Miguel M Fonseca

Miguel M Fonseca
University of Porto | UP · Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR)

PhD

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42
Publications
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816
Citations

Publications

Publications (42)
Article
The Atlantic chub mackerel, Scomber colias (Gmelin, 1789), is a medium-sized pelagic fish with substantial importance in the fisheries of the Atlantic Ocean and the Mediterranean Sea. Over the past decade, this species has gained special relevance, being one of the main targets of pelagic fisheries in the NE Atlantic. Here, we sequenced and annotat...
Article
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Mammalian spermatozoa are a notable example of metabolic compartmentalization.¹ Energy in the form of ATP production, vital for motility, capacitation, and fertilization, is subcellularly separated in sperm cells. While glycolysis provides a local, rapid, and low-yielding input of ATP along the flagellum fibrous sheath, oxidative phosphorylation (O...
Preprint
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Mammalia spermatozoa are a notable example of energetic compartmentalization. While mitochondrial oxidative phosphorylation is restricted to the midpiece, sperm-specific glycolysis operates in the flagellum. Consequently, these highly specialized cells exhibit a clear adaptability to fuel substrates. This plasticity is essential to ensure sperm mot...
Preprint
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Advances in phylogenetics and high-throughput sequencing have allowed the reconstruction of deep phylogenetic relationships in the evolution of eukaryotes. Yet, the root of the eukaryotic tree of life remains elusive. The most popular hypothesis in textbooks and reviews is a root between Unikonta (Opisthokonta + Amoebozoa) and Bikonta (all other eu...
Article
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The skin is a multi-layered organ, often displaying associated structures, that establishes a protective interface between the organism and the surrounding environment. In mammals, the skin provides a physical and immune barrier, while contributing to thermoregulation and water balance. Within cetaceans, the archetypal mammalian skin was drasticall...
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The rapid expansion of high-quality genome assemblies, exemplified by ongoing initiatives such as the Genome-10K and i5k, demands novel automated methods to approach comparative genomics. Of these, the study of inactivating mutations in the coding region of genes, or pseudogenization, as a source of evolutionary novelty is mostly overlooked. Thus,...
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Using a new fossil-calibrated mitogenome-based approach, we identified macroevolutionary shifts in mitochondrial gene order among the freshwater mussels (Unionoidea). We show that the early Mesozoic divergence of the two Unionoidea clades, Margaritiferidae and Unionidae, was accompanied by a synchronous split in the gene arrangement in the female m...
Article
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Estimating multiple sequence alignments (MSAs) and inferring phylogenies are essential for many aspects of comparative biology. Yet, many bioinformatics tools for such analyses have focused on specific clades, with greatest attention paid to plants, animals and fungi. The rapid increase of high-throughput sequencing (HTS) data from diverse lineages...
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The appearance of mammalian-specific skin features was a key evolutionary event contributing for the elaboration of physiological processes such as thermoregulation, adequate hydration, locomotion, and inflammation. Skin inflammatory and autoimmune processes engage a population of skin-infiltrating T cells expressing a specific C-C chemokine recept...
Article
Ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota are widespread in marine and terrestrial habitats, playing a major role in the global nitrogen cycle. However, their evolutionary history remains unexplored, which limits our understanding of their adaptation mechanisms. Here, our comprehensive phylogenomic tree of Thaumarchaeota supports...
Article
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Genomes are dynamic biological units, with processes of gene duplication and loss triggering evolutionary novelty. The mammalian skin provides a remarkable case study on the occurrence of adaptive morphological innovations. Skin sebaceous glands, for instance, emerged in the ancestor of mammals serving pivotal roles, such as lubrication, waterproof...
Preprint
Full-text available
The appearance of mammalian-specific skin features was a key evolutionary event contributing for the elaboration of physiological processes such as thermoregulation, adequate hydration, locomotion and inflammation. Skin inflammatory and autoimmune processes engage a population of skin-infiltrating T cells expressing a specific C-C chemokine recepto...
