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  1. Article ; Online: Deep structure, long-distance migration and admixture in the colour polymorphic land snail Cepaea nemoralis.

    Ramos-Gonzalez, Daniel / Saenko, Suzanne V / Davison, Angus

    Journal of evolutionary biology

    2022  Volume 35, Issue 8, Page(s) 1110–1125

    Abstract: Although snails of the genus Cepaea have historically been important in studying colour polymorphism, an ongoing issue is that there is a lack of knowledge of the underlying genetics of the polymorphism, as well as an absence of genomic data to put ... ...

    Abstract Although snails of the genus Cepaea have historically been important in studying colour polymorphism, an ongoing issue is that there is a lack of knowledge of the underlying genetics of the polymorphism, as well as an absence of genomic data to put findings in context. We, therefore, used phylogenomic methods to begin to investigate the post-glacial history of Cepaea nemoralis, with a long-term aim to understand the roles that selection and drift have in determining both European-wide and local patterns of colour polymorphism. By combining prior and new mitochondrial DNA data from over 1500 individuals with ddRAD genomic data from representative individuals across Europe, we show that patterns of differentiation are primarily due to multiple deeply diverged populations of snails. Minimally, there is a widespread Central European population and additional diverged groups in Northern Spain, the Pyrenees, as well as likely Italy and South Eastern Europe. The genomic analysis showed that the present-day snails in Ireland and possibly some other locations are likely descendants of admixture between snails from the Pyrenees and the Central European group, an observation that is consistent with prior inferences from mitochondrial DNA alone. The interpretation is that C. nemoralis may have arrived in Ireland via long-distance migration from the Pyrenean region, subsequently admixing with arrivals from elsewhere. This work, therefore, provides a baseline expectation for future studies on the genetics of the colour polymorphism, as well as providing a comparator for similar species.
    MeSH term(s) Animals ; Color ; DNA, Mitochondrial/genetics ; Gastropoda ; Humans ; Phylogeny ; Polymorphism, Genetic
    Chemical Substances DNA, Mitochondrial
    Language English
    Publishing date 2022-07-13
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1465318-7
    ISSN 1420-9101 ; 1010-061X
    ISSN (online) 1420-9101
    ISSN 1010-061X
    DOI 10.1111/jeb.14060
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Evo-devo of shell colour in gastropods and bivalves.

    Saenko, Suzanne V / Schilthuizen, Menno

    Current opinion in genetics & development

    2020  Volume 69, Page(s) 1–5

    Abstract: Recent technical innovations are revealing surprising patterns in mollusc shell pigmentation, such as an unexpectedly modest role for melanins and rapid divergences in the mix of pigments used to achieve similar colour patterns. The elucidation of the ... ...

    Abstract Recent technical innovations are revealing surprising patterns in mollusc shell pigmentation, such as an unexpectedly modest role for melanins and rapid divergences in the mix of pigments used to achieve similar colour patterns. The elucidation of the molecular genetic basis of shell pigmentation has been slow, probably because of the high genome complexity of gastropods and bivalves. Recent work within the old field of evolutionary ecology of shell pigmentation allows a greater role for the analysis of large-geographic-scale patterns (sometimes employing citizen-science data), as well as experimental field studies. However, the field remains dominated by land snails as model organisms, while colour pattern evolution in marine gastropods and bivalves, particularly those not exposed to visual predators, remains mysterious.
    MeSH term(s) Animal Shells/anatomy & histology ; Animals ; Biological Evolution ; Bivalvia/anatomy & histology ; Bivalvia/genetics ; Color ; Ecology ; Gastropoda/anatomy & histology ; Gastropoda/genetics ; Phenotype ; Pigmentation/genetics
    Language English
    Publishing date 2020-12-31
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1077312-5
    ISSN 1879-0380 ; 0959-437X
    ISSN (online) 1879-0380
    ISSN 0959-437X
    DOI 10.1016/j.gde.2020.11.009
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Dominance mechanisms in supergene alleles controlling butterfly wing pattern variation: insights from gene expression in Heliconius numata.

