Sandra Afonso

CIBIO Research Center in Biodiversity and Genetic Resources | CIBIO · CIBIO

Amphibians are increasingly threatened worldwide, but the availability of genomic resources that could be crucial for implementing informed conservation practices lags well behind that for other vertebrate groups. Here, we describe draft de novo genome, mitogenome and transcriptome assemblies for the Neotropical leaf-frog Phyllomedusa bahiana nativ...

Red coloration is a salient feature of the natural world. Many vertebrates produce red color by converting dietary yellow carotenoids into red ketocarotenoids via an unknown mechanism. Here, we show that two enzymes, cytochrome P450 2J19 (CYP2J19) and 3-hydroxybutyrate dehydrogenase 1-like (BDH1L), are sufficient to catalyze this conversion. In bir...

Long‐term maintenance of colour polymorphisms often depends on the interplay of multiple selective forces. In the common wall lizard (Podarcis muralis), up to three pure and two mosaic ventral colour morphs co‐exist across most of its range. Available evidence suggests that colour morphs in this species are maintained through the interaction betwee...

Grapevine (Vitis vinifera L.) diversity richness results from a complex domestication history over multiple historical periods. Here, we used whole-genome resequencing to elucidate different aspects of its recent evolutionary history. Our results support a model in which a central domestication event in grapevine was followed by postdomestication h...

The Eurasian Woodcock Scolopax rusticola is a widespread Palearctic migratory wader, with purportedly sedentary populations occurring in the Macaronesian archipelago of the Azores. Here we used microsatellite markers to investigate patterns of genetic diversity and differentiation in these insular birds, and compared Azorean populations to those fr...

Saltatorial locomotion is a type of hopping gait that in mammals can be found in rabbits, hares, kangaroos, and some species of rodents. The molecular mechanisms that control and fine-tune the formation of this type of gait are unknown. Here, we take advantage of one strain of domesticated rabbits, the sauteur d’Alfort, that exhibits an abnormal lo...

Grapevine ( Vitis vinifera L.) is one of the most significant crops in the world. Today’s richness in grapevine diversity results from a complex domestication history over multiple historical periods. Here, we employed whole genome resequencing to elucidate different aspects of the recent evolutionary history of this crop. Our results support a mod...

Birds exhibit striking variation in eye color that arises from interactions between specialized pigment cells named chromatophores. The types of chromatophores present in the avian iris are lacking from the integument of birds or mammals, but are remarkably similar to those found in the skin of ectothermic vertebrates. To investigate molecular mech...

Mitochondrial DNA (mtDNA) and cytochrome b (cyt b) gene sequences were used to determine the status of genetic diversity and phylogeny for 132 individuals from local rabbit breeds in Egypt and Spain. The Egyptian local rabbit breeds were Egyptian Red Baladi (ERB), Egyptian Black Baladi (EBB) and Egyptian Gabali Sinai (EGS). However, the Spanish loc...

Canaries changing colors Many animals are sexually dimorphic, with different phenotypes in males and females. To identify the genetic basis of sexual differences in bird coloration, Gazda et al. investigated red coloration in mosaic canaries and related species (see the Perspective by Chen). Using a combination of genetic crosses, genomic mapping,...

The flat periwinkles, Littorina fabalis and L. obtusata, comprise two sister gastropod species that have an enormous potential to elucidate the mechanisms involved in ecological speciation in the marine realm. However, the molecular resources currently available for these species are still scarce. In order to circumvent this limitation, we used RNA...

Unlike wild and domestic canaries (Serinus canaria), or any of the three dozen species of finches in genus Serinus, the domestic urucum breed of canaries exhibits bright red bills and legs. This novel trait offers a unique opportunity to understand the mechanisms of bare-part coloration in birds. To identify the mutation producing the colorful phen...

A BSTRACT Unlike wild and domestic canaries ( Serinus canaria ), or any of the three dozen species of finches in genus Serinus , the domestic urucum breed of canaries exhibits bright red bills and legs. This novel bare-part coloration offers a unique opportunity to understand how leg and bill coloration evolve in birds. To identify the causative lo...

Background: Venom has evolved in parallel in multiple animals for the purpose of self-defense, prey capture or both. These venoms typically consist of highly complex mixtures of toxins: diverse bioactive peptides and/or proteins each with a specific pharmacological activity. Because of their specificity, they can be used as experimental tools to s...

The evolution of gene expression in mammalian organ development remains largely uncharacterized. Here we report the transcriptomes of seven organs (cerebrum, cerebellum, heart, kidney, liver, ovary and testis) across developmental time points from early organogenesis to adulthood for human, rhesus macaque, mouse, rat, rabbit, opossum and chicken. C...

Background Iberian primitive breeds exhibit a remarkable phenotypic diversity over a very limited geographical space. While genomic data are accumulating for most commercial cattle, it is still lacking for these primitive breeds. Whole genome data is key to understand the consequences of historic breed formation and the putative role of earlier adm...

