Maria MANUELA Coelho

University of Lisbon | UL · Faculty of Science

Evidence for ancient interspecific gene flow through hybridization has been reported in many animal and plant taxa based on genetic markers. The study of genomic patterns of closely related species with allopatric distributions allows the assessment of the relative importance of vicariant isolating events and past gene flow. Here, we investigated t...

Background The circadian clock is a biological timing system that improves the ability of organisms to deal with environmental fluctuations. At the molecular level it consists of a network of transcription-translation feedback loops, involving genes that activate ( bmal and clock – positive loop) and repress expression (cryptochrome ( cry ) and per...

Background The circadian clock is a biological timing system that improves the ability of organisms to deal with environmental fluctuations. At the molecular level it consists of a network of transcription-translation feedback loops, involving genes that activate (bmal and clock – positive loop) and repress expression (cryptochrome (cry) and period...

Background The circadian clock is a biological timing system that improves the ability of organisms to deal with environmental fluctuations. At the molecular level it consists of a network of transcription-translation feedback loops, involving genes that activate (bmal and clock – positive loop) and repress expression (cryptochrome (cry) and period...

In freshwater fish, processes of population divergence and speciation are often linked to the geomorphology of rivers and lakes that isolate populations. However, current geographical isolation does not necessarily imply total absence of gene flow during the divergence process. Here, we focused on four species of the genus Squalius in Portuguese ri...

In freshwater fish, processes of population divergence and speciation are often linked to the geomorphology of rivers and lakes that isolate populations. However, current geographical isolation does not necessarily imply total absence of gene flow during the divergence process. Here, we focused on four species of the genus Squalius in Portuguese ri...

Background The circadian clock is a biological timing system that improves the ability of organisms to deal with environmental fluctuations. At the molecular level it consists of a network of transcription-translation feedback loops, involving genes that activate ( bmal and clock – positive loop) and repress expression (cryptochrome ( cry ) and per...

Future climate change scenarios predict threatening outcomes to biodiversity. Available empirical data concerning biological response of freshwater fish to climate change remains scarce. In this study, we investigated the physiological and biochemical responses of two Iberian freshwater fish species (Squalius carolitertii and the endangered S. torg...

Current knowledge on the biological responses of freshwater fish under projected scenarios of climate change remains limited. Here, we examine differences in the protein configuration of two endemic Iberian freshwater fish species, Squalius carolitertii and the critically endangered S. torgalensis that inhabit in the Atlantic-type northern and in t...

Protein structure predictions for proteins with minor or no differences between species. Regions in light grey have no differences between species, blue and red indicate the conformation of S. carolitertii and S. torgalensis for that specific region and yellow represents the amino acids which correspond to non-synonymous substitutions. (PDF)

Predicted proteins physical and chemical parameters. (XLSX)

Primer pairs used to re-sequence genes in Sanger with their PCR amplification conditions. (DOCX)

Real-time RT-PCR primer pairs for reference and target genes and their efficiency values calculated in LinRegPCR (Ruijter et al., 2009). Real-time PCRs were done in a final volume of 10 μL, containing 5 μL of Sso Advanced universal SYBR® Green supermix (2x) (Bio- Rad, Hercules, CA, USA) and 0.4 μL of each primer (with a concentration of 0.4 μM). Th...

Gene expression values of reference and target genes in the transcriptomes of both species described in Jesus et al. (2016). Reference genes have a column for the differential gene expression value between S. pyrenaicus males and females from (Genomic resources development consortium et al., 2015b). Non-DE and N/A stands for genes that are not sign...

Stability values calculated for the reference genes (rpsa, rpl35 and pabpc1a), showing their overall stability and for each organ and condition analyzed. The lower the stability value the better the reference gene and thus less variable across the experimental conditions. (PDF)

Schematic representation of the pathways discussed in this research for the genes involved in energy metabolism. Doted arrows indicate gene expression regulation from the source to the sink gene; dashed arrows represent a source gene that encodes a protein is responsible for substrate conversion; and full arrows indicate a direct conversion. Target...

Non-synonymous substitutions for the translated predicted protein structures (in a.a.). (DOCX)

Temperature is the main factor affecting the distribution of the sympatric Amazon fishes Paracheirodon axelrodi and Paracheirodon simulans. Both species are associated with flooded areas of the Negro river basin; P. axelrodi inhabits waters that do not exceed 30C, and P. simulans lives at temperatures that can surpass 35C. The present work aimed to...