    Bastide, Héloïse / Saenko, Suzanne V / Chouteau, Mathieu / Joron, Mathieu / Llaurens, Violaine

    Heredity

    2022  Volume 130, Issue 2, Page(s) 92–98

    Abstract: Loci under balancing selection, where multiple alleles are maintained, offer a relevant opportunity to investigate the role of natural selection in shaping genetic dominance: the high frequency of heterozygotes at these loci has been shown to enable the ... ...

    Abstract Loci under balancing selection, where multiple alleles are maintained, offer a relevant opportunity to investigate the role of natural selection in shaping genetic dominance: the high frequency of heterozygotes at these loci has been shown to enable the evolution of dominance among alleles. In the butterfly Heliconius numata, mimetic wing color variations are controlled by an inversion polymorphism of a circa 2 Mb genomic region (supergene P), with strong dominance between sympatric alleles. To test how differences in dominance observed on wing patterns correlate with variations in expression levels throughout the supergene region, we sequenced the complete transcriptome of heterozygotes at the prepupal stage and compared it to corresponding homozygotes. By defining dominance based on non-overlapping ranges of transcript expression between genotypes, we found contrasting patterns of dominance between the supergene and the rest of the genome; the patterns of transcript expression in the heterozygotes were more similar to the expression observed in the dominant homozygotes in the supergene region. Dominance also differed among the three subinversions of the supergene, suggesting possible epistatic interactions among their gene contents underlying dominance evolution. We found the expression pattern of the melanization gene cortex located in the P-region to predict wing pattern phenotype in the heterozygote. We also identify new candidate genes that are potentially involved in mimetic color pattern variations highlighting the relevance of transcriptomic analyses in heterozygotes to pinpoint candidate genes in non-recombining regions.
    MeSH term(s) Animals ; Alleles ; Genotype ; Polymorphism, Genetic ; Phenotype ; Gene Expression ; Butterflies/genetics ; Wings, Animal
    Language English
    Publishing date 2022-12-16
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2423-5
    ISSN 1365-2540 ; 0018-067X
    ISSN (online) 1365-2540
    ISSN 0018-067X
    DOI 10.1038/s41437-022-00583-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: The draft genome sequence of the grove snail Cepaea nemoralis.

    Saenko, Suzanne V / Groenenberg, Dick S J / Davison, Angus / Schilthuizen, Menno

    G3 (Bethesda, Md.)

    2021  Volume 11, Issue 2

    Abstract: Studies on the shell color and banding polymorphism of the grove snail Cepaea nemoralis and the sister taxon Cepaea hortensis have provided compelling evidence for the fundamental role of natural selection in promoting and maintaining intraspecific ... ...

    Abstract Studies on the shell color and banding polymorphism of the grove snail Cepaea nemoralis and the sister taxon Cepaea hortensis have provided compelling evidence for the fundamental role of natural selection in promoting and maintaining intraspecific variation. More recently, Cepaea has been the focus of citizen science projects on shell color evolution in relation to climate change and urbanization. C. nemoralis is particularly useful for studies on the genetics of shell polymorphism and the evolution of "supergenes," as well as evo-devo studies of shell biomineralization, because it is relatively easily maintained in captivity. However, an absence of genomic resources for C. nemoralis has generally hindered detailed genetic and molecular investigations. We therefore generated ∼23× coverage long-read data for the ∼3.5 Gb genome, and produced a draft assembly composed of 28,537 contigs with the N50 length of 333 kb. Genome completeness, estimated by BUSCO using the metazoa dataset, was 91%. Repetitive regions cover over 77% of the genome. A total of 43,519 protein-coding genes were predicted in the assembled genome, and 97.3% of these were functionally annotated from either sequence homology or protein signature searches. This first assembled and annotated genome sequence for a helicoid snail, a large group that includes edible species, agricultural pests, and parasite hosts, will be a core resource for identifying the loci that determine the shell polymorphism, as well as in a wide range of analyses in evolutionary and developmental biology, and snail biology in general.
    MeSH term(s) Animals ; Genome ; Genomics ; Molecular Sequence Annotation ; Polymorphism, Genetic ; Selection, Genetic ; Snails
    Language English
    Publishing date 2021-01-04
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2629978-1
    ISSN 2160-1836 ; 2160-1836
    ISSN (online) 2160-1836
    ISSN 2160-1836
    DOI 10.1093/g3journal/jkaa071
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Deep structure, long‐distance migration and admixture in the colour polymorphic land snail Cepaea nemoralis

