Browsing by Author "Seabra, Sofia G."
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- 4Pipe4 – A 454 data analysis pipeline for SNP detection in datasets with no reference sequence or strain informationPublication . Pina-Martins, Francisco; Vieira, Bruno M.; Seabra, Sofia G.; Batista, Dora; Paulo, Octávio S.Next-generation sequencing datasets are becoming more frequent, and their use in population studies is becoming widespread. For non-model species, without a reference genome, it is possible from a panel of individuals to identify a set of SNPs that can be used for further population genotyping. However the lack of a reference genome to which the sequenced data could be compared makes the finding of SNPs more troublesome. Additionally when the data sources (strains) are not identified (e.g. in datasets of pooled individuals), the problem of finding reliable variation in these datasets can become much more difficult due to the lack of specialized software for this specific task.
- Assessing genotype-phenotype associations in three dorsal colour morphs in the meadow spittlebug Philaenus spumarius (L.) (Hemiptera: Aphrophoridae) using genomic and transcriptomic resourcesPublication . Rodrigues, Ana S. B.; Silva, Sara Ema; Pina-Martins; Loureiro, João; Castro, Mariana; Gharbi, Karim; Johnson, Kevin P.; Dietrich, Christopher H.; Borges, Paulo A. V.; Quartau, J. A.; Jiggins, Chris D.; Paulo, Octávio S.; Seabra, Sofia G.Colour polymorphisms are common among animal species. When combined with genetic and ecological data, these polymorphisms can be excellent systems in which to understand adaptation and the molecular changes underlying phenotypic evolution. The meadow spittlebug, Philaenus spumarius (L.) (Hemiptera, Aphrophoridae), a widespread insect species in the Holarctic region, exhibits a striking dorsal colour/pattern balanced polymorphism. Although experimental crosses have revealed the Mendelian inheritance of this trait, its genetic basis remains unknown. In this study we aimed to identify candidate genomic regions associated with the colour balanced polymorphism in this species.
- Assessing genotype-phenotype associations in three dorsal colour morphs in the meadow spittlebug Philaenus spumarius (L.) (Hemiptera: Aphrophoridae) using genomic and transcriptomic resourcesPublication . Rodrigues, Ana S. B.; Silva, Sara E.; Pina-Martins, Francisco; Loureiro, João; Castro, Mariana; Gharbi, Karim; Johnson, Kevin P.; Dietrich, Christopher H.; Borges, P.A.V.; Quartau, J. A.; Jiggins, Chris D.; Paulo, Octávio S.; Seabra, Sofia G.Colour polymorphisms are common among animal species. When combined with genetic and ecological data, these polymorphisms can be excellent systems in which to understand adaptation and the molecular changes underlying phenotypic evolution. The meadow spittlebug, Philaenus spumarius (L.) (Hemiptera, Aphrophoridae), a widespread insect species in the Holarctic region, exhibits a striking dorsal colour/pattern balanced polymorphism. Although experimental crosses have revealed the Mendelian inheritance of this trait, its genetic basis remains unknown. In this study we aimed to identify candidate genomic regions associated with the colour balanced polymorphism in this species.
- Correction to: Assessing genotype-phenotype associations in three dorsal colour morphs in the meadow spittlebug Philaenus spumarius (L.) (Hemiptera: Aphrophoridae) using genomic and transcriptomic resourcesPublication . Rodrigues, Ana S. B.; Silva, Sara Ema; Pina Martins, Francisco; Loureiro, João; Castro, Mariana; Gharbi, Karim; Johnson, Kevin P.; Dietrich, Christopher H.; Borges, Paulo .A.V.; Quartau, José A.; Jiggins, Chris D.; Paulo, Octávio S.; Seabra, Sofia G.Following publication of the original article [1], it has been brought to the authors’ attention that in their paper (Rodrigues et al. 2016) they reported the genome size based on 2C values (diploid genome) when it is more common to present it as 1C value. This has led to a misinterpretation of the percentage of the genome that was sequenced. However, none of the remaining analyses were affected.
- Correction to: Assessing genotype-phenotype associations in three dorsal colour morphs in the meadow spittlebug Philaenus spumarius (L.) (Hemiptera: Aphrophoridae) using genomic and transcriptomic resourcesPublication . Rodrigues, Ana S. B.; Silva, Sara Ema; Pina-Martins; Loureiro, João; Castro, Mariana; Gharbi, Karim; Johnson, Kevin P.; Dietrich, Christopher H.; Borges, Paulo A. V.; Quartau, José A.; Jiggins, Chris D.; Paulo, Octávio S.; Seabra, Sofia G.Following publication of the original article [1], it has been brought to the authors' attention that in their paper (Rodrigues et al. 2016) they reported the genome size based on 2C values (diploid genome) when it is more common to present it as 1C value.
