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- The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomicsPublication . Mc Cartney, Ann M.; Formenti, Giulio; Mouton, Alice; De Panis, Diego; Marins, Luísa S.; Leitão, Henrique G.; Diedericks, Genevieve; Kirangwa, Joseph; Morselli, Marco; Salces-Ortiz, Judit; Escudero, Nuria; Iannucci, Alessio; Natali, Chiara; Svardal, Hannes; Fernández, Rosa; De Pooter, Tim; Joris, Geert; Strazisar, Mojca; Wood, Jonathan M. D.; Herron, Katie E.; Seehausen, Ole; Watts, Phillip C.; Shaw, Felix; Davey, Robert P.; Minotto, Alice; Fernández, José M.; Böhne, Astrid; Alegria, Carla; Alioto, Tyler; Alves, Paulo C.; Amorim, Isabel R.; Aury, Jean-Marc; Backstrom, Niclas; Baldrian, Petr; Baltrunaite, Laima; Barta, Endre; BedHom, Bertrand; Belser, Caroline; Bergsten, Johannes; Bertrand, Laurie; Bilandija, Helena; Binzer-Panchal, Mahesh; Bista, Iliana; Blaxter, Mark; Borges, Paulo A. V.; Dias, Guilherme Borges; Bosse, Mirte; Brown, Tom; Bruggmann, Rémy; Buena-Atienza, Elena; Burgin, Josephine; Buzan, Elena; Cariani, Alessia; Casadei, Nicolas; Chiara, Matteo; Chozas, Sergio; Čiampor, Fedor; Crottini, Angelica; Cruaud, Corinne; Cruz, Fernando; Dalen, Love; De Biase, Alessio; del Campo, Javier; Delic, Teo; Dennis, Alice B.; Derks, Martijn F. L.; Diroma, Maria Angela; Djan, Mihajla; Duprat, Simone; Eleftheriadi, Klara; Feulner, Philine G. D.; Flot, Jean-François; Forni, Giobbe; Fosso, Bruno; Fournier, Pascal; Fournier-Chambrillon, Christine; Gabaldon, Toni; Garg, Shilpa; Gissi, Carmela; Giupponi, Luca; Gomez-Garrido, Jessica; González, Josefa; Grilo, Miguel L.; Grüning, Björn; Guerin, Thomas; Guiglielmoni, Nadege; Gut, Marta; Haesler, Marcel P.; Hahn, Christoph; Halpern, Balint; Harrison, Peter W.; Heintz, Julia; Hindrikson, Maris; Höglund, Jacob; Howe, Kerstin; Hughes, Graham M.; Istace, Benjamin; Cock, Mark J.; Janžekovič, Franc; Jonsson, Zophonias O.; Joye-Dind, Sagane; Koskimäki, Janne J.; Krystufek, Boris; Kubacka, Justyna; Kuhl, Heiner; Kusza, Szilvia; Labadie, Karine; Lähteenaro, Meri; Lantz, Henrik; Lavrinienko, Anton; Leclère, Lucas; Lopes, Ricardo Jorge; Madsen, Ole; Magdelenat, Ghislaine; Magoga, Giulia; Manousaki, Tereza; Mappes, Tapio; Marques, Joao Pedro; Redondo, Gemma I. Martinez; Maumus, Florian; McCarthy, Shane A.; Megens, Hendrik-Jan; Melo-Ferreira, Jose; Mendes, Sofia L.; Montagna, Matteo; Moreno, Joao; Mosbech, Mai-Britt; Moura, Mónica; Musilova, Zuzana; Myers, Eugene; Nash, Will J.; Nater, Alexander; Nicholson, Pamela; Niell, Manuel; Nijland, Reindert; Noel, Benjamin; Noren, Karin; Oliveira, Pedro H.; Olsen, Remi-Andre; Ometto, Lino; Oomen, Rebekah A.; Ossowski, Stephan; Palinauskas, Vaidas; Palsson, Snaebjorn; Panibe, Jerome P.; Pauperio, Joana; Pavlek, Martina; Payen, Emilie; Pawlowska, Julia; Pellicer, Jaume; Pesole, Graziano; Pimenta, Joao; Pippel, Martin; Pirttilä, Anna Maria; Poulakakis, Nikos; Rajan, Jeena; M.C. Rego, Rúben; Resendes, Roberto; Resl, Philipp; Riesgo, Ana; Rodin-Morch, Patrik; Soares, Andre E. R.; Fernandes, Carlos Rodriguez; Romeiras, Maria M.; Roxo, Guilherme; Rüber, Lukas; Ruiz-Lopez, Maria Jose; Saarma, Urmas; da Silva, Luis P.; Sim-Sim, Manuela; Soler, Lucile; Sousa, Vitor C.; Santos, Carla Sousa; Spada, Alberto; Stefanovic, Milomir; Steger, Viktor; Stiller, Josefin; Stöck, Matthias; Struck, Torsten H.; Sudasinghe, Hiranya; Tapanainen, Riikka; Tellgren-Roth, Christian; Trindade, Helena; Tukalenko, Yevhen; Urso, Ilenia; Vacherie, Benoit; Van Belleghem, Steven M.; Van Oers, Kees; Vargas-Chavez, Carlos; Velickovic, Nevena; Vella, Noel; Vella, Adriana; Vernesi, Cristiano; Vicente, Sara; Villa, Sara; Pettersson, Olga Vinnere; Volckaert, Filip