Reptiles use pterin and carotenoid pigments to produce yellow, orange, and red colors. These conspicuous colors serve a diversity of signaling functions, but their molecular basis remains unresolved. Here, we show that the genomes of sympatric color morphs of the European common wall lizard (Podarcis muralis), which differ in orange and yellow pigm...

Locating myxomatosis resistance Myxomatosis is a viral infection that was deliberately introduced from American cottontail rabbits into European rabbit populations to control their population. Over the past 60 years or so, similar resistance variants have emerged in parallel in the United Kingdom, France, and Australia. Alves et al. discovered that...

Reptiles use pterin and carotenoid pigments to produce yellow, orange, and red colors. These conspicuous colors serve a diversity of signaling functions, but their molecular basis remains unresolved. Here, we show that the genomes of sympatric color morphs of the European common wall lizard, which differ in orange and yellow pigmentation and in the...

Background Iberian primitive breeds exhibit a remarkable phenotypic diversity over a very limited geographical space. While genomic data are accumulating for most commercial cattle, it is still lacking for these primitive breeds. Whole genome data is key to understand the consequences of historic breed formation and the putative role of earlier adm...

Discrete colour morphs coexisting within a single population are common in nature. In a broad range of organisms, sympatric colour morphs often display major differences in other traits, including morphology, physiology or behaviour. Despite the repeated occurrence of this phenomenon, our understanding of the genetics that underlie multi-trait diff...

Significance A common feature of all domestic animals is their tame behavior and lack of fear for humans. Consistent with this, we have previously demonstrated that genes with a role in brain or neural development have been particularly targeted during rabbit domestication. Here we show, using high-resolution magnetic resonance imaging, that domest...

Racing pigeons have been selectively bred to find their way home quickly over what are often extremely long distances. This breed is of substantial commercial value and is also an excellent avian model to gain empirical insights into the evolution of traits associated with flying performance and spatial orientation. Here, we investigate the molecul...

Speciation is a process proceeding from weak to complete reproductive isolation. In this continuum, naturally hybridizing taxa provide a promising avenue for revealing the genetic changes associated with the incipient stages of speciation. To identify such changes between two subspecies of rabbits that display partial reproductive isolation, we stu...

Significance The yellow, orange, and red colors of birds are produced through the deposition of carotenoid pigments into feathers and skin, and often function as signals in aggressive interactions and mate choice. These colors are hypothesized to communicate information about individual quality because their expression is linked to vital cellular p...

The dwarf phenotype characterizes the smallest of rabbit breeds and is governed largely by the effects of a single dwarfing allele with an incompletely dominant effect on growth. Dwarf rabbits typically weigh under 1 kg and have altered craniofacial morphology. The dwarf allele is a recessive lethal and dwarf homozygotes die within a few days of bi...

The Small Five-toed Jerboa, Allactaga elater, is a small rodent adapted to desert and semi-arid habitats with a widespread distribution around the Caucasus. Previous studies have suggested the occurrence of subspecific variation within the species but, except for a recent phylogeny of the genus Allactaga, most of the work done on the taxonomy of th...

Nineteen microsatellite loci were used to identify the genetic diversity for 3 Egyptian and Spanish common rabbit. Egyptian breeds were Egyptian Red Baladi (ERB), Egyptian Black Baladi (EBB) and Egyptian Gabali Sinai (EGS). The previous breeds were compared with European Wild rabbits (EWR). This study recorded that lower genetic diversity exists in...

Mitochondrial DNA (mtDNA) cytochrome b (cyt b) gene sequences were used to determine the phylogeny and the origin of local rabbit breeds in Egypt and Spain. Egyptian local rabbit breeds were Egyptian Red Baladi (ERB), Egyptian Black Baladi (EBB) and Egyptian Gabali Sinai (EGS), while the Spanish local rabbit breed was Spanish common rabbit (SCR). P...

Nineteen microsatellite loci were used to identify the genetic diversity for 3 Egyptian and Spanish common rabbit. Egyptian breeds were Egyptian Red Baladi (ERB), Egyptian Black Baladi (EBB) and Egyptian Gabali Sinai (EGS). The previous breeds were compared with European Wild rabbits (EWR). This study recorded that lower genetic diversity exists in...

Over thousands of years humans changed the genetic and phenotypic composition of several organisms and in the process transformed wild species into domesticated forms. From this close association, domestic animals emerged as important models in biomedical and fundamental research, in addition to their intrinsic economical and cultural value. The do...

Geographical location of the wild rabbit samples used in this study. The background layer reflects the elevation (increasing elevation from light to dark tones) highlighting the Pyrenees mountain range that separates the Iberian Peninsula from France. (PDF)

Average percentage of genetic diversity lost with different processes. Bars show values of genetic diversity lost for the colonization of France (green), domestication process (red), breed formation process (blue) and for each one of the 16 breeds (grey). Values were estimated using a resampling methodology (described in Methods). Error bars repres...

