Browsing by Author "Filipe, Ana Filipa"
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- Can invasive alien fish species act as effective hosts of native freshwater mussels (Unionidae) in Iberia?Publication . Teixeira, Amílcar; Dias, Ana Rita; Miranda, Fernando Jorge Veloso; Lopes-Lima, Manuel; Varandas, Simone; Froufe, Elsa; Filipe, Ana Filipa; Beja, Pedro; Sousa, RonaldoThe freshwater biodiversity of Mediterranean areas is severely threatened by several human activities, including habitat loss and fragmentation, river regulation, pollution, overexploitation, climate change and introduction of invasive alien species (IAS). These human disturbances drastically affect native fish and mussel populations and possibly conservation measures are needed to implement to revert major problems. Particularly at risk may be affiliate species such as freshwater mussels (Bivalvia, Unionoida) that have an obligatory parasitic phase of a short-term larval stage on fish host gills and fins. In Iberia, the identification of effective fish hosts for unionid species and the impact of IAS remain unclear. In this study, field and laboratorial studies were performed to assess the fish hosts for Anodonta anatina, Unio delphinus and Potomida littoralis. For in situ monitoring done in Douro basin (Northern Portugal), results showed an effective infestation for native (Luciobarbus bocagei, Squalius carolitertii, Squalius alburnoides and Pseudochondrostoma duriense) but also for non-native (Lepomis gibbosus, Alburnus alburnus, Gambusia holbrooki and Gobio lozanoi) fishes. The highest infestation rate and prevalence were observed for L. bocagei and S. carolitertii, but also for L. gibbosus. However, in laboratorial experiments significant differences were found. In fact, for U. delphinus and P. littoralis only native fishes (mainly endemic cyprinids) showed to be effective hosts, since viable juveniles were produced. A. anatina exhibited a more generalist behavior, with a wide range of native (endemic cyprinids of north and south Iberia) and non-native (Australoheros facetus, Oncorhynchus mykiss, Esox lucius, Phoxinus phoxinus, A. alburnus and G. lozanoi) fish host species. Overall, our results showed: 1) the importance of native fish species for the maintenance of a good conservation status of native unionids; 2) some invasive fish species can also function as hosts of A. anatina and 3) basic ecological data using field monitoring and laboratorial experiments are fundamental to design future conservation measures such as reproduction in captivity and propagation of threatened unionids.
- Effect of moisture on the characteristics of hazelnut kernel during storagePublication . Correia, Paula; Filipe, Ana Filipa; Ferrão, Ana Cristina; Ramalhosa, Elsa; Guiné, Raquel P.F.The organoleptic and nutritional quality of hazelnuts during storage can be greatly influenced by environment conditions. The aim of this study was to evaluate the effect of moisture on the physicochemical characteristics of hazelnut kernels when stored under controlled conditions of temperature (25 °C) and different relative humidities (RH) (57.6, 68.9, and 78.6%). To obtain these RH in the hazelnut storage atmospheres, the salts NaBr, KI, and NH4Cl were used, respectively. The following properties were evaluated: moisture, water activity (aw), color, texture, and fat oxidative stability, both in the initial sample and after 1, 2, 4 and 6 months of storage. The results showed that there was a progressive increase over time in moisture and water activity, with growth being most pronounced from 4 months onwards. Moreover, hazelnuts stored at a RH of 78.6%, at 6 months of storage were completely spoiled, making their evaluation of impossible. The hardness and friability of the hazelnuts decreased over the storage time, with the differences being more pronounced for the samples subjected to higher RH. In general, the color of the skin and core of the fruits showed little variation over the storage time for all parameters evaluated (L*, a*, b*) and for all RH conditions tested. The hazelnuts stored at a RH of 78,6% could only be preserved until the 4th month, but presented low oxidative stability, being comparable to the hazelnuts with 6 months at RH of 57,6%, meaning that with a reduction of about 10% of RH it is possible to increase the oxidative stability about 2 months. Thus, it can be concluded that high relative humidities lead to a lower conservation of the quality characteristics of hazelnuts. Moreover, during the 6 months of storage the color of the fruits was little affected for the different RH tested, however all the other evaluated characteristics presented significant alterations, namely the texture and the oxidative stability of the fats.