    Ramos‐Gonzalez, Daniel / Saenko, Suzanne V. / Davison, Angus

    Journal of evolutionary biology. 2022 Aug., v. 35, no. 8

    2022  

    Abstract: Although snails of the genus Cepaea have historically been important in studying colour polymorphism, an ongoing issue is that there is a lack of knowledge of the underlying genetics of the polymorphism, as well as an absence of genomic data to put ... ...

    Abstract Although snails of the genus Cepaea have historically been important in studying colour polymorphism, an ongoing issue is that there is a lack of knowledge of the underlying genetics of the polymorphism, as well as an absence of genomic data to put findings in context. We, therefore, used phylogenomic methods to begin to investigate the post‐glacial history of Cepaea nemoralis, with a long‐term aim to understand the roles that selection and drift have in determining both European‐wide and local patterns of colour polymorphism. By combining prior and new mitochondrial DNA data from over 1500 individuals with ddRAD genomic data from representative individuals across Europe, we show that patterns of differentiation are primarily due to multiple deeply diverged populations of snails. Minimally, there is a widespread Central European population and additional diverged groups in Northern Spain, the Pyrenees, as well as likely Italy and South Eastern Europe. The genomic analysis showed that the present‐day snails in Ireland and possibly some other locations are likely descendants of admixture between snails from the Pyrenees and the Central European group, an observation that is consistent with prior inferences from mitochondrial DNA alone. The interpretation is that C. nemoralis may have arrived in Ireland via long‐distance migration from the Pyrenean region, subsequently admixing with arrivals from elsewhere. This work, therefore, provides a baseline expectation for future studies on the genetics of the colour polymorphism, as well as providing a comparator for similar species.
    Keywords Cepaea nemoralis ; color ; evolutionary biology ; genomics ; mitochondrial DNA ; snails ; Ireland ; Italy ; Southern European region ; Spain
    Language English
    Dates of publication 2022-08
    Size p. 1110-1125.
    Publishing place John Wiley & Sons, Ltd
    Document type Article
    Note JOURNAL ARTICLE
    ZDB-ID 1465318-7
    ISSN 1420-9101 ; 1010-061X
    ISSN (online) 1420-9101
    ISSN 1010-061X
    DOI 10.1111/jeb.14060
    Database NAL-Catalogue (AGRICOLA)

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  6. Article: Unravelling the genes forming the wing pattern supergene in the polymorphic butterfly

    Saenko, Suzanne V / Chouteau, Mathieu / Piron-Prunier, Florence / Blugeon, Corinne / Joron, Mathieu / Llaurens, Violaine

    EvoDevo

    2019  Volume 10, Page(s) 16

    Abstract: Background: Unravelling the genetic basis of polymorphic characters is central to our understanding of the origins and diversification of living organisms. Recently, supergenes have been implicated in a wide range of complex polymorphisms, from adaptive ...

    Abstract Background: Unravelling the genetic basis of polymorphic characters is central to our understanding of the origins and diversification of living organisms. Recently, supergenes have been implicated in a wide range of complex polymorphisms, from adaptive colouration in butterflies and fish to reproductive strategies in birds and plants. The concept of a supergene is now a hot topic in biology, and identification of its functional elements is needed to shed light on the evolution of highly divergent adaptive traits. Here, we apply different gene expression analyses to study the supergene
    Results: We performed de novo transcriptome assembly and differential expression analyses using high-throughput Illumina RNA sequencing on developing wing discs of different
    Conclusions: This study found the majority of genes in the
    Language English
    Publishing date 2019-08-08
    Publishing country England
    Document type Journal Article
    ZDB-ID 2563566-9
    ISSN 2041-9139
    ISSN 2041-9139
    DOI 10.1186/s13227-019-0129-2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Photonic crystals cause active colour change in chameleons.