Article
Full-text available
Clupeiformes, such as sardines and herrings, represent an important share of worldwide fisheries. Among those, the European sardine (Sardina pilchardus, Walbaum 1792) exhibits significant commercial relevance. While the last decade showed a steady and sharp decline in capture levels, recent advances in culture husbandry represent promising research...
Preprint
Full-text available
Clupeiformes, such as sardines and herrings, represent an important share of worldwide fisheries. Among those, the European sardine (Sardina pilchardus, Walbaum 1792) exhibits significant commercial relevance. While the last decade showed a steady and sharp decline in capture levels, recent advances in culture husbandry represent promising research...
Article
The Cetacea infraorder comprises a very unique group within the mammalian lineage. While sharing common ancestors with terrestrial mammals, their exclusive dependence on aquatic environments makes them attractive models to explore the landscape of molecular shifts in radical habitat transitions. Among their diverse anatomical and physiological solu...
Article
Two Unionida (freshwater mussel) families are present in the Northern Hemisphere; the Margaritiferidae, representing the most threatened of unionid families, and the Unionidae, which include several genera of unresolved taxonomic placement. The recent reassignment of the poorly studied Lamprotula rochechouartii from the Unionidae to the Margaritife...
Data
Supplementary Materials for Genes for de novo biosynthesis of omega-3 polyunsaturated fatty acids are widespread in animals fig. S1. Complete view of the phylogenetic tree presented in Fig. 1A, with major metazoan taxonomic clades colored as in Fig. 1. fig. S2. Summary tree (cladogram) showing relationships between major well- supported clades to...
Article
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Marine ecosystems are responsible for virtually all production of omega-3 (ω3) long-chain polyunsaturated fatty acids (PUFA), which are essential nutrients for vertebrates. Current consensus is that marine microbes account for this production, given their possession of key enzymes including methyl-end (or “ωx”) desaturases. ωx desaturases have also...
Article
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The unionid family Margaritiferidae, comprising 12 extant species, is widely distributed across the northern hemisphere in North America, Europe and Asia (Bolotov et al., 2016). Most species in this family have dramatically declined over the last century, with nine out of the 12 species assessed as threatened in the most recent IUCN Red List (IUCN,...
Article
Full-text available
The unionid family Margaritiferidae, comprising 12 extant species, is widely distributed across the northern hemisphere in North America, Europe and Asia (Bolotov et al., 2016). Most species in this family have dramatically declined over the last century, with nine of the 12 species assessed as threatened in the most recent IUCN Red List (IUCN, 201...
Article
Full-text available
We have sequenced the female and male mtDNA of Unio delphinus and inferred the Unionidae phylogeny using 41 complete mtDNA sequences. Additionally, we compared the concatenated mtDNA trees with those using single or combination of two mtDNA genes to identify the best genes to use in the absence of complete mitogenomes. The gender-specific mtDNAs of...
Article
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Mitochondrial genomes are known to have a strong strand-specific compositional bias that is more pronounced at fourfold redundant sites of mtDNA protein-coding genes. This observation suggests that strand asymmetries, to a large extent, are caused by mutational asymmetric mechanisms. In vertebrate mitogenomes, replication and not transcription seem...
Article
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Mitochondria play a fundamental role in cellular metabolism, being responsible for most of the energy production of the cell in the oxidative phosphorylation (OXPHOS) pathway. Mitochondrial DNA (mtDNA) encodes for key components of this process but its direct role in adaptation remains far from understood. Hares (Lepus spp.) are privileged models t...
Article
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Prokaryotic unidirectional overlapping genes can be originated with the disruption and replacement of the start or stop codon of one protein-coding gene by another start or stop codon within the adjacent gene. However, the probability of disruption and replacement of a start or stop codon may differ significantly depending on the number and redunda...
Article
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Vertebrate mitochondrial genomes typically have one transfer RNA (tRNA) for each synonymous codon family. This limited anticodon repertoire implies that each tRNA anticodon needs to wobble (establish a non-Watson-Crick base pairing between two nucleotides in RNA molecules) to recognize one or more synonymous codons. Different hypotheses have been p...