- Have the cake and eat it: optimizing nondestructive DNA metabarcoding of macroinvertebrate samples for freshwater biomonitoringPublication . Martins, Filipa M.S.; Galhardo, Mafalda; Filipe, Ana Filipa; Teixeira, Amílcar; Pinheiro, Paulo; Paupério, Joana; Alves, Paulo C.; Beja, PedroDNA metabarcoding can contribute to improving cost‐effectiveness and accuracy of biological assessments of aquatic ecosystems, but significant optimization and standardization efforts are still required to mainstream its application into biomonitoring programmes. In assessments based on freshwater macroinvertebrates, a key challenge is that DNA is often extracted from cleaned, sorted and homogenized bulk samples, which is time‐consuming and may be incompatible with sample preservation requirements of regulatory agencies. Here, we optimize and evaluate metabarcoding procedures based on DNA recovered from 96% ethanol used to preserve field samples and thus including potential PCR inhibitors and nontarget organisms. We sampled macroinvertebrates at five sites and subsampled the preservative ethanol at 1 to 14 days thereafter. DNA was extracted using column‐based enzymatic (TISSUE) or mechanic (SOIL) protocols, or with a new magnetic‐based enzymatic protocol (BEAD), and a 313‐bp COI fragment was amplified. Metabarcoding detected at least 200 macroinvertebrate taxa, including most taxa detected through morphology and for which there was a reference barcode. Better results were obtained with BEAD than SOIL or TISSUE, and with subsamples taken 7–14 than 1–7 days after sampling, in terms of DNA concentration and integrity, taxa diversity and matching between metabarcoding and morphology. Most variation in community composition was explained by differences among sites, with small but significant contributions of subsampling day and extraction method, and negligible contributions of extraction and PCR replication. Our methods enhance reliability of preservative ethanol as a potential source of DNA for macroinvertebrate metabarcoding, with a strong potential application in freshwater biomonitoring.
- Identifying freshwater priority areas for cross-taxa interactionsPublication . Nogueira, Joana Garrido; Lopes-Lima, Manuel; Beja, Pedro; Filipe, Ana Filipa; Froufe, Elsa; Gonçalves, Duarte V.; Silva, Janine P.; Sousa, Ronaldo; Teixeira, Amílcar; Varandas, Simone; Hermoso, VirgilioInformation about biotic interactions (e.g. competition, predation, parasitism, diseases, mutualism, allelopathy) is fundamental to better understand species distribution and abundance, ecosystem functioning, and ultimately guide conservation efforts. However, conservation planning often overlooks these important interactions. Here, we aim to demonstrate a new framework to include biotic interactions into Marxan. For that, we use freshwater mussels and fish interaction (as mussels rely on fishes to complete their life cycle) in the Douro River basin (Iberian Peninsula) as a case study. While doing that, we also test the importance of including biotic interactions into conservation planning exercises, by running spatial prioritisation analysis considering either: 1) only the target species (freshwater mussels); 2) freshwater mussels and their obligatory hosts (freshwater fishes); 3) freshwater mussels, fishes and their interactions.With this framework we found that biotic interactions tend to be under represented when the data on both freshwater mussels and fishes is not simultaneously included in the spatial prioritisation. Overall, the priority areas selected across all scenarios are mostly located in the western part of the Douro River basin, where most freshwater mussels and fishes still occur. Given the low overlap of priority areas identified here and the current Natura 2000 network, our approach may be useful for establishing (or enlarging) protected areas, especially in light of the EU Biodiversity Strategy for 2030. Also, this work may provide guidance for future habitat restoration and management of main threats to freshwater biodiversity.