    Teyssier, Jérémie / Saenko, Suzanne V / van der Marel, Dirk / Milinkovitch, Michel C

    Nature communications

    2015  Volume 6, Page(s) 6368

    Abstract: Many chameleons, and panther chameleons in particular, have the remarkable ability to exhibit complex and rapid colour changes during social interactions such as male contests or courtship. It is generally interpreted that these changes are due to ... ...

    Abstract Many chameleons, and panther chameleons in particular, have the remarkable ability to exhibit complex and rapid colour changes during social interactions such as male contests or courtship. It is generally interpreted that these changes are due to dispersion/aggregation of pigment-containing organelles within dermal chromatophores. Here, combining microscopy, photometric videography and photonic band-gap modelling, we show that chameleons shift colour through active tuning of a lattice of guanine nanocrystals within a superficial thick layer of dermal iridophores. In addition, we show that a deeper population of iridophores with larger crystals reflects a substantial proportion of sunlight especially in the near-infrared range. The organization of iridophores into two superposed layers constitutes an evolutionary novelty for chameleons, which allows some species to combine efficient camouflage with spectacular display, while potentially providing passive thermal protection.
    MeSH term(s) Animals ; Biological Evolution ; Chromatophores/chemistry ; Chromatophores/physiology ; Color ; Guanine/chemistry ; Guanine/physiology ; Male ; Nanoparticles/chemistry ; Optical Phenomena ; Photons ; Pigments, Biological/chemistry ; Pigments, Biological/physiology ; Skin Pigmentation/physiology ; Skin Pigmentation/radiation effects
    Chemical Substances Pigments, Biological ; Guanine (5Z93L87A1R)
    Language English
    Publishing date 2015-03-10
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2041-1723
    ISSN (online) 2041-1723
    DOI 10.1038/ncomms7368
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Involvement of the conserved Hox gene Antennapedia in the development and evolution of a novel trait.

    Saenko, Suzanne V / Marialva, Marta Sp / Beldade, Patrícia

    EvoDevo

    2011  Volume 2, Page(s) 9

    Abstract: Background: Hox proteins specify segment identity during embryogenesis and have typical associated expression patterns. Changes in embryonic expression and activity of Hox genes were crucial in the evolution of animal body plans, but their role in the ... ...

    Abstract Background: Hox proteins specify segment identity during embryogenesis and have typical associated expression patterns. Changes in embryonic expression and activity of Hox genes were crucial in the evolution of animal body plans, but their role in the post-embryonic development of lineage-specific traits remains largely unexplored. Here, we focus on the insect Hox genes Ultrabithorax (Ubx) and Antennapedia (Antp), and implicate the latter in the formation and diversification of novel, butterfly-specific wing patterns.
    Results: First, we describe a conserved pattern of Ubx expression and a novel pattern of Antp expression in wing discs of Bicyclus anynana butterflies. The discrete, reiterated domains of Antp contrast with the typical expression of Hox genes in single continuous regions in arthropod embryos. Second, we show that this pattern is associated with the establishment of the organizing centres of eyespots. Antp upregulation is the earliest event in organizer development described to date, and in contrast to all genes implicated in eyespot formation, is exclusive to those centres. Third, our comparative analysis of gene expression across nymphalids reveals unexpected differences in organizer determination.
    Conclusions: We show that the Antp's recruitment for the formation of novel traits in butterfly wing discs involved the evolution of new expression domains, and is restricted to a particular lineage. This study contributes novel insights into the evolution of Antp expression, as well as into the genetic mechanisms underlying morphological diversification. Our results also underscore how a wider representation of morphological and phylogenetic diversity is essential in evolutionary developmental biology.
    Language English
    Publishing date 2011-04-19
    Publishing country England
    Document type Journal Article
    ZDB-ID 2563566-9
    ISSN 2041-9139 ; 2041-9139
    ISSN (online) 2041-9139
    ISSN 2041-9139
    DOI 10.1186/2041-9139-2-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Amelanism in the corn snake is associated with the insertion of an LTR-retrotransposon in the OCA2 gene.