Sex determination is a highly variable process that utilizes many different mechanisms to initiate the cascade of differentiation processes. The molecular pathways controlling sexual development are less conserved than previously assumed, and appear to require active maintenance in some species; indeed, the developmental decision of gonad phenotype...

Allelic silencing is an important mechanism for coping with gene dosage changes in polyploid organisms that is well known in allopolyploid plants. Only recently, it was shown in the allotriploid fish Squalius alburnoides that this process also occurs in vertebrates. However, it is still unknown whether this silencing mechanism is common to other al...

The evolutionary mechanisms underlying the geographic distribution of gene lineages in the marine environment are not as well understood as those affecting terrestrial groups. The continuous nature of the pelagic marine environment may limit opportunities for divergence to occur and lineages to spatially segregate, particularly in highly mobile spe...

The evolutionary mechanisms underlying the geographic distribution of gene lineages in the marine environment are not as well understood as those affecting terrestrial groups. The continuous nature of the pelagic marine environment may limit opportunities for divergence to occur and lineages to spatially segregate, particularly in highly mobile spe...

The congeneric freshwater fish Squalius carolitertii and S. torgalensis inhabit different Iberian regions with distinct climates; Atlantic in the North and Mediterranean in the South, respectively. While northern regions present mild temperatures, fish in southern regions often experience harsh temperatures and droughts. Previous work with two hsp7...

This article documents the public availability of (i) microbiomes in diet and gut of larvae from the dipteran Dilophus febrilis using massive parallel sequencing, (ii) SNP and SSR discovery and characterization in the transcriptome of the Atlantic mackerel (Scomber scombrus, L) and (iii) assembled transcriptome for an endangered, endemic Iberian cy...

This article documents the public availability of transcriptomic resources for (i) the stellate sturgeon Acipenser stellatus, (ii) the flowering plant Campanula gentilis and (iii) two endemic Iberian fish, Squalius carolitertii and Squalius torgalensis. © 2015 John Wiley & Sons Ltd.

Analytical methods that apply coalescent theory to multi-locus data have improved inferences of demographic parameters that are critical to understanding population divergence and speciation. In particular, at the early stages of speciation it is important to implement models that accommodate conflicting gene trees, and benefit from the presence of...

How allopolyploids are able not only to cope but profit from their condition is a question that remain elusive, but of great importance within the context of successful allopolyploid evolution. One outstanding example of successful allopolyploidy is the endemic Iberian cyprinid Squalius alburnoides. Previously, based on the evaluation of a few gene...

Assessing allele-specific gene expression (ASE) on a large scale continues to be a technically challenging problem. Certain biological phenomena, such as X chromosome inactivation and parental imprinting, affect ASE most drastically by completely shutting down the expression of a whole set of alleles. Other more subtle effects on ASE are likely to...

Natural hybridization may result in the exchange of genetic material between divergent lineages and even the formation of new taxa. Many of the Neo-Darwinian architects argued that, particularly for animal clades, natural hybridization was maladaptive. Recent evidence, however, has falsified this hypothesis, instead indicating that this process may...

Iberochondrostoma almacai is an endemic cyprinid fish from the southwest of the Iberian Peninsula, with a distribution area restricted to three independent Portuguese river basins. This species is critically endangered due to water abstraction, pollution, habitat destruction and introduction of exotic species. Captive breeding for restocking purpos...

The phylogeography of Iberian freshwater fish species strongly reflects the geomorphological history of Iberian water drainages and formation of mountain ranges. In particular, the Iberian Central Massif limits two ichthyogeographical districts based on fish distribution assemblages: the Northwest district, which comprises all river basins north of...

When comparing the known picture of polyploidy in animals and in plants, it is possible to recognize some similarities, namely: (i) multiple and recurrent origins in several well-established taxonomic groups; (ii) a strong and regular association with hybridization events; (iii) the production of genotypic diversity; (iv) a rapid genomic reshufflin...

Comprehension of the mechanisms by which ectotherms, such as fish, respond to thermal stress is paramount for understanding the threats that environmental changes may pose to wild populations. Heat shock proteins are molecular chaperones with an important role in several stress conditions such as high temperatures. In the Iberian Peninsula, particu...

The conservation status of seabird populations has been deteriorating at a fast pace in recent decades. Studies of population genetic variation provide important insights regarding the evolutionary history of species, but also crucial information for conservation and management strategies. We report isolation and characterization of twelve anonymou...