- Improving freshwater biodiversity assessment: application of molecular tools on preservative ethanol from macroinvertebrate bulksPublication . Martins, Filipa; Galhardo, M.; Teixeira, Amílcar; Pinheiro, Paulo; Filipe, Ana Filipa; Alves, Paulo C.; Beja, PedroTraditional biodiversity assessment methods rely on morphological identification of bioindicators species such as benthic macroinvertebrates. This is the case of the Water Framework Directive (WFD), the key legislation for the protection and sustainable use of European freshwater resources (2000/60/EC). The possibility of identifying all life stages is particularly relevant, but it requires high levels of specialization and expertise and entail procedures that are expensive and time consuming. Also, the majority of these bioindicator taxa are in their larval stage, which imposes constrains on their morphological identification at lower taxonomic levels (e.g. genus or species). Advanced molecular tools, such as metabarcoding, allow the processing of complex multi-species assemblages at greater resolution (up to species level), by combining DNA taxonomy with high-throughput DNA sequencing. Here, we demonstrate the potential use of preservative ethanol from macroinvertebrate bulk and metabarcoding tools to assess macroinvertebrate communities and biological quality of surface water bodies. We examined etanol samples collected from five macroinvertebrate bulks of Tua subbasin (Douro) and morphologically identified organisms down to the lowest practical taxonomic level. Our results showed that 60% of the taxa found in ethanol were macroinvertebrate taxa targeted by WFD, while the remaining percentage was identified as e.g. Bacteria, Stramenopiles, terrestrial invertebrates, amphibians and fishes. In comparison with morphological identification, molecular methods detected in average 70% of the WFD families and 86% of the EPTO (Ephemeroptera, Plecoptera, Trichoptera and Odonata) families. Yet, the percentage of families matching between etanol metabarcoding and morphological identification increased when rare families (<5 individuals) were excluded (80 and 92.2% respectively) and was maximum on groups well represented in DNA reference databases, such as the order Trichoptera. Also, 113 species were successfully identified from ethanol samples but only half was detected morphologically. Ethanol metabarcoding can potentially be a faster, low-priced and more refined approach for assessing biological quality than traditional methods, by increasing taxonomic resolution and thus sensitivity of metrics to fine variations in stream Ecosystem functioning. Nevertheless, further validation is needed as well as expanding the existing DNA reference databases.
- Joint species distribution models unveil co-occurrences between freshwater mussels and their fish hostsPublication . Silva, Janine P.; Goncalves, Duarte Vasconcelos; Garcia-Raventós, Aina; Lopes-Lima, Manuel; Varandas, Simone; Froufe, Elsa; Teixeira, Amílcar; Hui, Francis K.C.; Filipe, Ana Filipa; Sousa, RonaldoFreshwater mussels are among the most threatened taxa in the world, partially due to the dependence on fish hosts to complete their life cycle. Knowledge about the role of environmental and biotic drivers in determining mussels' distribution is currently lacking. We aimed to assess the role of environmental and biotic drivers in determining the distribution of mussels and their fish hosts and to test if co-occurrence patterns were able to identify mussel-host interactions.Location: Douro River basin (Iberian Peninsula).Taxon: Four freshwater mussels and ten fish hosts.Methods: Joint species distribution models (JSDMs) were fitted to presence-absence records for mussel and fish assemblages. Variance partitioning among environmental variables and latent variables was conducted to determine the environmental versus biotic drivers of species distributions. Resulting matrices of pairwise species co-occurrences were used to identify co-occurrence patterns.Results: The distribution of host generalist mussel species was mainly explained by environmental variables related to climate and topography. The distribution of the host specialist Margaritifera margaritifera was mainly explained by land use. Strong positive correlations between mussels and the most relevant fish hosts were consistently captured by JSDMs. Co-occurrence patterns were mainly explained by residual factors, indicating the potential role of biotic interactions.Main Conclusions: Biotic interactions were expected to play an important role in explaining mussels' distribution, but the contribution of this factor was only meaningful for the host specialist M. margaritifera. Correlations between mussels and suitable hosts allowed to infer important fish hosts for freshwater mussels in the Douro River basin from distributional data alone. By finding similarities between the ecological requirements of co-occurring species, conservation measures can be oriented towards several species, which brings a more holistic perspective to the protection of biodiversity.
