predictions were further filtered by removing genes shorter than 50 aa in length, or that had high sequence similarity (diamond blastp --sensitive --evalue 1e-10) to the repeat database included in funannotate, or that had more than 90% of the model intersecting regions masked by RepeatMasker. The filtered set of gene models was updated in order to include UTR information by two executions of the PASA annotation comparison using the Trinity transcripts and filtering gene models according to transcripts per million as calculated by Kallisto. Alternative transcripts were only kept if they were at least 10% as highly expressed as the most highly expressed transcript per gene.<br>Non-coding genes were annotated with the following tools: tRNA genes, tRNAscan-SE v.2.0; rRNA genes, RNAmmer v.1.2; and for a variety of other RNA genes, Infernal v1.1.1. Specifically, for miRNA-encoding genes, we used BLASTn to locate the most recent annotation of these genes. Lastly, FEELnc classified lncRNAs from the transcripts assembled by StringTie v1.3.2d, and considering protein-coding predictions described above.</p><p>Homology relationships of the predicted protein coding genes were inferred with OrthoFinder (v2.2.6) relative to <i>Bombyx mori, Plutella xylostella, Papilio xuthus, Amyelois transitella, Heliconius melpomene, Plodia interpunctella </i>and<i> Drosophila melanogaster</i>. OrthoFinder was run with the settings "-S diamond -M msa".</p>
Host plant specificity of the monarch butterfly Danaus plexippus: A systematic review and meta-analysis
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Plant water limitation and its impact on the oviposition preferences of the monarch butterfly, Danaus plexippus (Lepidoptera: Nymphalidae)
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Data from: Habitat type influences Danaus plexippus (Lepidoptera: Nymphalidae) oviposition and egg survival on Asclepias syriaca (Gentianales: Apocynaceae)
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Monarch (Danaus plexippus) larval records in the western U.S
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Data from: Beyond preference and performance: host plant selection by monarch butterflies, Danaus plexippus
The connection between adult preferences and offspring performance is long-standing issue in understanding the evolutionary and ecological forces that dictate host associations and specialization in herbivorous insects. Indeed, decisions made by females about where to lay their eggs have direct consequences for fitness and are influenced by interacting factors including offspring performance, defence, and competition. Nonetheless, in addition to these attributes of the offspring, a female's choices may be affected by her own prior experience. Here we examined oviposition preference, larval performance, and the role of learning in the monarch butterfly, Danaus plexippus, which encounters diverse milkweed host species across its broad range and over the course of migration. Monarch females consistently preferred to oviposit on Asclepias incarnata subspecies pulchra. This plant, however, was associated with poor caterpillar growth, low sequestration of toxins, and the highest plant defences (latex and trichomes). We examined flexibility in this apparently maladaptive preference by testing the impact of previous experience and competition on preference. Experience laying on an alternative plant species enhanced preference for that species in contrast to A. i. pulchra. In addition, presence of a (competing) conspecific caterpillar on A. i. pulchra had a strongly deterrent effect and reversed host plant preferences. Thus, monarch butterflies exhibit preferences contrary to what would be expected based on offspring development and sequestered defences, but their preferences are altered by learning and competition, which may allow butterflies to shift preferences as they encounter diverse milkweeds across the landscape. Learning and perception of threats (i.e., competition or predation) may be critical for most herbivorous insects, which universally experience heterogeneity among their potential host plants.
Data from: Population genetics of overwintering monarch butterflies, Danaus plexippus (Linnaeus), from central Mexico inferred from mitochondrial DNA and microsatellite markers
Population genetic variation and demographic history in Danaus plexippus (L.), from Mexico were assessed based on analyses of mitochondrial cytochrome c oxidase subunit I (COI; 658 bp) and subunit II (COII; 503 bp) gene segments and seven microsatellite loci. The sample of 133 individuals included both migratory monarchs, mainly from four overwintering sites within the Monarch Butterfly Biosphere Reserve (MBBR) in central Mexico (states of Michoacán and México), and a nonmigratory population from Irapuato, Guanajuato. Haplotype (h) and nucleotide (π) diversities were relatively low, averaging 0.466 and 0.00073, respectively, for COI, and 0.629 and 0.00245 for COII. Analysis of molecular variance (AMOVA) of the COI data set, which included additional GenBank sequences from a nonmigratory Costa Rican population, showed significant population structure between Mexican migratory monarchs and nonmigratory monarchs from both Mexico and Costa Rica, suggesting limited gene flow between the two behaviorally distinct groups. Interestingly, while the COI haplotype frequencies of the nonmigratory populations differed from the migratory, they were similar to each other, despite the great physical distance between them. Microsatellite analyses, however, suggested a lack of structure between the two groups, possibly owing to the number of significant deviations from Hardy Weinberg equilibrium resulting from heterzoygote deficiencies found for most of the loci. Estimates of demographic history of the combined migratory MBBR monarch population, based on the mismatch distribution and Bayesian skyline analyses of the concatenated COI and COII data set (n = 89) suggested a population expansion dating to the late Pleistocene (~35,000 to 40,000 years before present) followed by a stable effective female population size (Nef) of about six million over the last 10,000 years.
