Even seemingly homogeneous on the surface, the oceans display high environmental heterogeneity ac... more Even seemingly homogeneous on the surface, the oceans display high environmental heterogeneity across space and time. Indeed, different soft barriers structure the marine environment, which offers an appealing opportunity to study various evolutionary processes such as population differentiation and speciation. Here, we focus onAmphiprion clarkii(Actinopterygii; Perciformes), the most widespread of clownfishes that exhibits the highest colour polymorphism. Clownfishes can only disperse during a short pelagic larval phase before their sessile adult lifestyle, which might limit connectivity among populations, thus facilitating speciation events. Consequently, the taxonomic status ofA. clarkiihas been under debate. We used whole-genome resequencing data of 67A. clarkiispecimens spread across the Indian and Pacific Oceans to characterise the species' population structure, demographic history, and colour polymorphism. We found thatA. clarkiispread from the Indo-Pacific Ocean to the P...
The Réunion grey white-eye, Zosterops borbonicus, a passerine bird endemic to Réunion Island in t... more The Réunion grey white-eye, Zosterops borbonicus, a passerine bird endemic to Réunion Island in the Mascarene archipelago, represents an extreme case of microgeographical plumage colour variation in birds, with four distinct colour forms occupying different parts of this small island (2512 km2). To understand whether such population differentiation may reflect low levels of dispersal and gene flow at a very small spatial scale, we examined population structure and gene flow by analysing variation at 11 microsatellite loci among four geographically close localities (<26 km apart) sampled within the distribution range of one of the colour forms, the brown-headed brown form. Our results revealed levels of genetic differentiation that are exceptionally high for birds at such a small spatial scale. This strong population structure appears to reflect low levels of historical and contemporary gene flow among populations, unless very close geographically (<10 km). Thus, we suggest that the Réunion grey white-eye shows an extremely reduced propensity to disperse, which is likely to be related to behavioural processes
Recently diverged taxa showing marked phenotypic and ecological diversity are optimal systems to ... more Recently diverged taxa showing marked phenotypic and ecological diversity are optimal systems to understand the genetic processes underlying speciation. We used genome-wide markers to investigate the diversification of the Reunion grey white eye (Zosterops borbonicus) on the small volcanic island of Reunion (Mascarene archipelago), where this species complex exhibits four geographic forms that are parapatrically distributed across the island and differ strikingly in plumage colour. One form restricted to the highlands is separated by a steep ecological gradient from three distinct lowland forms which meet at narrow hybrid zones that are not associated with environmental variables. Analyses of genomic variation based on SNP data from genotyping-by-sequencing and pooled RADseq approaches, reveal that signatures of selection associated with elevation can be found at multiple regions across the genome, whereas most loci associated with the lowland forms are located on the Z sex chromoso...
Predicted protein sequences from Amphiprion frenatus genome assembly, in fasta format. Each prote... more Predicted protein sequences from Amphiprion frenatus genome assembly, in fasta format. Each protein is annotated with the best blast hit with SwissProt database. For more information, please refer to the publication
Structural genome annotation of Amphiprion frenatus genome, in gff3 format. Structural annotation... more Structural genome annotation of Amphiprion frenatus genome, in gff3 format. Structural annotation was obtained with a combination of ab initio and RNAseq-data based approaches. Final gene models were obtained with MAKER2. For more information, please refer to the publication
Genome assembly of A. frenatus in fasta format. The genome was obtained with a combination of hig... more Genome assembly of A. frenatus in fasta format. The genome was obtained with a combination of high-coverage Illumina short paired-end reads (350 bo insertion size), Illumina mate-pairs (3 kb insertion sizes) and low-coverage long Pacbio reads. For more information, please refer to the publication
Mitochondrial genome annotation for Amphiprion frenatus, in csv format. MitoAnnotator and MitoFis... more Mitochondrial genome annotation for Amphiprion frenatus, in csv format. MitoAnnotator and MitoFish were used to obtain the mitochondrial genome annotation. For more information, please refer to the publicatio
The mitochondrial genome of Amphiprion frenatus, in fasta format. The mitochondrial genome was ob... more The mitochondrial genome of Amphiprion frenatus, in fasta format. The mitochondrial genome was obtained by assembling short Illumina reads with MITObim. For further information, please refer to the publication
Predicted coding sequences (CDS) sequences from Amphiprion frenatus genome assembly, in fasta for... more Predicted coding sequences (CDS) sequences from Amphiprion frenatus genome assembly, in fasta format. Each CDS is annotated with the best blast hit with SwissProt database. For more information, please refer to the publication