Climatic oscillations during the Pleistocene have greatly influenced the distribution and connectivity of many organisms, leading to extinctions but also generating biodiversity. While the effects of such changes have been extensively studied in the terrestrial environment, studies focusing on the marine realm are still scarce. Here we used sequenc...

The Squalius alburnoides complex (Steindachner) is one of the most intricate hybrid polyploid systems known in vertebrates. In this complex, the constant switch of the genome composition in consecutive generations, very frequently involving a change on the ploidy level, promotes repetitive situations of potential genomic shock. Previously in this c...

Annotation of small RNA tags. (DOCX)

Differences between real expression values and expected values in case of additivity. Results are logarithmized log2 (real/expected)) and presented in an ascending order. In grey background are values higher than 1 and lower than −1. (DOCX)

Differences in the expression levels of each miRNA for all the possible pairwise comparisons – PAA/PA, PAA/PP, PAA/AA, AA/PP, PA/PP, PA/AA. Fold differences are logarithmized and presented in an ascending order. In grey background are values higher than 1 and lower than −1. (DOCX)

MicroRNAs grouped according to their differential expression in microarrays and smallRNAseq. Differences in the expression for each miRNA in two different libraries were analyzed by ratios of expression. Fold differences were grouped according to their values (<0.5; >2 or between).The majority of miRNAs shows a fold differences between 0.5 and 2. (...

Conserved miRNAs annotated in S. alburnoides and S. pyrenaicus from the small RNA data and their presence in the microarray miRNA chip. (DOCX)

This article documents the addition of 171 microsatellite marker loci and 27 pairs of single nucleotide polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Bombus pauloensis, Cephalorhynchus heavisidii, Cercospora sojina, Harpyhaliaetus coronatus, Hordeum vulgare, Lachnol...

This article documents the addition of 171 microsatellite marker loci and 27 pairs of single nucleotide polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Bombus pauloensis, Cephalorhynchus heavisidii, Cercospora sojina, Harpyhaliaetus coronatus, Hordeum vulgare, Lachnol...

The genus Delphinus comprises two species and one subspecies: the short-beaked common dolphin, Delphinus delphis (Linnaeus, 1758), distributed in continental shelf and pelagic waters of the Atlantic and Pacific Oceans, the long-beaked common dolphin, D. capensis (Gray, 1828), distributed in nearshore tropical and temperate waters of the Pacific and...

Interplay between the complex geography, hydrogeomorphological history, past climatic changes, and anthropogenic pressures is likely responsible for the current diversity and species' distribution of freshwater fishes in the Iberian Peninsula. To further disentangle the evolutionary processes promoting the diversification of endemic Iberian Cyprini...

Identifying which factors shape the distribution of intraspecific genetic diversity is central in evolutionary and conservation biology. In the marine realm, the absence of obvious barriers to dispersal can make this task more difficult. Nevertheless, recent studies have provided valuable insights into which factors may be shaping genetic structure...

Annual fluctuation of oceanographic predictor values. Annual average values for (a) sea surface temperature, (b) chlorophyll concentration and (c) water turbidity for the different oceanographic regions. (PDF)

Mean pairwise difference between average values of a) sea surface temperature (SST), b) chlorophyll concentration (CHL) and c) water turbidity (KD490) obtained for each oceanographic region where short-beaked common dolphins were sampled for this study, with significant values of paired t-tests indicated in bold. (XLS)

Individual runs for the Bayesian analysis implemented in the program STRUCTURE with a burn-in phase of 4×105 and 4×106 MCMC replicates. The log-likelihood of the data (LnP(D)) for each run and an average across 10 runs for each K are shown. The K with the highest averaged maximum log-likelihood was considered the most likely number of clusters that...

Genetic data have been widely used to reconstruct the demographic history of populations, including the estimation of migration rates, divergence times and relative admixture contribution from different populations. Recently, increasing interest has been given to the ability of genetic data to distinguish alternative models. One of the issues that...

Figure S1-Distribution of S. alburnoides in Portugal and areas of sympatry with other Squalius species involved in the S. alburnoides polyploid reproductive complex. Figure S1-Distribution of S. alburnoides in Portugal and areas of sympatry with other Squalius species involved in the S. alburnoides polyploidy reproductive complex. Distribution of S...

Table S1. Primer sequences and references for each gene. Table S1. Primer sequences and references for each gene. Primer sequences and references for each gene amplified for this work..

