105,314 research outputs found
A conserved supergene locus controls colour pattern diversity in Heliconius butterflies
No full textWe studied whether similar developmental genetic mechanisms are involved in both convergent and divergent evolution. Mimetic insects are known for their diversity of patterns as well as their remarkable evolutionary convergence, and they have played an important role in controversies over the respective roles of selection and constraints in adaptive evolution. Here we contrast three butterfly species, all classic examples of Müllerian mimicry. We used a genetic linkage map to show that a locus, Yb, which controls the presence of a yellow band in geographic races of Heliconius melpomene, maps precisely to the same location as the locus Cr, which has very similar phenotypic effects in its co-mimic H. erato. Furthermore, the same genomic location acts as a “supergene”, determining multiple sympatric morphs in a third species, H. numata. H. numata is a species with a very different phenotypic appearance, whose many forms mimic different unrelated ithomiine butterflies in the genus Melinaea. Other unlinked colour pattern loci map to a homologous linkage group in the co-mimics H. melpomene and H. erato, but they are not involved in mimetic polymorphism in H. numata. Hence, a single region from the multilocus colour pattern architecture of H. melpomene and H. erato appears to have gained control of the entire wing-pattern variability in H. numata, presumably as a result of selection for mimetic “supergene” polymorphism without intermediates. Although we cannot at this stage confirm the homology of the loci segregating in the three species, our results imply that a conserved yet relatively unconstrained mechanism underlying pattern switching can affect mimicry in radically different ways. We also show that adaptive evolution, both convergent and diversifying, can occur by the repeated involvement of the same genomic regions
Variable Selection and the Coexistence of Multiple mimetic forms of the Butterfly Heliconius numata
No full textInternational audiencePolymorphism in aposematic animals and coexistence of multiple mimicry rings within a habitat are not predicted by classical Müllerian mimicry. The butterfly Heliconius numata Cramer (Lepidoptera: Nymphalidae; Heliconiinae) is both polymorphic and aposematic. The polymorphism is due to variation at a single locus (or `supergene') which determines colour patterns involved in Müllerian mimicry. We sampled 11 sites in a small area (approx. 60×30km) of North-eastern Peru for H. numata and its co-mimics in the genus Melinaea and Athyrtis (Ithomiinae), and examined the role of temporal and spatial heterogeneity in the maintenance of polymorphism. Colour-patterns of Melinaea communities, which constitute the likely `mimetic environment' for H. numata, are differentiated on a more local scale than morphs of H. numata, but the latter do show a strong and significant response to local selection for colour-pattern. In contrast, analysis of enzyme polymorphism in H. numata across the region revealed no spatial structure, which is consistent with a high mobility of this species. Differences in spatial variability in the two taxa may have caused H. numata to become polymorphic, while temporal variability, not significant in this study, probably has a lesser effect. The mimetic polymorphism is therefore explained by means of multiple selection-migration clines at a single locus, a similar process to that which explains narrow hybrid zones between geographic races of other Heliconius butterflies
Colour Pattern Diversity of <i>H. numata, H. melpomene,</i> and their Respective Co-Mimics
No full text<p>The upper half of the figure shows five sympatric forms of H. numata from northern Peru (second row, left to right: <i>H. n.</i> f. <i>tarapotensis, H. n.</i> f. <i>silvana, H. n.</i> f. <i>aurora, H. n.</i> f. <i>bicoloratus,</i> and <i>H. n.</i> f. <i>arcuella</i>) with their distantly related comimetic <i>Melinaea</i> species (Nymphalidae: Ithomiinae) from the same area (first row: M. menophilus ssp. nov<i>.</i>, <i>M. ludovica ludovica, M. marsaeus rileyi, M. marsaeus mothone,</i> and <i>M. marsaeus phasiana</i>) [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0040303#pbio-0040303-b020" target="_blank">20</a>]. The lower half of the figure shows five colour pattern races of <i>H. melpomene,</i> each from a different area of South America (third row: <i>H. m. rosina, H. m. cythera, H. m. aglaope, H. m. melpomene,</i> and <i>H. m. plesseni</i>) with their distantly related comimetic H. erato races from the same areas (fourth row: <i>H. e.</i> cf. <i>petiveranus, H. e. cyrbia, H. e. emma, H. e. hydara,</i> and <i>H. e. notabilis</i>). <i>H. m. aglaope</i> and <i>H. e. emma</i> are known as rayed forms, whereas <i>H. m. rosina, H. m. melpomene,</i> and co-mimics are known as postman forms. H. melpomene and H. erato are from divergent clades of <i>Heliconius</i> and are identified in the field using minor morphological characters, such as the different form of the red rays on the hindwing between <i>H. m. aglaope</i> and <i>H. e. emma</i> (third from left) or the arrangement of red versus white patches in <i>H. m. plesseni</i> and <i>H. e. notabilis</i> (first from right). Co-mimics H. numata and Melinaea spp. belong to different subfamilies of the Nymphalidae and have very different body morphology and wing venation. The phylogram on the left is a maximum-likelihood tree based on 1,541 bases of mitochondrial DNA (scale bar in substitutions per site, all bootstrap values over 99).</p