- Genomic signatures of introgression between commercial and native bumblebees, Bombus terrestris, in Western Iberian Peninsula - implications for conservation and trade regulationPublication . Seabra, Sofia G.; Silva, Sara E.; Nunes, Vera L.; Sousa, Vitor C.; Martins, Joana; Marabuto, Eduardo; Rodrigues, Ana S.B.; Pina-Martins, Francisco; Laurentino, Telma G.; Rebelo, Maria Teresa; Figueiredo, Elisabete; Paulo, Octávio S.Human‐mediated introductions of species may have profound impacts on native ecosystems. One potential impact with largely unforeseen consequences is the potential admixture of introduced with autochthonous species through hybridization. Throughout the world, bumblebees have been deliberately introduced for crop pollination with known negative impacts on native pollinators. Given the likely allochthonous origin of commercial bumblebees used in Portugal (subspecies Bombus terrestris terrestris and B. t. dalmatinus), our aim was to assess their putative introgression with the native Iberian subspecies B. terrestris lusitanicus. We analysed one mitochondrial gene, cytochrome c oxidase subunit I (COX1) and genomic data involving thousands of genome‐wide restriction‐site‐associated DNA markers (RAD‐seq). In the mitochondrial COX1 analyses, we detected one relatively common haplotype in commercial bumblebees, also present in wild samples collected nearby the greenhouses where the commercial hives are used. In the RAD‐seq analysis, we found a clear genetic differentiation between native and commercial lineages. Furthermore, we detected candidate hybrids in the wild, as well as putatively escaped commercial bumblebees, some of which being potentially fertile males. Although we cannot assess directly the fitness effects of introgressed alleles, there is a risk of maladaptive allele introgression to the local bumblebee subspecies, which can negatively impact autochthon populations. One immediate recommendation to farmers is for the proper disposal of hive boxes, after their use in greenhouses, so as to minimize the risk of escapees contaminating native populations. On the other hand, the feasibility of using local subspecies B. t. lusitanicus, preferably with local production, should be evaluated
- Genomic signatures of introgression between commercial and native bumblebees, Bombus terrestris, in western Iberian Peninsula—Implications for conservation and trade regulationPublication . Seabra, Sofia G.; Silva, Sara E.; Nunes, Vera L.; Sousa, Vitor C; Martins, Joana; Marabuto, Eduardo; Rodrigues, Ana S. B.; Pina Martins, Francisco; Laurentino, Telma G.; Rebelo, Maria Teresa; Figueiredo, Elisabete; Paulo, Octávio S.Human‐mediated introductions of species may have profound impacts on native eco ‐systems. One potential impact with largely unforeseen consequences is the potential admixture of introduced with autochthonous species through hybridization. Throughout the world, bumblebees have been deliberately introduced for crop pol ‐lination with known negative impacts on native pollinators. Given the likely alloch ‐thonous origin of commercial bumblebees used in Portugal (subspecies Bombus terrestris terrestris and B. t. dalmatinus), our aim was to assess their putative introgres‐sion with the native Iberian subspecies B. terrestris lusitanicus. We analysed one mito ‐chondrial gene, cytochrome c oxidase subunit I (COX1) and genomic data involving thousands of genome‐wide restriction‐site‐associated DNA markers (RAD‐seq). In the mitochondrial COX1 analyses, we detected one relatively common haplotype in commercial bumblebees, also present in wild samples collected nearby the green ‐houses where the commercial hives are used. In the RAD‐seq analysis, we found a clear genetic differentiation between native and commercial lineages. Furthermore,we detected candidate hybrids in the wild, as well as putatively escaped commercialbumblebees, some of which being potentially fertile males. Although we cannot as ‐sess directly the fitness effects of introgressed alleles, there is a risk of maladaptive allele introgression to the local bumblebee subspecies, which can negatively impact autochthon populations. One immediate recommendation to farmers is for the proper disposal of hive boxes, after their use in greenhouses, so as to minimize the risk of escapees contaminating native populations. On the other hand, the feasibilityof using local subspecies B. t. lusitanicus, preferably with local production, should be evaluated.
- Integrative analysis reveals the divergence and speciation between sister Sooty Copper butterflies Lycaena bleusei and L. tityrusPublication . Marabuto, Eduardo; Nunes, Miguel S.; Martins, Renata; Gonçalves Mendes, Raquel; Moreira-Pinhal, Tatiana C.; Raimundo, João; Seabra, Sofia G.; Paulo, Octávio S.The comparison of closely related taxa is cornerstone in biology, as understanding mechanisms leading up to differentiation in relation to extant shared characters are powerful tools in interpreting the evolutionary process. Hotspots of biodiversity such as the west-Mediterranean, where many lineages meet are ideal grounds to study these processes. We set to explore the interesting example of Sooty Copper butterflies: widespread Eurasian Lycaena tityrus (Poda, 1761) comes into contact in Iberia with closely related and local endemic, L. bleusei (Oberthür, 1884), which hasn’t always been considered a distinct species. An integrative analysis was designed, combining the use of extensive molecular data (five genes), geometric morphometrics analyses, verified and up-to-date distribution data, and environmental niche modelling, aimed at deciphering their true relationship, their placement within European Lycaena and trace their evolutionary history. We revealed several levels of differentiation: L. bleusei and L. tityrus appear to be reciprocally monophyletic independent gene-pools, distinct in all genes analysed, having mutually diverged 4.8 Ma ago. L. tityrus but not L. bleusei, further displays a genetic structure compatible with several glacial refugia, where populations assignable to infraspecific taxa surface. Conversely, L. bleusei shows a loss in mtDNA diversity in relation to nuDNA. Morphological analyses differentiate both species according to size and shape but also discriminate strong seasonal and sexual traits and a geographical phenotype segregation in L. tityrus. Finally, updated distribution and its modelling for current and glacial timeframes reveal both species respond differently to environmental variables, defining a mostly parapatric distribution and an overlapping belt where sympatry was recovered. During the last glacial maximum, a wider expansion in L. bleusei distribution explains current isolated populations. Our study highlights the importance of gathering several lines of evidence when deciphering the relationships between closely related populations in the fringe of cryptic species realm.
