Raquel Xavier
Universidade do Porto, Age, Post-Doc
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Research Interests: Zoology, Biology, Ecology, Habitat, Root-Mean Square Error, and 3 moreLacertidae, Lizard, and Microbiome
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Global warming is challenging wild species in land and water. In the intertidal zone, species are already living at their thermal limits, being vulnerable even to small increases in maximum habitat temperatures. Knowledge of the... more
Global warming is challenging wild species in land and water. In the intertidal zone, species are already living at their thermal limits, being vulnerable even to small increases in maximum habitat temperatures. Knowledge of the mechanisms by which many intertidal zone species cope with elevated temperatures is limited. We analysed the molecular thermal stress response of the limpet Patella vulgata under slight and frequent (one-day), and extreme and rare (three-day) warming events. Using RNA-seq to assess differential gene expression among treatments, differing molecular responses were obtained in the two treatments, with more changes in gene expression after the three-day event; with one-third of the differentially expressed transcripts being down-regulated. However, across treatments we observed shifts in gene expression for common aspects of the heat stress response including intra-cellular communication, protein chaperoning, proteolysis and cell cycle arrest. Of the 71,675 transcripts obtained, only 259 were differentially expressed after both heating events. From these, 218 defined the core group (i.e. genes induced by thermal stress with similar expression patterns irrespective of the magnitude of the warming event). The core group was composed of already well-studied genes in heat stress responses in intertidal organisms (e.g. heat shock proteins), but also genes from less explored metabolic pathways, e.g. the ubiquitin system, which were also fundamental regardless of the magnitude of the imposed warming. Moreover, we have also identified 41 signaling genes (i.e. a set of genes responding to both events and with expression patterns specific to the intensity of thermal stress), principally including genes involved in the maintenance of extracellular structure that have previously not been identified as part of the response to thermal stress in intertidal zone organisms. These signaling genes will be useful heat stress molecular biomarkers for monitoring heat stress in natural populations.
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<p>Values of nodes correspond to bootstrap support and Bayesian posterior probability, respectively. The three major clades corresponding to <i>Gyrodactylus</i> morphospecies are surrounded by a dotted line. Cryptic... more
<p>Values of nodes correspond to bootstrap support and Bayesian posterior probability, respectively. The three major clades corresponding to <i>Gyrodactylus</i> morphospecies are surrounded by a dotted line. Cryptic lineages within these clades are signaled with black bars.</p
Research Interests: Biology, Ecology, Biological Sciences, Maximum Likelihood, Parasite, and 3 moreCOII, PLoS one, and Host Range
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ABSTRACT The caprellid Caprella scaura, native to the western Indian Ocean, is one striking example of a successful invader. It was first recorded in the Iberian Peninsula in Gerona (north-eastern coast of Spain), in 2005, and has... more
ABSTRACT The caprellid Caprella scaura, native to the western Indian Ocean, is one striking example of a successful invader. It was first recorded in the Iberian Peninsula in Gerona (north-eastern coast of Spain), in 2005, and has recently been reported throughout the Mediterranean and Atlantic coasts of this region. The most likely vector of introduction and distribution is within the hull-fouling community on recreational craft. However, beyond the dates of detection, the introduction history of C. scaura remains unclear. Direct sequencing of mitochondrial DNA (cytochrome c oxidase subunit I) was used to compare genetic composition in native and introduced populations in order to infer the invasion history of this species. In addition, 18S rDNA sequences were used to resolve phylogenetic relationships within this species and with the morphologically closest species Caprella californica and Caprella scauroides. The high genetic divergence and population subdivision found between non-native Iberian populations together with a high level of genetic diversity in some populations indicate multiple geographical sources and introduction points for this caprellid. Our data suggest that Iberian populations may derive from at least two sources: (1) Pacific Australian, and (2) Indian Ocean, either directly, or, more likely, through stepping-stone events from central Mediterranean population(s). Atlantic Iberian populations seem to be the most recently established populations. On the other hand, this is the first study providing molecular evidence confirming C. scaura, C. californica and C. scauroides as distinct species. It also provides strong molecular evidence that C. scaura typica and C. scaura scaura correspond to the same subspecies, and the Japanese C. scaura diceros and the Chilean C. scaura spinirostris could merit specific rank.