This file contains 1) microsatellites data in GENPOP format, 2) morphometric data for birds inclu... more This file contains 1) microsatellites data in GENPOP format, 2) morphometric data for birds included in the pedigree analysis, 3) Spectrophotometry measurements and 4) Results from the dosage of melanins for 12 individuals. Localities coordinates are also provided
Understanding the mechanisms responsible for phenotypic diversification within and among species ... more Understanding the mechanisms responsible for phenotypic diversification within and among species ultimately rests with linking naturally occurring mutations to functionally and ecologically significant traits. Colour polymorphisms are of great interest in this context because discrete colour patterns within a population are often controlled by just a few genes in a common environment. We investigated how and why phenotypic diversity arose and persists in the Zosterops borbonicus white-eye of Reunion (Mascarene archipelago), a colour polymorphic songbird in which all highland populations contain individuals belonging to either a brown or a grey plumage morph. Using extensive phenotypic and genomic data, we demonstrate that this melanin-based colour polymorphism is controlled by a single locus on chromosome 1 with two large-effect alleles, which was not previously described as affecting hair or feather colour. Differences between colour morphs appear to rely upon complex cis-regulatory variation that either prevents the synthesis of pheomelanin in grey feathers, or increases its production in brown ones. We used coalescent analyses to show that, from a ‘brown’ ancestral population, the dominant ‘grey’ allele spread quickly once it arose from a new mutation. Since colour morphs are always found in mixture, this implies that the selected allele does not go to fixation, but instead reaches an intermediate frequency, as would be expected under balancing selection
Even seemingly homogeneous on the surface, the oceans display high environmental heterogeneity ac... more Even seemingly homogeneous on the surface, the oceans display high environmental heterogeneity across space and time. Indeed, different soft barriers structure the marine environment, which offers an appealing opportunity to study various evolutionary processes such as population differentiation and speciation. Here, we focus onAmphiprion clarkii(Actinopterygii; Perciformes), the most widespread of clownfishes that exhibits the highest colour polymorphism. Clownfishes can only disperse during a short pelagic larval phase before their sessile adult lifestyle, which might limit connectivity among populations, thus facilitating speciation events. Consequently, the taxonomic status ofA. clarkiihas been under debate. We used whole-genome resequencing data of 67A. clarkiispecimens spread across the Indian and Pacific Oceans to characterise the species' population structure, demographic history, and colour polymorphism. We found thatA. clarkiispread from the Indo-Pacific Ocean to the P...
The Réunion grey white-eye, Zosterops borbonicus, a passerine bird endemic to Réunion Island in t... more The Réunion grey white-eye, Zosterops borbonicus, a passerine bird endemic to Réunion Island in the Mascarene archipelago, represents an extreme case of microgeographical plumage colour variation in birds, with four distinct colour forms occupying different parts of this small island (2512 km2). To understand whether such population differentiation may reflect low levels of dispersal and gene flow at a very small spatial scale, we examined population structure and gene flow by analysing variation at 11 microsatellite loci among four geographically close localities (<26 km apart) sampled within the distribution range of one of the colour forms, the brown-headed brown form. Our results revealed levels of genetic differentiation that are exceptionally high for birds at such a small spatial scale. This strong population structure appears to reflect low levels of historical and contemporary gene flow among populations, unless very close geographically (<10 km). Thus, we suggest that the Réunion grey white-eye shows an extremely reduced propensity to disperse, which is likely to be related to behavioural processes
Recently diverged taxa showing marked phenotypic and ecological diversity are optimal systems to ... more Recently diverged taxa showing marked phenotypic and ecological diversity are optimal systems to understand the genetic processes underlying speciation. We used genome-wide markers to investigate the diversification of the Reunion grey white eye (Zosterops borbonicus) on the small volcanic island of Reunion (Mascarene archipelago), where this species complex exhibits four geographic forms that are parapatrically distributed across the island and differ strikingly in plumage colour. One form restricted to the highlands is separated by a steep ecological gradient from three distinct lowland forms which meet at narrow hybrid zones that are not associated with environmental variables. Analyses of genomic variation based on SNP data from genotyping-by-sequencing and pooled RADseq approaches, reveal that signatures of selection associated with elevation can be found at multiple regions across the genome, whereas most loci associated with the lowland forms are located on the Z sex chromoso...