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The phylogenetic affinities of Acanthodactylus beershebensis, a highly endangered lacertid lizard en-demic to the Neguev (Israel), were assessed using mtDNA markers. Fragments of 12S and 16S rRNA were analysed and compared with already published sequences of Acanthodactylus. Results corroborate the taxo-nomic placement of A. beershebensis as a memb...
Article
We have used mitochondrial 12S rRNA, 16S rRNA and nuclear beta-fibrinogen (intron 7) sequences to investigate the phylogenetic and phylogeographic relationships between Acanthodactylus erythrurus group species (except for A. boueti). The phylogenetic analyses of the Acanthodactylus genus did not cluster A. guineensis and A. savignyi with the remain...
Article
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After analyzing the base composition asymmetry of coding regions in vertebrate mitochondria, we identified 2 fishes, Albula glossodonta and Bathygadus antrodes, with inverted compositional patterns. Both species appear to have an unusual control region (CR), and in B. antrodes, it has switched from the light strand to the heavy strand. To our knowl...
Article
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The systematics of the genus Acanthodactylus was classically based on external morphological traits, osteological characters and morphology of the hemipenes. Although the identification of species complexes is relatively easy, the distinction within some groups is difficult due to a high variability of the external morphology. Partial mitochondrial...
Article
The systematics of the genus Acanthodactylus was classically based on external morphological traits, osteological characters and morphology of the hemipenes. Although the identification of species complexes is relatively easy, the distinction within some groups is difficult due to a high variability of the external morphology. Partial mitochondrial...
Article
Full-text available
We studied the fish assemblag-es of thirty one, 2 nd –4 th order "least-impacted" streams with a varying degree of low-level man-agement in central Portugal, using a standardised survey to document the river habitat. Channel, banks and riparian landuse, described separately according to principal component scores, were significantly related to alti...
Article
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Mitochondrial gene rearrangements are much more frequent in vertebrates than initially thought. It has been suggested that the origin of light strand replication could have an important role in the process of gene rearrangements, but this hypothesis has never been tested before. We used amphibians to test the correlation between light-strand replic...
Article
Full-text available
Mitochondrial gene rearrangements are much more frequent in vertebrates than initially thought. It has been suggested that the origin of light strand replication could have an important role in the process of gene rearrangements, but this hypothesis has never been tested before. We used amphibians to test the correlation between light-strand replic...
Article
Retrieving and organizing data from complete genomes is a time-consuming task, even more so if the interest lies only in part of the genome (for nongenomic analysis). Furthermore, when comparing several genomes or genes, data retrieval has to be repeated multiple times. We present baca, a software for retrieving, organizing and visualizing multiple...
Article
Asymmetric compositional and mutation bias between the two strands occurs in mitochondrial genomes, and an asymmetric mechanism of mtDNA replication is a potential source of this bias. Some evidence indicates that during replication the heavy strand is subject to a gradient of time spent in a single-stranded state (D (ssH)) and a gradient of mutati...
Article
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It has been suggested that dorsal colour patterns and defence strategies could have coevolved in reptiles, the striped species being more prone to flee compared with the spotted species that rely more on crypsis. Because of the confounding effects of phylogeny and habitat, we compared closely related forms that share the same habi- tats and predati...

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Projects (2)
Project
To define the most important freshwater mussel taxa and areas of critical importance for conservation, at European and Global levels, to inform the most relevant policy makers. This will be reached by joining a genomics approach with scattered available distribution data, to determine and map global species richness, weighted endemism, phylogenetic diversity and endemism. Additionally as these animals have an extraordinary unusual pattern of mtDNA inheritance, they will also be used as model-taxa to tackle several issues related with mtDNA evolution.