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Fish-associated microorganisms are known to be affected by the environment and other external factors, such as microbial transfer between interacting partners. One of the most iconic mutualistic interactions on coral reefs is the cleaning... more
Fish-associated microorganisms are known to be affected by the environment and other external factors, such as microbial transfer between interacting partners. One of the most iconic mutualistic interactions on coral reefs is the cleaning interactions between cleaner fishes and their clients, during which direct physical contact occurs. Here, we characterized the skin bacteria of the Caribbean cleaner sharknose goby, Elacatinus evelynae, in four coral reefs of the US Virgin Islands using sequencing of the V4 region of the 16S rRNA gene. We specifically tested the relationship between gobies' level of interaction with clients and skin microbiota diversity and composition. Our results showed differences in microbial alpha- and beta-diversity in the skin of gobies from different reef habitats and high inter-individual variation in microbiota diversity and structure. Overall, the results showed that fish-to-fish direct contact and specifically, access to a diverse clientele, influences the bacterial diversity and structure of cleaner gobies' skin. Because of their frequent contact with clients, and therefore, high potential for microbial exchange, cleaner fish may serve as models in future studies aiming to understand the role of social microbial transfer in reef fish communities.
Research Interests: Microbiology, Microbial Ecology, Biology, Ecology, Medicine, and 4 moreCoral Reef, Microbiome, Coral Reef Fish, and Reef
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The activity of the microbiome of fish mucosae provides functions related to immune response, digestion, or metabolism. Several biotic and abiotic factors help maintaining microbial homeostasis, with disruptions leading to dysbiosis.... more
The activity of the microbiome of fish mucosae provides functions related to immune response, digestion, or metabolism. Several biotic and abiotic factors help maintaining microbial homeostasis, with disruptions leading to dysbiosis. Diseases and antibiotic administration are known to cause dysbiosis in farmed fish. Pathogen infections greatly affect the production of gilthead seabream, and antibiotic treatment is still frequently required. Here, we employed a 16S rRNA high-throughput metataxonomics approach to characterize changes in the gut, skin, and gill microbiomes occurring due to infection with Photobacterium damselae subsp. piscicida and subsequent antibiotic treatment with oxytetracycline (OTC), as well as during recovery. Although microbiota response differed between studied tissues, overall changes in composition, diversity, structure, and predicted function were observed in all mucosae. The skin and gill microbiomes of diseased fish became largely dominated by taxa that ...
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Natural history museum collections hold extremely rare, extinct species often described from a single known specimen. On occasions, rediscoveries open new opportunities to understand selective forces acting on phenotypic traits. Recent... more
Natural history museum collections hold extremely rare, extinct species often described from a single known specimen. On occasions, rediscoveries open new opportunities to understand selective forces acting on phenotypic traits. Recent rediscovery of few individuals of Bocourt´s Terrific Skink Phoboscincus bocourti, from a small and remote islet in New Caledonia allowed to genetically identify a species of land crab in its diet. To explore this further, we CT- and MRI-scanned the head of the holotype, the only preserved specimen dated to about 1870, segmented the adductor muscles of the jaw and bones, and estimated bite force through biomechanical models. These data were compared with those gathered for 332 specimens belonging to 44 other skink species. Thereafter we recorded the maximum force needed to generate mechanical failure of the exoskeleton of a crab specimen. The bite force is greater than the prey hardness, suggesting that predation on hard-shelled crabs may be an importa...
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Host‐associated microbial communities are essential for host homeostasis and health. Most research on microbiotas is restricted to model host species and, since microbe–host dynamics can be species‐specific, we still lack a good... more
Host‐associated microbial communities are essential for host homeostasis and health. Most research on microbiotas is restricted to model host species and, since microbe–host dynamics can be species‐specific, we still lack a good taxonomic, ecological and evolutionary understanding of microbiotas in wild hosts, including birds. Given the diversity of avian host species, their habitat specializations, ecological requirements and life‐history traits, we need to characterize the dynamics of microbiotas from taxonomically diverse bird species. Here we describe cloaca and feather microbiotas of a population of common waxbills Estrilda astrild living in a large open‐air mesocosm, and compare it to microbiotas sampled one year later for a subset of this population, and to the microbiotas of free‐ranging waxbills from the same region. We found clear differences between microbiota from the cloaca, which contained some taxa that may be found in seeds, and from feathers, which contained some ta...
Research Interests: Zoology, Biology, Ecology, Avian Biology, Biological Sciences, and 4 morePopulation, Feather, Cloaca, and Taxon
Omobranchus punctatus is native to the Indo-Pacific region and invasive in the Atlantic region, currently being considered one of the most widely distributed blenny species. However, recent molecular studies indicated that O. punctatus is... more
Omobranchus punctatus is native to the Indo-Pacific region and invasive in the Atlantic region, currently being considered one of the most widely distributed blenny species. However, recent molecular studies indicated that O. punctatus is a complex of species, with three divergent mtDNA lineages identified to date, stressing the need for a taxonomic revision. In this study, we used an integrative approach, combining morphological and genetic data, to shed light on the taxonomy and distribution of O. punctatus. Moreover, we provide the first genetic records of introduced populations in Brazil and discuss the introduction pattern of this species in this region. Morphological data shows that O. punctatus consists of at least five distinct and geographically restricted species: O. punctatus sensu stricto, O. dispar, O. sewalli, O. cf. kochi, and O. cf. japonicus. Species delimitation analyses performed using the mtDNA data available confirmed that O. punctatus sensu stricto, O. dispar a...