Influence of habitat quality and resource density on breeding-season female monarch butterfly (Danaus plexippus) movement and space use in north-central USA agroecosystem landscapes
<ol> <li> The eastern North American monarch butterfly is at risk of quasi-extinction due, in part, to the loss of breeding habitat in agricultural landscapes of the USA Midwest. Because adult females are not patch residents, egg abundance and distribution across the landscape are a function of their perceptual range, flight directionality, and flight step lengths. Conservation actions that account for habitat use in agricultural landscapes can enhance functional connectivity.</li> <li>Field-captured females (n=114) were released in a 64-ha area containing restored prairies, grass-dominated fields, and crop fields in Floyd County, Iowa, USA, and two 1,000 m linear north-south sections of grass-dominated roadside along secondary roads (~ 35 ha) with different proximity to prairie habitat in rural Story County, Iowa. Radio-tagged or untagged monarchs were released in areas with high-density, low-density, and zero density of forage and oviposition resources, as well as on habitat edges between high and zero-density habitats. Monarchs were observed for one hour. Radio-tagged individuals that flew beyond visual detection were relocated using handheld radio telemetry.</li> <li>Monarchs moved within and between habitat classes and typically performed up-wind search behavior. Monarchs successfully located resources, with some flying over 500 m to find high-density areas, providing evidence that the monarch's perceptual distance is > 100 m. Regardless of habitat class or field site, most step lengths were < 50 m, and turn angles were directional. Large steps (≥ 50 m) crossing habitat boundaries occurred with approximately half of the monarchs, which may indicate initiation of long-range searches for suitable habitat, consistent with their vagile behavior. Establishing habitat patches 50 m apart in agricultural landscapes would facilitate efficient movement.</li> <li>This study provides an extensive dataset of directly observed breeding-season monarch butterflies to assess the utilization of agricultural landscapes. Documentation of step lengths > 50 m in complex, agricultural landscapes would not have been possible without the aid of radio telemetry. Results provide improved estimates of perceptual range and flight patterns within and between habitat patches that support models that simulate natural population dynamics to enable conservation planning at a landscape scale.</li> </ol>
Supplementary material 1 from: Palma L, Vasconcelos S, Palmeirim AF, Cancela JP (2023) History of colonisation and updated distribution of the Monarch butterfly Danaus plexippus (Linnaeus, 1758) and its hostplants in mainland Portugal, Azores and Madeira. Nota Lepidopterologica 46: 83-101. https://doi.org/10.3897/nl.46.89665
Summary of occurrence and colonisation records of the monarch butterfly and its hostplants in the Iberian Peninsula
Supplementary material 3 from: Palma L, Vasconcelos S, Palmeirim AF, Cancela JP (2023) History of colonisation and updated distribution of the Monarch butterfly Danaus plexippus (Linnaeus, 1758) and its hostplants in mainland Portugal, Azores and Madeira. Nota Lepidopterologica 46: 83-101. https://doi.org/10.3897/nl.46.89665
Frequencies (%) of hostplant patch size classes arranged in geometric progression (2× ratio) (N patches = 78)
Influence of habitat quality and resource density on breeding-season female monarch butterfly (Danaus plexippus) movement and space use in north-central USA agroecosystem landscapes
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Data from: The effects of milkweed induced defense on parasite resistance in monarch butterflies, Danaus plexippus
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Data from: Transcriptomics of monarch butterflies (Danaus plexippus) reveals that toxic host plants alter expression of detoxification genes and down-regulate a small number of immune genes
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Data from: Population genetics of overwintering monarch butterflies, Danaus plexippus (Linnaeus), from central Mexico inferred from mitochondrial DNA and microsatellite markers
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Data from: Beyond preference and performance: host plant selection by monarch butterflies, Danaus plexippus
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