Miguel Carneiro

Miguel Carneiro
University of Porto | UP · Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO)

PhD

About

187
Publications
31,288
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3,110
Citations
Citations since 2017
68 Research Items
2375 Citations
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20172018201920202021202220230100200300400500600
20172018201920202021202220230100200300400500600
Additional affiliations
January 2008 - December 2013
University of Porto

Publications

Publications (187)
Article
Full-text available
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...
Article
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In many vertebrates, the enzymatic oxidation of dietary yellow carotenoids generates red keto‐carotenoids giving color to ornaments. The oxidase CYP2J19 is here a key effector. Its purported intracellular location suggests a shared biochemical pathway between trait expression and cell functioning. This might guarantee the reliability of red colorat...
Article
Biological invasions are a major cause of environmental and economic disruption. While ecological factors are key determinants of their success, the role of genetics has been more challenging to demonstrate. The colonization of Australia by the European rabbit is one of the most iconic and devastating biological invasions in recorded history. Here,...
Article
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...
Article
Full-text available
Studying the genetics of phenotypic convergence can yield important insights into adaptive evolution. Here, we conducted a comparative genomic study of four lineages (species and subspecies) of anadromous shad (Alosa) that have independently evolved life cycles entirely completed in freshwater. Three naturally diverged (A. fallax lacustris, A. f. k...
Article
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...
Preprint
Full-text available
Sexual and social selections promote the evolution of many conspicuous colorations in animals. These traits would act as individual quality signals when they transmit reliable information. Reliability should be assured by production costs unaffordable for low-quality trait bearers or guaranteed if trait expression is tightly linked to individual qu...
Article
Pterins are one of the major sources of bright coloration in animals. They are produced endogenously, participate in vital physiological processes and serve a variety of signalling functions. Despite their ubiquity in nature, pterin-based pigmentation has received little attention when compared to other major pigment classes. Here, we summarize maj...
Article
Background and Aims The characterisation of plant microbiomes using metabarcoding strategies is expected to be progressively replaced by shotgun metagenomic (SMg) approaches. In the present report we explore the potential of applying SMg to grapevine leaf, rhizosphere and soil samples. Methods and Results Our strategy involved combining a single m...
Article
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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...
Preprint
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...
Article
Full-text available
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...
Article
The study of phenotypic evolution in island birds following colonization is a classic topic in island biogeography. However, few studies explicitly test for the role of selection in shaping trait evolution in these taxa. Here, we studied the Azores woodpigeon (Columba palumbus azorica) to investigate differences between island and mainland populati...
Article
Full-text available
Ornaments can evolve to reveal individual quality when their production/maintenance costs make them reliable as “signals” or if their expression level is intrinsically linked to condition by some unfalsifiable mechanism (“indices”). The latter has been mostly associated with traits constrained by body size. In red ketocarotenoid-based colourations,...
Article
Full-text available
Domestication has resulted in immense phenotypic changes in animals despite their relatively short evolutionary history. The European rabbit is one of the most recently domesticated animals, but exhibits distinct morphological, physiological and behavioural differences from their wild conspecifics. A previous study revealed that sequence variants w...
Article
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,...
Preprint
Full-text available
Conspicuous ornaments in animals can evolve to reveal individual quality when their production/maintenance costs make them reliable as signals or if their expression level is intrinsically linked to quality by some unfalsifiable mechanism (quality indices). The latter has been mostly associated with traits constrained by body size. However, red ket...
Article
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...
Article
Black and tan animals have tan‐coloured ventral body surfaces separated by sharp boundaries from black‐coloured dorsal body surfaces. In the at mouse mutant, a retroviral 6 kb insertion located in the hair cycle‐specific promoter of the murine Asip gene encoding agouti signalling protein causes the black and tan phenotype. In rabbits, three ASIP al...
Preprint
Full-text available
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...
Article
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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...
Poster
Full-text available
The European rabbit (Oryctolagus cuniculus) is a keystone species in Mediterranean ecosystems and also is one of the most appreciated small game species in the Iberian Peninsula. Over the last decades, however, natural populations have encompassed steep fluctuations in numbers and distribution as a consequence of habitat loss, infectious diseases,...