Discriminant Analysis of Principal Components (DAPC) of 16 breeds. The scatterplot shows the first two principal components (Y-axis and X-axis, respectively) using breeds as prior for genetic clusters. Each dot represents an individual, and genetic clusters are depicted by colours and 95% inertia ellipses. The eigenvalue components are show in the...

List of all 45 microsatellites used in this study. (PDF)

PCR profiles for the nine multiplex reactions. (PDF)

Genetic diversity and sample sizes for each microsatellite. Values for domestic rabbits (DOM), wild rabbits from France (WF), and wild rabbits from the Iberian Peninsula (WIP). (PDF)

Average percentage of genetic diversity lost during the colonization of France, domestication process, and the breed formation process. Values for breed formation process were averaged across breeds and for each individual breed. Values were estimated using a resampling methodology (described in the Methods section). (PDF)

Consensus Fitch-Margoliash trees for 20 populations. Trees include domestic rabbits, wild French rabbits and is rooted with wild Iberian rabbits. (A) Tree based on chord genetic distance B) Tree based on allele-sharing genetic distance. Domestic rabbits include 16 breeds, two of which composed by two different strains. The node values correspond to...

Domestic breeds and strains with respective sample sizes. (PDF)

Chromosome positions of the 12 microsatellites developed for this study. (PDF)

Phylogenies of wild and domestic rabbits based on allele-sharing genetic distance. (A) Neighbour-joining tree for 471 individuals rooted with wild rabbits from the Iberian Peninsula. (B) Unrooted Neighbour-joining tree for 340 domestic individuals from 16 different breeds. Branches are coloured according to individual’s origin. (PDF)

STRUCTURE plots for different values of K for all 16 breeds. Five independent runs were performed for each K value, and K varied from 2 to 30. (PDF)

Primers used for the 12 microsatellites developed for this study. (PDF)

Thermal cycler conditions for the nine multiplex PCRs. (PDF)

Pairwise FST genetic distances for all 16 domestic breeds. (PDF)

Chi-square test for Hardy-Weinberg equilibrium for all loci and across all 16 breeds (PDF)

Modal Distribution of ΔK for different values of K in STRUCTURE analysis with all domestic individuals. (PDF)

Microsatellite genotypes. The table contains individual rabbit genotypes for each microsatellite. Microsatellites are ordered according to the multiplex number order and group code represents breed/population. (XLSX)

Wild rabbit samples. (PDF)

Mean Similarity Coefficient for STRUCTURE runs from K = 2 to K = 9 (PDF)

The genetic changes underlying the initial steps of animal domestication are still poorly understood. We generated a high-quality reference genome for the rabbit and compared it to resequencing data from populations of wild and domestic rabbits. We identified more than 100 selective sweeps specific to domestic rabbits but only a relatively small nu...

The analysis of introgression of genomic regions between divergent populations provides an excellent opportunity to determine the genetic basis of reproductive isolation during the early stages of speciation. However, hybridization and subsequent gene flow must be relatively common in order to localize individual loci that resist introgression. In...

T-complex testis expressed protein 1 domain containing 4 (TCTEX1D4) contains the canonical phosphoprotein phosphatase 1 (PPP1) binding motif, composed by the amino acid sequence RVSF. We identified and validated the binding of TCTEX1D4 to PPP1 and demonstrated that indeed this protein is a novel PPP1 interacting protein. Analyses of twenty-one mamm...

Maintenance of genetic distinction in the face of gene flow is an important aspect of the speciation process. Here, we provide a detailed spatial and genetic characterization of a hybrid zone between two subspecies of the European rabbit. We examined patterns of allele frequency change for 22 markers located on the autosomes, X-chromosome, Y-chromo...

Background Recent studies in human have highlighted the importance of the monocyte chemotactic proteins (MCP) in leukocyte trafficking and their effects in inflammatory processes, tumor progression, and HIV-1 infection. In European rabbit (Oryctolagus cuniculus) one of the prime MCP targets, the chemokine receptor CCR5 underwent a unique structural...

Genbank Accessions and Links of MCP-Eotaxin mRNA sequences of Placental Mammals used or consulted.

Alignment of Oryctolagus cuniculus and Homo sapiens WGS sequences: identifying the rabbit ortholog of human CCL8 .

GenBank Features file for Rabbit NC_013687 REGION: 23720000.23798000.

Alignment of Oryctolagus cuniculus and Homo sapiens WGS sequences: identifying rabbit ortholog of human CCL7 .

Alignment of Oryctolagus cuniculus and Homo sapiens WGS sequences: identifying rabbit ortholog of human CCL13 .

Alignment of MCP encoding regions of rabbit and human in Fasta format.

Nucleotide variation at CCL8 genes within and among leporid species.

Rabbit CCL13 ortholog named ‘ CCL8’ or ‘ CCL7’.

Detailed PCR procedures.

Understanding the genetic structure of domestic species provides a window into the process of domestication and motivates the design of studies aimed at making links between genotype and phenotype. Rabbits exhibit exceptional phenotypic diversity, are of great commercial value, and serve as important animal models in biomedical research. Here, we p...