Gene annotation in Heliconius numata colouring the black box
No full textTese de mestrado, Biologia (Biologia Evolutiva e do Desenvolvimento, Universidade de Lisboa, Faculdade de Ciências, 2010O presente projecto teve por objectivo a identificação e anotação de genes que se sabe estarem ligados num arranjo de genes inquebrável por recombinação e que controla a padronização das asas da borboleta Heliconius numata. Este complexo é homologo posicional de complexos em outras espécies de Heliconius, nomeadamente o complexo Yb/Sb em H. melpomene e Cr em H. erato. Este “supergene” é visto como um hotspot de desenvolvimento (sensu Richardson & Brakefield 2003) que controla divergência fenotípica entre espécies próximas e convergência fenotípica entre espécies mais distantes. Em H. numata o supergene sofreu rearranjos genómicos que se pensa estarem correlacionados com a preservação das combinações alélicas necessárias para manter os fenótipos discretos característicos das relações miméticas locais (mimicry rings) que estes organismos estabelecem na natureza. Estes rearranjos podem estar a modificar ou perturbar expressão genica e é, portanto, de extrema importância identificar tais genes bem como compreender a sua estrutura, nomeadamente no que diz respeito a eventuais eventos de clivagem alternativa que possam estar correlacionados com as diferentes raças locais observáveis na natureza. Usando uma combinação de ferramentas bioinformáticas e sequências de transcriptoma de raças com fenótipos diferentes, modelos de genes serão estabelecidos para desenhar primers específicos de modo a amplificar os genes modelizados e testar hipóteses relativamente a diferenças na sua estrutura e distribuição na região de interesse.The present project aims at the identification and annotation of the specific genes known to be in a cluster of tighly linked genes known to control wing patterning in H. numata. This cluster is positionally homologous with cluster in other species of Heliconius, namely Yb/Sb in H. melpomene and Cr in H. erato. This “supergene” is seen as a developmental hotspot (sensu Richardson and Brakefield 2003) controlling both phenotypic divergence between closely related species and convergence between more distantly related species. In H. numata the supergene suffered genomic rearrangements that are thought to be preserving the necessary combination of loci to attain the concrete phenotypes typical in mimicry relations these butterflies establish in nature. These rearrangements may be disturbing or modifying gene expression. Therefore, it is extremely valuable to identify the genes in the genomic region of interest, and address eventual alternative splicing events that could be associated with the different locally adapted races. Using a combination of bioinformatics’ tools and transcriptome sequences from two phenotypically different races, I generated gene models in order to design primers and amplify these genes, testing hypothesis regarding splice variants and validating the models
MOESM1 of Unravelling the genes forming the wing pattern supergene in the polymorphic butterfly Heliconius numata
No full textAdditional file 1: Table S1. Information on probes used for ISH in H. numata larval wing discs. Figure S1. Principal component analysis (PCA) plot of read counts matrix from RNA-seq data. Table S2. Gene set enrichment analysis comparing the rank of differential expression in transcripts mapped to the supergene P to the rest of the transcriptome using 1,000 transcript permutations. Table S3. Analysis of splicing sites in the first intron of cortex. Figure S2. Examples of expression patterns observed in larval wing discs of H. numata. A. Ubiquitous expression, B. Expression in the trachea, C. No detectable signal. Figure S3. Expression patterns of cortex in larval wing discs of H. numata (all samples)
Gene annotation in Heliconius numata colouring the black box
No full textTese de mestrado, Biologia (Biologia Evolutiva e do Desenvolvimento, Universidade de Lisboa, Faculdade de Ciências, 2010O presente projecto teve por objectivo a identificação e anotação de genes que se sabe estarem ligados num arranjo de genes inquebrável por recombinação e que controla a padronização das asas da borboleta Heliconius numata. Este complexo é homologo posicional de complexos em outras espécies de Heliconius, nomeadamente o complexo Yb/Sb em H. melpomene e Cr em H. erato. Este “supergene” é visto como um hotspot de desenvolvimento (sensu Richardson & Brakefield 2003) que controla divergência fenotípica entre espécies próximas e convergência fenotípica entre espécies mais distantes. Em H. numata o supergene sofreu rearranjos genómicos que se pensa estarem correlacionados com a preservação das combinações alélicas necessárias para manter os fenótipos discretos característicos das relações miméticas locais (mimicry rings) que estes organismos estabelecem na natureza. Estes rearranjos podem estar a modificar ou perturbar expressão genica e é, portanto, de extrema importância identificar tais genes bem como compreender a sua estrutura, nomeadamente no que diz respeito a eventuais eventos de clivagem alternativa que possam estar correlacionados com as diferentes raças locais observáveis na natureza. Usando uma combinação de ferramentas bioinformáticas e sequências de transcriptoma de raças com fenótipos diferentes, modelos de genes serão estabelecidos para desenhar primers específicos de modo a amplificar os genes modelizados e testar hipóteses relativamente a diferenças na sua estrutura e distribuição na região de interesse.The present project aims at the identification and annotation