Article
Full-text available
Genome-wide assessment of genetic diversity has the potential to increase the ability to understand admixture, inbreeding, kinship and erosion of genetic diversity affecting both captive (ex situ) and wild (in situ) populations of threatened species. The sable antelope (Hippotragus niger), native to the savannah woodlands of sub-Saharan Africa, is...
Cover Page
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Pictured is a wall lizard exhibiting orange coloration, a phenotype controlled by a genetic variant of the gene for the sepiapterin reductase enzyme. Pedro Andrade et al. analyzed the genes of European common wall lizards (Podarcis muralis), which exhibit distinct colors, and found that changes in the genes associated with carotenoid and pterin met...
Article
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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...
Cover Page
Full-text available
Regulatory changes in pterin and carotenoid genes underlie balanced color polymorphisms in the wall lizard
Article
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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...
Preprint
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
Background The cane toad (Rhinella marina formerly Bufo marinus) is a species native to Central and South America that has spread across many regions of the globe. Cane toads are known for their rapid adaptation and deleterious impacts on native fauna in invaded regions. However, despite an iconic status, there are major gaps in our understanding o...
Article
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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...
Article
Platelet integrin αIIbβ3 is crucial for platelet aggregation. Although structural and functional characteristics of this protein have been extensively studied, the evolutionary pattern studies of this protein complex in mammals are scarce. Here, we addressed this question using maximum likelihood approaches to identify codons that are evolving unde...
Article
Full-text available
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...
Article
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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...
Article
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A fraction of genetic variants segregating in any population are deleterious, which negatively impacts individual fitness. The domestication of animals and plants is associated with population bottlenecks and artificial selection, which are predicted to increase the proportion of deleterious variants. However, the extent to which this is a general...
Article
Full-text available
Background Cane toads (Rhinella marina) are an iconic invasive species introduced to four continents and well utilized for studies of rapid evolution in introduced environments. Despite the long introduction history of this species, its profound ecological impacts and its utility for demonstrating evolutionary principles, genetic information is spa...
Article
Genetic data generated by high-throughput sequencing and deposited in public databases are increasing exponentially. A substantial amount of these data is generated from wild animals, and can contain information from nontarget organisms, such as parasites. Methodologies that leverage this available information are warranted and can help to answer q...
Article
Full-text available
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...
Article
Full-text available
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...
Preprint
Full-text available
Background Next generation sequencing (NGS) technology has made it possible to perform high-resolution screens for structural variants. Computational methods for detection of structural variants utilize paired-end mapping information, depth of coverage, split reads, or some combination of such data. The available methods are particularly designed t...
Article
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The complete mitochondrial genome of Salamandra salamandra was reconstructed using bycatch sequences from an RNAseq library generated from muscle tissue. This study shows the potential of using data originally produced for transcriptome assembly to additionally generate complete mitochondrial genomes. The resulting mitogenome was circular, consiste...
Article
This article reports the de novo transcriptome assemblies of two highly divergent evolutionary units of the Iberian endemic Bosca's newt, Lissotriton boscai. These two units are distributed mostly allopatrically but overlap in the central-southwestern coastal region of Portugal. The resources we provide include the raw sequence reads, the assembled...
Article
Full-text available
The yellow and red feather pigmentation of many bird species [1] plays pivotal roles in social signaling and mate choice [2, 3]. To produce red pigments, birds ingest yellow carotenoids and endogenously convert them into red ketocarotenoids via an oxidation reaction catalyzed by a previously unknown ketolase [4-6]. We investigated the genetic basis...
Article
Recent studies have revealed repeated patterns of genomic divergence associated with species formation. Such patterns suggest that natural selection tends to target a set of available genes, but is also indicative that closely related taxa share evolutionary constraints that limit genetic variability. Studying patterns of genomic divergence among p...
Article
Full-text available
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...
Data
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)
Data
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...