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Assessing the importance of intrinsic and extrinsic factors that shape the spatial distribution of genetic diversity of symbionts has been a topic of debate for decades. While host-mediated dispersal is an important driver of gene flow in... more
Assessing the importance of intrinsic and extrinsic factors that shape the spatial distribution of genetic diversity of symbionts has been a topic of debate for decades. While host-mediated dispersal is an important driver of gene flow in many terrestrial metazoan symbionts, few studies have identified the drivers of symbiont genetic differentiation in the marine realm, where habitats are comparatively more homogeneous and long-distance dispersal is common. In the present study, we perform a meta-analysis of existing studies examining symbiont spatial genetic diversity to determine which symbiont- and host-related traits shape the patterns of genetic differentiation of metazoan symbionts, while also considering technical aspects of each study. Specifically, we wanted to assess the influence of biological traits and/ or technical aspects in (1) detecting genetic differentiation in marine symbionts, and (2) shaping the minimum spatial scale at which genetic differentiation was detecte...
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Fish-associated microorganisms are known to be affected by the environment and other external factors, such as microbial transfer between interacting partners. One of the most iconic mutualistic interactions on coral reefs is the cleaning... more
Fish-associated microorganisms are known to be affected by the environment and other external factors, such as microbial transfer between interacting partners. One of the most iconic mutualistic interactions on coral reefs is the cleaning interactions between cleaner fishes and their clients, during which direct physical contact occurs. Here, we characterized the skin bacteria of the Caribbean cleaner sharknose goby, Elacatinus evelynae, in four coral reefs of the US Virgin Islands using sequencing of the V4 region of the 16S rRNA gene. We specifically tested the relationship between gobies' level of interaction with clients and skin microbiota diversity and composition. Our results showed differences in microbial alpha- and beta-diversity in the skin of gobies from different reef habitats and high inter-individual variation in microbiota diversity and structure. Overall, the results showed that fish-to-fish direct contact and specifically, access to a diverse clientele, influences the bacterial diversity and structure of cleaner gobies' skin. Because of their frequent contact with clients, and therefore, high potential for microbial exchange, cleaner fish may serve as models in future studies aiming to understand the role of social microbial transfer in reef fish communities.
Research Interests: Microbiology, Microbial Ecology, Biology, Ecology, Medicine, and 4 moreCoral Reef, Microbiome, Coral Reef Fish, and Reef
Additional file 6.
Additional file 7 PCoA plot computed using Bray-Curtis distances for water, skin and gills microbiota of the seabass Dicentrarchus labrax (A) and the seabream Sparus aurata (B) (n = 60 per species x age group for tissues; n = 10 per... more
Additional file 7 PCoA plot computed using Bray-Curtis distances for water, skin and gills microbiota of the seabass Dicentrarchus labrax (A) and the seabream Sparus aurata (B) (n = 60 per species x age group for tissues; n = 10 per species x age group for water). Each dot represents a microbiome sample and is coloured by tissue/origin (skin, gill and water).
<p>Values of nodes correspond to bootstrap support and Bayesian posterior probability, respectively. The three major clades corresponding to <i>Gyrodactylus</i> morphospecies are surrounded by a dotted line. Cryptic... more
<p>Values of nodes correspond to bootstrap support and Bayesian posterior probability, respectively. The three major clades corresponding to <i>Gyrodactylus</i> morphospecies are surrounded by a dotted line. Cryptic lineages within these clades are signaled with black bars.</p
Research Interests: Biology, Ecology, Biological Sciences, Maximum Likelihood, Parasite, and 3 moreCOII, PLoS one, and Host Range
The development of an inventory of earth’s biodiversity—identifying and naming all living species—is a central tenet of biological science. For over 250 years, the Linnean system has been the predominant naming approach, with new species... more
The development of an inventory of earth’s biodiversity—identifying and naming all living species—is a central tenet of biological science. For over 250 years, the Linnean system has been the predominant naming approach, with new species designated by a unique Latinized binomina following rules laid out by the International Code of Zoological Nomenclature (Anonymous 1999; “the Code” below) for animal taxa, while the International Code of Nomenclature for algae, fungi and plants (Turland et al. 2018) is the set of rules dealing with formal botanical names.