Predicted protein sequences from Amphiprion frenatus genome assembly, in fasta format. Each prote... more Predicted protein sequences from Amphiprion frenatus genome assembly, in fasta format. Each protein is annotated with the best blast hit with SwissProt database. For more information, please refer to the publication
Structural genome annotation of Amphiprion frenatus genome, in gff3 format. Structural annotation... more Structural genome annotation of Amphiprion frenatus genome, in gff3 format. Structural annotation was obtained with a combination of ab initio and RNAseq-data based approaches. Final gene models were obtained with MAKER2. For more information, please refer to the publication
Genome assembly of A. frenatus in fasta format. The genome was obtained with a combination of hig... more Genome assembly of A. frenatus in fasta format. The genome was obtained with a combination of high-coverage Illumina short paired-end reads (350 bo insertion size), Illumina mate-pairs (3 kb insertion sizes) and low-coverage long Pacbio reads. For more information, please refer to the publication
Mitochondrial genome annotation for Amphiprion frenatus, in csv format. MitoAnnotator and MitoFis... more Mitochondrial genome annotation for Amphiprion frenatus, in csv format. MitoAnnotator and MitoFish were used to obtain the mitochondrial genome annotation. For more information, please refer to the publicatio
The mitochondrial genome of Amphiprion frenatus, in fasta format. The mitochondrial genome was ob... more The mitochondrial genome of Amphiprion frenatus, in fasta format. The mitochondrial genome was obtained by assembling short Illumina reads with MITObim. For further information, please refer to the publication
Predicted coding sequences (CDS) sequences from Amphiprion frenatus genome assembly, in fasta for... more Predicted coding sequences (CDS) sequences from Amphiprion frenatus genome assembly, in fasta format. Each CDS is annotated with the best blast hit with SwissProt database. For more information, please refer to the publication
This file contains 1) microsatellites data in GENPOP format, 2) morphometric data for birds inclu... more This file contains 1) microsatellites data in GENPOP format, 2) morphometric data for birds included in the pedigree analysis, 3) Spectrophotometry measurements and 4) Results from the dosage of melanins for 12 individuals. Localities coordinates are also provided
Understanding the mechanisms responsible for phenotypic diversification within and among species ... more Understanding the mechanisms responsible for phenotypic diversification within and among species ultimately rests with linking naturally occurring mutations to functionally and ecologically significant traits. Colour polymorphisms are of great interest in this context because discrete colour patterns within a population are often controlled by just a few genes in a common environment. We investigated how and why phenotypic diversity arose and persists in the Zosterops borbonicus white-eye of Reunion (Mascarene archipelago), a colour polymorphic songbird in which all highland populations contain individuals belonging to either a brown or a grey plumage morph. Using extensive phenotypic and genomic data, we demonstrate that this melanin-based colour polymorphism is controlled by a single locus on chromosome 1 with two large-effect alleles, which was not previously described as affecting hair or feather colour. Differences between colour morphs appear to rely upon complex cis-regulatory variation that either prevents the synthesis of pheomelanin in grey feathers, or increases its production in brown ones. We used coalescent analyses to show that, from a ‘brown’ ancestral population, the dominant ‘grey’ allele spread quickly once it arose from a new mutation. Since colour morphs are always found in mixture, this implies that the selected allele does not go to fixation, but instead reaches an intermediate frequency, as would be expected under balancing selection
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