- Multiple introductions and first record of Phoxinus phoxinus in the Douro basin revealed by molecular dataPublication . Garcia-Raventós, Aina; Martins, Filipa; Magalhães, Maria Filomena; Ramião, José; Ferreira, Mário; Carona, Sara; Carvalho, Francisco; Sousa, Ronaldo; Froufe, Elsa; Teixeira, Amílcar; Varandas, Simone; Lopes-Lima, Manuel; Beja, Pedro; Filipe, Ana FilipaBiological invasions are a major threat to global biodiversity. Freshwater ecosystems are particularly vulnerable to anthropogenic introductions. This is the case of the minnows (Phoxinus genus), which have been used as a live bait since the 1900s. Until recently, Phoxinus phoxinus was thought to be distributed across most of the European watercourses, including the Iberian Peninsula (Ebro Basin and Cantabrian region). In 2007, these Iberian populations were identified as Phoxinus bigerri, including the traslocated populations in the Douro Basin near Burgos (Spain). Currently, little is known about the distribution of Phoxinus bigerri in the Douro Basin. During early summer 2017, we sampled 75 stream reaches using electrofishing across the Douro Basin (Portugal and Spain). We identified 267 individuals as the Pyrenean minnow P. bigerri, and we cliped and stored fin tissues from 153 individuals in 96% ethanol for DNA reference collection. Among those, 26 were barcoded for cytochrome oxidase I (COI) and cytochrome b (Cytb) genes to confirm the taxonomic identification at the species level. Results confirmed for the first time the presence of the common minnow P. phoxinus in the Douro basin, being five individuals collected in the western Douro (Portugal near Porto) closely related to populations from Adour Basin in France. The remaining 21 individuals from eastern Douro (Spain near Brugos) were identified as P. bigerri, as expected. Our study is the first record of P. phoxinus in the Douro Basin, which can be easly missidentified when using only morphologically identifications. The study highlights the value of using molecular approaches for detecting new introductions and tracking spread histories, which can be relevant for designing proper management plans. The P. phoxinus introduction in western Douro (Portugal) seem to be related with human activities (sport fisheries by Portuguese immigrants living in France) rather than geographical proximity.
- Multiple introductions and first record of Phoxinus phoxinus in the Douro basin revealed by molecular dataPublication . Garcia-Raventós, Aina; Martins, Filipa; Magalhães, Maria Filomena; Ramião, José; Ferreira, Mário; Carona, Sara; Carvalho, Francisco; Sousa, Ronaldo; Froufe, Elsa; Teixeira, Amílcar; Varandas, Simone; Lopes-Lima, Manuel; Beja, Pedro; Filipe, Ana FilipaBiological invasions are a major threat to global biodiversity. Freshwater ecosystems are particularly vulnerable to anthropogenic introductions, including in the Iberian Peninsula where the number of introduced species has been increasing during the last decades. This is the case of the minnows (Phoxinus genus), which have been used as a live bait since the 1900s. Until recently, Phoxinus phoxinus was thought to be distributed across most of the European watercourses, including the Iberian Peninsula in the Ebro Basin and some streams of the Cantabrian region. In 2007, these Iberian populations were identified as Phoxinus bigerri, including the traslocated populations in the Douro Basin near Burgos (Spain). Currently, little is known about the distribution of Phoxinus bigerri in the Douro Basin. During early summer 2017, we sampled 75 stream reaches using electrofishing across the Douro Basin (Portugal and Spain). We identified 267 individuals as the Pyrenean minnow P. bigerri, and we cliped and stored fin tissues from 153 individuals in 96% etanol for DNA reference collection. Among those, 26 were barcoded for cytochrome oxidase I (COI) and cytochrome b (Cytb) genes to confirm the taxonomic identification at the species level. Results confirmed, for the first time, the presence of the common minnow P. phoxinus in the Douro basin, being five individuals collected in the western Douro (Portugal near Porto) closely related to populations from Adour Basin in France. The remaining 21 individuals from eastern Douro (Spain near Brugos) were identified as P. bigerri, as expected. Our study is the first record of P. phoxinus in the Douro Basin, which can be easly missidentified when using only morphologically identifications. The study highlights the value of using molecular approaches for detecting new introductions and tracking spread histories, which can be relevant for designing proper management plans dealing with erradication, control or containemnt of invasive species. Importantly, the P. phoxinus introduction in western Douro river (Potugal) seem to be related with human activities (sport fisheries by Portuguese immigrants living in France) rather than geographical proximity.