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Background Host-gut microbiota interactions are complex and can have a profound impact on the ecology and evolution of both counterparts. Several host traits such as systematics, diet and social behavior, and external factors such as prey... more
Background Host-gut microbiota interactions are complex and can have a profound impact on the ecology and evolution of both counterparts. Several host traits such as systematics, diet and social behavior, and external factors such as prey availability and local environment are known to influence the composition and diversity of the gut microbiota. Methods In this study, we investigate the influence of systematics, sex, host size, and locality/habitat on gut microbiota diversity in five lizard species from two different sites in Portugal: Podarcis bocagei and Podarcis lusitanicus, living in syntopy in a rural area in northern Portugal (Moledo); the invasive Podarcis siculus and the native Podarcis virescens, living in sympatry in an urbanized environment (Lisbon); and the invasive Teira dugesii also living in an urban area (Lisbon). We also infer the potential microbial transmission occurring between species living in sympatry and syntopy. To achieve these goals, we use a metabarcodi...
Several freshwater crayfish species, including Procambarus clarkii, are both ecologically important and commercially important benthic macroinvertebrates, remarkable for their potential to adapt and reproduce but also for their unique... more
Several freshwater crayfish species, including Procambarus clarkii, are both ecologically important and commercially important benthic macroinvertebrates, remarkable for their potential to adapt and reproduce but also for their unique abilities to face distinct abiotic and biotic environments and become successful invaders. While much work has been done to study crayfish introductions, less focus has been given to how crayfish cope with pollution and other environmental stressors, in terms of physiological responses, and whether crayfish responses can be used to assess the effective state of their living environment. Here, we used a mixed approach combining laboratory experiments with field data to validate the use of hemolymph glucose as a relevant biomarker of red swamp crayfish (Procambarus clarkii) stress response. Three meaningful sampling locations were chosen across southern Portugal that are representative of different environments where crayfish live and are frequently captured for human consumption but also correspond to different pollution levels. To reference field measurements of glucose levels, we performed two lab-based experiments: (a) crayfish were exposed to different levels of stress (stress challenge) and (b) crawfish were exposed to a maze dispersal test, with or without water. Crayfish glucose levels were responsive to induced stress but were not correlated with dispersal efforts. Wild crayfish’s body condition and stress levels responded differently to environmental conditions, with more challenged individuals showing higher glycemia levels but similar body condition. The glucose levels of the more stressed wild crayfish were visually similar to lab-based crayfish subjected to the higher stress levels (electric shocks), while the levels of glucose of crayfish at the less polluted site corresponded to those measured before the start of the challenge (baseline). The maintenance of high levels of glycemia in crayfish inhabiting more challenging habitats is revealing of their higher energetic demand state. Since P. clarkii ia globally distributed and easily sampled invasive species, quantifying its hemolymph glucose levels can be a particularly useful proxy for assessing environmental quality.
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Additional file 4.
The snowflake coral Carijoa riisei is one of the most invasive and successfully adapting species in the coastal marine environment. This species can disperse through ballast waters or fouling on the hull of ships, which allows it to... more
The snowflake coral Carijoa riisei is one of the most invasive and successfully adapting species in the coastal marine environment. This species can disperse through ballast waters or fouling on the hull of ships, which allows it to expand very quickly to areas where it is not native. Recently C. riisei was identified in the Porto Grande Bay in São Vicente island in Cabo Verde Islands. We analysed mitochondrial and nuclear DNA sequences from specimens collected at this locality to determine the potential origin of this invasion. Lack of genetic variation in both mitochondrial and nuclear genes suggest a very recent invasion (bottleneck effect) but did not permit to establish its origin with total confidence.
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DNA metabarcoding is a fast and simple alternative to traditional microscopy methods, which have been the main tool for identification of prey in dietary studies of lizards. In this study, we applied a metabarcoding approach based on COI... more
DNA metabarcoding is a fast and simple alternative to traditional microscopy methods, which have been the main tool for identification of prey in dietary studies of lizards. In this study, we applied a metabarcoding approach based on COI and 16S rRNA amplicons to assess diet partitioning and feeding strategies in three syntopic lizards from Taza, Morocco: Scelarcis perspicillata chabanaudi, Scelarcis perspicillata pellegrini and Podarcis vaucheri. In order to avoid competition, these lizards are expected to consume different prey species because they occupy distinct trophic niches, use different foraging strategies and express different dorsal pigmentation patterns. Given the spotted pattern of S. p. chabanaudi, we hypothesize a sit-and-wait foraging strategy with a less diverse diet and a higher consumption of mobile prey relative to the striped S. p. pellegrini and P. vaucheri which, as potential active foragers, are expected to have a higher diet diversity. Previous diet assessme...