of the specific genes known to be in a cluster of tighly linked genes known to control wing patterning in H. numata. This cluster is positionally homologous with cluster in other species of Heliconius, namely Yb/Sb in H. melpomene and Cr in H. erato. This “supergene” is seen as a developmental hotspot (sensu Richardson and Brakefield 2003) controlling both phenotypic divergence between closely related species and convergence between more distantly related species. In H. numata the supergene suffered genomic rearrangements that are thought to be preserving the necessary combination of loci to attain the concrete phenotypes typical in mimicry relations these butterflies establish in nature. These rearrangements may be disturbing or modifying gene expression. Therefore, it is extremely valuable to identify the genes in the genomic region of interest, and address eventual alternative splicing events that could be associated with the different locally adapted races. Using a combination of bioinformatics’ tools and transcriptome sequences from two phenotypically different races, I generated gene models in order to design primers and amplify these genes, testing hypothesis regarding splice variants and validating the models
Gene annotation in Heliconius numata colouring the black box
No full textTese de mestrado, Biologia (Biologia Evolutiva e do Desenvolvimento, Universidade de Lisboa, Faculdade de Ciências, 2010O presente projecto teve por objectivo a identificação e anotação de genes que se sabe estarem ligados num arranjo de genes inquebrável por recombinação e que controla a padronização das asas da borboleta Heliconius numata. Este complexo é homologo posicional de complexos em outras espécies de Heliconius, nomeadamente o complexo Yb/Sb em H. melpomene e Cr em H. erato. Este “supergene” é visto como um hotspot de desenvolvimento (sensu Richardson & Brakefield 2003) que controla divergência fenotípica entre espécies próximas e convergência fenotípica entre espécies mais distantes. Em H. numata o supergene sofreu rearranjos genómicos que se pensa estarem correlacionados com a preservação das combinações alélicas necessárias para manter os fenótipos discretos característicos das relações miméticas locais (mimicry rings) que estes organismos estabelecem na natureza. Estes rearranjos podem estar a modificar ou perturbar expressão genica e é, portanto, de extrema importância identificar tais genes bem como compreender a sua estrutura, nomeadamente no que diz respeito a eventuais eventos de clivagem alternativa que possam estar correlacionados com as diferentes raças locais observáveis na natureza. Usando uma combinação de ferramentas bioinformáticas e sequências de transcriptoma de raças com fenótipos diferentes, modelos de genes serão estabelecidos para desenhar primers específicos de modo a amplificar os genes modelizados e testar hipóteses relativamente a diferenças na sua estrutura e distribuição na região de interesse.The present project aims at the identification and annotation of the specific genes known to be in a cluster of tighly linked genes known to control wing patterning in H. numata. This cluster is positionally homologous with cluster in other species of Heliconius, namely Yb/Sb in H. melpomene and Cr in H. erato. This “supergene” is seen as a developmental hotspot (sensu Richardson and Brakefield 2003) controlling both phenotypic divergence between closely related species and convergence between more distantly related species. In H. numata the supergene suffered genomic rearrangements that are thought to be preserving the necessary combination of loci to attain the concrete phenotypes typical in mimicry relations these butterflies establish in nature. These rearrangements may be disturbing or modifying gene expression. Therefore, it is extremely valuable to identify the genes in the genomic region of interest, and address eventual alternative splicing events that could be associated with the different locally adapted races. Using a combination of bioinformatics’ tools and transcriptome sequences from two phenotypically different races, I generated gene models in order to design primers and amplify these genes, testing hypothesis regarding splice variants and validating the models
Chromosomal Maps for Linkage Group Homologues in H. melpomene (LG15), H. numata (LG15), and H. erato (LG02)
No full text<p>Distances are in Haldane centimorgans. The alternative orders for <i>P</i> and <i>a41</i> relative to <i>Hm01</i> in H. numata are not significantly different (ΔLn<i>L</i> = −1.40). Similarly, most orders of <i>N, Sb, Yb,</i> and <i>a41</i> in H. melpomene are not significantly different (from ΔLn<i>L</i> = −0.15 for the order <i>a41–Yb</i>–<i>N–Sb–</i> to ΔLn<i>L</i> = −0.77 for <i>a41–N–Yb–Sb–</i>). Finally, the two orders for <i>Cr</i> and <i>GerTra</i> in H. erato are also equally significant. Therefore, we here show the most likely gene orders but cannot exclude that the colour loci are on the other side of the anchor loci <i>a41, Fox,</i> or <i>GerTra</i>. In contrast, anchor loci order <i>GerTra–RpP40–Hm01–Hm08</i> is robust, with alternative orders significantly worse (ΔLn<i>L</i> < −2), although the relative placement of <i>RpL22</i> and <i>eIF3</i>-<i>S9</i> is uncertain in H. melpomene and H. erato (ΔLn<i>L</i> > −2).</p
Going Beyond Counting First Authors in Author Co-citation Analysis
No full textThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Appropriate Similarity Measures for Author Cocitation Analysis
No full textWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
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