Squalius alburnoides is an Iberian cyprinid fish resulting from an interspecific hybridisation between Squalius pyrenaicus females (P genome) and males of an unknown Anaecypris hispanica-like species (A genome). S. alburnoides is an allopolyploid hybridogenetic complex, which makes it a likely candidate for ploidy mosaicism occurrence, and is also...

Common dolphins (genus Delphinus) presently comprise two species and four subspecies: the short-beaked common dolphin, D. delphis delphis Linnaeus, 1758 distributed in temperate waters of the Atlantic and Pacific Oceans; D. delphis ponticus Barabash, 1935 restricted to the Black Sea; the long-beaked common dolphin, D. capensis capensis Gray, 1828 d...

The phylogenetic relationships of the genus Squalius are believed to be well established based on the mitochondrial cytochrome b gene. Here, we inferred the phylogenetic relationships of all species inhabiting most of the western Iberia river systems using a nuclear multi-locus approach and different species tree methods: concatenation and coalesce...

The rapid evolution of proteins involved in reproduction has been documented in several animal taxa. This is thought to be the result of forces involved in sexual selection and is expected to be particularly strong in promiscuous mating systems. In this study, a range of cetacean species were used to analyze the patterns of evolution in 2 reproduct...

Procellariiform seabirds are among the avian species with the fastest rates of extinction due to interactions with fisheries and introduction of alien predators to the breeding colonies. Conservation and management policies targeting populations of these species must include information on colony demographics and levels of isolation and genetic mar...

Understanding the population structure, population dynamics and processes that give rise to polyploidy and helps to maintain it is central to our knowledge of the evolution of asexual vertebrates. Previous studies revealed high genetic diversity and several reproductive pathways in the southern populations of the Squalius alburnoides hybrid complex...

The evolution of hybrid polyploid vertebrates, their viability and their perpetuation over evolutionary time have always been questions of great interest. However, little is known about the impact of hybridization and polyploidization on the regulatory networks that guarantee the appropriate quantitative and qualitative gene expression programme. T...

Freshwater species with small distribution ranges are vulnerable to extinction, especially when they exhibit small effective population sizes. Squalius torgalensis, Cyprinidae, is an endemic critically endangered fish species from southwestern Portugal, confined to the intermittent streams of the Mira drainage. Assessment of genetic diversity and p...

Isolation by distance analysis for the microsatellite dataset. Mantel test comparing minimal river geographic distance (km) with genetic differentiation (FST/(1 − FST)) among pairs of samples .

Isolation by distance analysis for the cyt b dataset. Mantel test comparing minimal river geographic distance (km) with genetic differentiation (FST/(1 − FST)) among pairs of samples

The impact of genetic drift in population divergence can be elucidated using replicated laboratory experiments. In the present study we used microsatellite loci to study the genetic variability and differentiation of laboratory populations of Drosophila subobscura derived from a common ancestral natural population after 49 generations in the labora...

Here we report the development and characterization of 17 anonymous nuclear markers for cetacean species. These markers were isolated from a genomic library built from a common dolphin (genus Delphinus), and tested across several families within Cetacea. An average of 1 SNP per 272bp was found in 10 anonymous markers screened for polymorphism withi...

Fish show an amazing variety of mechanisms of sex determination and modes of reproduction. Of these, simultaneous hermaphroditism has rarely been described. Here, we report a novel case of this phenomenon in adults of the Squalius alburnoides allopolyploid cyprinid complex. We found evidence for the simultaneous presence of mature male and female g...

A new method for the fast identification of the genomic composition of the cyprinid Squalius alburnoides is presented. The method is based on a length polymorphism detected in the beta-actin gene, which serves as the basis for the development of a semi-quantitative PCR.

The endangered minnow Iberochondrostoma almacai is an endemic Iberian cyprinid with a restricted and fragmented distribution. Here, we describe the genetic structure of the species and infer its demographic history from six nuclear-encoded microsatellite loci and mitochondrial cytochrome b sequences. Genetic diversity was low (microsatellite He<0.4...

Pseudochondrostoma duriense and Achondrostoma oligolepis are two Iberian endemic cyprinid fish species that occur in sympatry over most of their distribution range and that are suspected to hybridize in nature. Here, we employed a combination of mitochondrial and microsatellite markers to explore the extent of introgressive hybridization between th...

The recent allocation of the cyprinid complex Squalius alburnoides to the genus Iberocypris in the Handbook of European Freshwater Fishes is refuted by confirming evidence of a close relationship with the genus Squalius. Squalius alburnoides is here defined as a complex based on the existence of a hybrid form with distinct genome combinations and p...