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Supplementary material 5 from: Cabezas MP, Ros M, Santos AM, Martínez-Laiz G, Xavier R, Montelli L, Hoffman R, Fersi A, Dauvin JC, Guerra-García JM (2019) Unravelling the origin and introduction pattern of the tropical species Paracaprella pusilla Mayer, 1890 (Crustacea, Amphipoda, Caprellidae) i...more
The genus Quedenfeldtia is composed of two species, Q. moerens and Q. trachyblepharus, both endemic to the Atlas Mountains region of Morocco. Previous studies recovered two main genetic lineages within each Quedenfeldtia species, although... more
The genus Quedenfeldtia is composed of two species, Q. moerens and Q. trachyblepharus, both endemic to the Atlas Mountains region of Morocco. Previous studies recovered two main genetic lineages within each Quedenfeldtia species, although sampling did not cover a substantial portion of their known distribution. In this study we collected individuals from previously unsampled localities of Quedenfeldtia and carried out genetic analyses in order to assess the range of previously identified lineages and the occurrence of additional lineages. Phylogenetic reconstruction based on both mitochondrial (12S and ND4 + tRNA) and nuclear (MC1R) markers revealed that while the new individuals of Q. moerens belong to previously described lineages, two new lineages of Q. trachyblepharus were uncovered from the northern and southern parts of the range. Genetic divergence of these new lineages (8-9% ND4 + tRNA p-distance) was higher than values observed between other lizard sister species. In the fu...
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Bayesian inference analysis of epicellular Goussia spp. and the unknown apicomplexan clade based on sequences generated in the present study plus previously public sequences retrieved from GenBank. The newly generated sequences are... more
Bayesian inference analysis of epicellular Goussia spp. and the unknown apicomplexan clade based on sequences generated in the present study plus previously public sequences retrieved from GenBank. The newly generated sequences are depicted in bold. Host species and infected organs or tissues were detailed for all aquatic hosts. (EPS 3990 kb)
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Bayesian inference analysis of dispersed and nodular Goussia, Caryospora-, Calyptospora- and Eimeria-like sequences generated in the present study, plus previously published or public sequences retrieved from GenBank. Node support values... more
Bayesian inference analysis of dispersed and nodular Goussia, Caryospora-, Calyptospora- and Eimeria-like sequences generated in the present study, plus previously published or public sequences retrieved from GenBank. Node support values correspond to posterior probabilities and consensus support (%) obtained from Bayesian inference and Maximum Likelihood analyses, respectively. The major phylogenetic groups infecting aquatic hosts are highlighted according to the legend, and the newly generated sequences are indicated in bold. Host species and infected organs or tissues were detailed for all aquatic hosts. (EPS 3133 kb)
Additional file 3 Mean values and standard deviations of Faith's phylogenetic (PD), ACE and Fisher alpha-diversity estimates plotted for the early juveniles/juveniles (green), late juveniles (yellow) and mature adults (orange) of the... more
Additional file 3 Mean values and standard deviations of Faith's phylogenetic (PD), ACE and Fisher alpha-diversity estimates plotted for the early juveniles/juveniles (green), late juveniles (yellow) and mature adults (orange) of the seabass Dicentrarchus labrax (A) and seabream Sparus aurata (B) (n = 60 per species x age group x tissue). Pairwise comparisons of alpha-diversity were assessed using Linear Mixed Effect models with age groups as a fixed factor and sampling date as a random factor. Statistically significant differences are denoted with an asterisk and non statistically significant differences are denoted with "ns".
Additional file 5.
Tissue samples from wildlife from South Africa were opportunistically collected and screened for haemoprotozoan parasites using nonspecific PCR primers. Samples of 127 individuals were tested, comprising over 50 different species.... more
Tissue samples from wildlife from South Africa were opportunistically collected and screened for haemoprotozoan parasites using nonspecific PCR primers. Samples of 127 individuals were tested, comprising over 50 different species. Haemogregarines were the most commonly identified parasites, but sarcocystids and piroplasmids were also detected. Phylogenetic analyses estimated from the 18S rDNA marker highlighted the occurrence of several novel parasite forms and the detection of parasites in novel hosts. Phylogenetic relationships, which have been recently reviewed, appear to be much more complex than previously considered. Our study highlights the high diversity of parasites circulating in wildlife in this biodiverse region, and the need for further studies to resolve taxonomic issues.