- Multiple introductions and first record of Phoxinus phoxinus in the Douro Basin revealed by molecular dataPublication . Garcia-Raventós, Aina; Martins, Filipa; Magalhães, Maria Filomena; Ramião, José; Ferreira, Mário; Carona, Sara; Carvalho, Francisco; Sousa, Ronaldo; Froufe, Elsa; Teixeira, Amílcar; Varandas, Simone; Lopes-Lima, Manuel; Beja, Pedro; Filipe, Ana FilipaBiological invasions are a major threat to global biodiversity. Freshwater ecosystems are particularly vulnerable to anthropogenic introductions. This is the case of the minnows (Phoxinus genus), which have been used as a live bait since the 1900s. Until recently, Phoxinus phoxinus was thought to be distributed across most of the European watercourses, including the Iberian Peninsula (Ebro Basin and Cantabrian region). In 2007, these Iberian populations were identified as Phoxinus bigerri, including the traslocated populations in the Douro Basin near Burgos (Spain). Currently, little is known about the distribution of Phoxinus bigerri in the Douro Basin. During early summer 2017, we sampled 75 stream reaches using electrofishing across the Douro Basin (Portugal and Spain). We identified 267 individuals as the Pyrenean minnow P. bigerri, and we cliped and stored fin tissues from 153 individuals in 96% ethanol for DNA reference collection. Among those, 26 were barcoded for cytochrome oxidase I (COI) and cytochrome b (Cytb) genes to confirm the taxonomic identification at the species level. Results confirmed for the first time the presence of the common minnow P. phoxinus in the Douro basin, being five individuals collected in the western Douro (Portugal near Porto) closely related to populations from Adour Basin in France. The remaining 21 individuals from eastern Douro (Spain near Brugos) were identified as P. bigerri, as expected. Our study is the first record of P. phoxinus in the Douro Basin, which can be easly missidentified when using only morphologically identifications. The study highlights the value of using molecular approaches for detecting new introductions and tracking spread histories, which can be relevant for designing proper management plans. The P. phoxinus introduction in western Douro (Portugal) seem to be related with human activities (sport fisheries by Portuguese immigrants living in France) rather than geographical proximity.
- Origin and history of Phoxinus (Cyprinidae) introductions in the Douro Basin (Iberian Peninsula): an update inferred from genetic dataPublication . Garcia-Raventós, Aina; Martins, Filipa M.S.; Teixeira, Amílcar; Sousa, Ronaldo; Froufe, Elsa; Varandas, Simone; Lopes-Lima, Manuel; Beja, Pedro; Filipe, Ana FilipaThe number of non-native freshwater fishes in the Iberian Peninsula has been greatly increasing. In this study, individuals of the genus Phoxinus were detected in 18 out of 138 stream sites sampled across the Douro Basin in 2017 and 2018. A total of 26 individuals were barcoded using partial cytochrome c oxidase subunit I (COI) and cytochrome b (cytb) genes for species identification and determination of geographical origin. Molecular data provided the first record of a second Phoxinus species in western Douro (Portugal, Iberian Peninsula), with haplotypes closely matching those found in the Charente River (southern France). This species is suspected to be a recent introduction associated with the use of minnows as live bait by freshwater anglers, which was facilitated by human movements between France and Portugal. Individuals from watercourses in eastern Douro (Spain) were genetically assigned to Phoxinus bigerri, an introduced species previously known for that region, which confirms reports of introduction events from Ebro to Douro Basin probably also related to freshwater angling and facilitated by geographic proximity. The potential ecological impacts of this genus in the region are unknown and need further investigation.