- New Mitochondrial and Nuclear Evidences Support Recent Demographic Expansion and an Atypical Phylogeographic Pattern in the Spittlebug Philaenus spumarius (Hemiptera, Aphrophoridae)Publication . Rodrigues, Ana S. B.; Silva, Sara E.; Marabuto, Eduardo; Silva, Diogo N.; Wilson, Mike R.; Thompson, Vinton; Yurtsever, Selçuk; Halkka, Antti; Borges, P.A.V.; Quartau, J. A.; Paulo, Octávio S.; Seabra, Sofia G.Philaenus spumarius is a widespread insect species in the Holarctic region. Here, by focusing on the mtDNA gene COI but also using the COII and Cyt b genes and the nuclear gene EF-1α, we tried to explain how and when its current biogeographic pattern evolved by providing time estimates of the main demographic and evolutionary events and investigating its colonization patterns in and out of Eurasia. Evidence of recent divergence and expansion events at less than 0.5 Ma ago indicate that climate fluctuations in the Mid-Late Pleistocene were important in shaping the current phylogeographic pattern of the species. Data support a first split and differentiation of P. spumarius into two main mitochondrial lineages: the "western", in the Mediterranean region and the "eastern", in Anatolia/Caucasus. It also supports a following differentiation of the "western" lineage into two sub-lineages: the "western-Mediterranean", in Iberia and the "eastern-Mediterranean" in the Balkans. The recent pattern seems to result from postglacial range expansion from Iberia and Caucasus/Anatolia, thus not following one of the four common paradigms. Unexpected patterns of recent gene-flow events between Mediterranean peninsulas, a close relationship between Iberia and North Africa, as well as high levels of genetic diversity being maintained in northern Europe were found. The mitochondrial pattern does not exactly match to the nuclear pattern suggesting that the current biogeographic pattern of P. spumarius may be the result of both secondary admixture and incomplete lineage sorting. The hypothesis of recent colonization of North America from both western and northern Europe is corroborated by our data and probably resulted from accidental human translocations. A probable British origin for the populations of the Azores and New Zealand was revealed, however, for the Azores the distribution of populations in high altitude native forests is somewhat puzzling and may imply a natural colonization of the archipelago.
- PCR-based detection of prey DNA in the gut contents of thr tiger-fly, Coenosia attenuata (Diptera: Muscidae), a biological control agent in Mediterranean greenhousesPublication . Seabra, Sofia G.; Martins, Joana; Brás, Patrícia; Tavares, Ana M.; Freitas, Inês; Barata, António; Rebelo, Maria Teresa; Mateus, Célia; Paulo, Octávio S.; Figueiredo, ElisabeteThe tiger-fl y Coenosia attenuata Stein (Diptera: Muscidae: Coenosiini) is a generalist predator that preys on several pests of greenhouse crops and is considered a biological control agent in the Mediterranean region. Previous behavioural observations identifi ed its preferred prey, but a more in-depth evaluation will benefi t from using Polymerase Chain Reaction amplifi cation of prey DNA remains in the gut of this predator. To evaluate the rate of decay and suitability of this method for use in the fi eld assessments, we carried out a laboratory feeding calibration experiment on 355 females of C. attenuata, which were killed at different intervals of time after ingestion (10 time points from 0 to 48 h). The prey species tested were: Trialeurodes vaporariorum (Westwood) (Hemiptera: Aleyrodidae: Trialeurodini), Liriomyza huidobrensis (Blanchard) (Diptera: Agromyzidae), Diglyphus isaea (Walker) (Hymenoptera: Eulophidae: Cirrospilini), Bradysia impatiens (Johannsen) (Diptera: Sciaridae) and Drosophila mercatorum Patterson & Wheeler (Diptera: Drosophilidae: Drosophilini). Based on a probit model, amplifi cation success of prey DNA declined exponentially with increasing time after ingestion. The half-time molecular detection differed between species, ranging from an average of 5 h for T. vaporariorum and D. isaea, 6 h for B. impatiens, 15 h for L. huidobrensis to more than 40 h for D. mercatorum. This study confi rmed the feasibility of using DNA based detection to identify prey species in the gut contents of C. attenuata and provided calibration curves for a better understanding of predation activity in this agroecosystem