    Saenko, Suzanne V / Lamichhaney, Sangeet / Martinez Barrio, Alvaro / Rafati, Nima / Andersson, Leif / Milinkovitch, Michel C

    Scientific reports

    2015  Volume 5, Page(s) 17118

    Abstract: The corn snake (Pantherophis guttatus) is a new model species particularly appropriate for investigating the processes generating colours in reptiles because numerous colour and pattern mutants have been isolated in the last five decades. Using our ... ...

    Abstract The corn snake (Pantherophis guttatus) is a new model species particularly appropriate for investigating the processes generating colours in reptiles because numerous colour and pattern mutants have been isolated in the last five decades. Using our captive-bred colony of corn snakes, transcriptomic and genomic next-generation sequencing, exome assembly, and genotyping of SNPs in multiple families, we delimit the genomic interval bearing the causal mutation of amelanism, the oldest colour variant observed in that species. Proceeding with sequencing the candidate gene OCA2 in the uncovered genomic interval, we identify that the insertion of an LTR-retrotransposon in its 11(th) intron results in a considerable truncation of the p protein and likely constitutes the causal mutation of amelanism in corn snakes. As amelanistic snakes exhibit white, instead of black, borders around an otherwise normal pattern of dorsal orange saddles and lateral blotches, our results indicate that melanocytes lacking melanin are able to participate to the normal patterning of other colours in the skin. In combination with research in the zebrafish, this work opens the perspective of using corn snake colour and pattern variants to investigate the generative processes of skin colour patterning shared among major vertebrate lineages.
    MeSH term(s) Animals ; Colubridae/genetics ; Colubridae/metabolism ; Melanins/metabolism ; Mutagenesis, Insertional ; Reptilian Proteins/genetics ; Retroelements ; Sequence Analysis, DNA ; Skin Pigmentation
    Chemical Substances Melanins ; Reptilian Proteins ; Retroelements
    Language English
    Publishing date 2015-11-24
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/srep17118
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: (with research data) Phylogeography and support vector machine classification of colour variation in panther chameleons.

    Grbic, Djordje / Saenko, Suzanne V / Randriamoria, Toky M / Debry, Adrien / Raselimanana, Achille P / Milinkovitch, Michel C

    Molecular ecology

    2015  Volume 24, Issue 13, Page(s) 3455–3466

    Abstract: Lizards and snakes exhibit colour variation of adaptive value for thermoregulation, camouflage, predator avoidance, sexual selection and speciation. Furcifer pardalis, the panther chameleon, is one of the most spectacular reptilian endemic species in ... ...

    Abstract Lizards and snakes exhibit colour variation of adaptive value for thermoregulation, camouflage, predator avoidance, sexual selection and speciation. Furcifer pardalis, the panther chameleon, is one of the most spectacular reptilian endemic species in Madagascar, with pronounced sexual dimorphism and exceptionally large intraspecific variation in male coloration. We perform here an integrative analysis of molecular phylogeography and colour variation after collecting high-resolution colour photographs and blood samples from 324 F. pardalis individuals in locations spanning the whole species distribution. First, mitochondrial and nuclear DNA sequence analyses uncover strong genetic structure among geographically restricted haplogroups, revealing limited gene flow among populations. Bayesian coalescent modelling suggests that most of the mitochondrial haplogroups could be considered as separate species. Second, using a supervised multiclass support vector machine approach on five anatomical components, we identify patterns in 3D colour space that efficiently predict assignment of male individuals to mitochondrial haplogroups. We converted the results of this analysis into a simple visual classification key that can assist trade managers to avoid local population overharvesting.
    MeSH term(s) Animals ; Bayes Theorem ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Female ; Gene Flow ; Genetics, Population ; Lizards/genetics ; Madagascar ; Male ; Models, Genetic ; Molecular Sequence Data ; Phylogeography ; Pigmentation/genetics ; Sequence Analysis, DNA ; Support Vector Machine
    Chemical Substances DNA, Mitochondrial
    Language English
    Publishing date 2015-05-24
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1126687-9
    ISSN 1365-294X ; 0962-1083
    ISSN (online) 1365-294X
    ISSN 0962-1083
    DOI 10.1111/mec.13241
    Database MEDical Literature Analysis and Retrieval System OnLINE

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