A. M.; Voros, Judit; Wincker, Patrick; Winkler, Sylke; Ciofi, Claudio; Waterhouse, Robert M.; Mazzoni, Camila J.A genomic database of all Earth’s eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction of species have genomic information available. In 2018, scientists across the world united under the Earth BioGenome Project (EBP), aiming to produce a database of high-quality reference genomes containing all ~1.5 million recognized eukaryotic species. As the European node of the EBP, the European Reference Genome Atlas (ERGA) sought to implement a new decentralised, equitable and inclusive model for producing reference genomes. For this, ERGA launched a Pilot Project establishing the first distributed reference genome production infrastructure and testing it on 98 eukaryotic species from 33 European countries. Here we outline the infrastructure and explore its effectiveness for scaling high-quality reference genome production, whilst considering equity and inclusion. The outcomes and lessons learned provide a solid foundation for ERGA while offering key learnings to other transnational, national genomic resource projects and the EBP.
- Unravelling the complexities of biotic homogenization and heterogenization in the British avifaunaPublication . Wayman, Joseph P.; Sadler, Jonathan P.; Martin, Thomas E; Graham, Laura J; White, Hannah J; Tobias, Joseph; Matthews, Thomas J.Biotic homogenization is a process whereby species assemblages become more similar through time. The standard way of identifying the process of biotic homogenization is to look for decreases in spatial beta–diversity. However, using a single assemblage-level metric to assess homogenization can mask important changes in the occupancy patterns of individual species. Here, we analysed changes in the spatial beta–diversity patterns (i.e. biotic heterogenization or homogenization) of British bird assemblages within 30 km × 30 km regions between two periods (1988–1991 and 2008–2011). We partitioned the change in spatial beta–diversity into extirpation and colonization-resultant change (i.e. change in spatial beta–diversity within each region resulting from both extirpation and colonization). We used measures of abiotic change in combination with Bayesian modelling to disentangle the drivers of biotic heterogenization and homogenization. We detected both heterogenization and homogenization across the two time periods and three measures of diversity (taxonomic, phylogenetic, and functional). In addition, both extirpation and colonization contributed to the observed changes, with heterogenization mainly driven by extirpation and homogenization by colonization. These assemblage-level changes were primarily due to shifting occupancy patterns of generalist species. Compared to habitat generalists, habitat specialists had significantly (i) higher average contributions to colonization-resultant change (indicating heterogenization within a region due to colonization) and (ii) lower average contributions to extirpation-resultant change (indicating homogenization from extirpation). Generalists showed the opposite pattern. Increased extirpation-resultant homogenization within regions was associated with increased urban land cover and decreased habitat diversity, precipitation, and temperature. Changes in extirpation-resultant heterogenization and colonization-resultant heterogenization were associated with differences in elevation between regions and changes in temperature and land cover. Many of the ‘winners’ (i.e. species that increased in occupancy) were species that had benefitted from conservation action (e.g. buzzard (Buteo buteo). The ‘losers’ (i.e. those that decreased in occupancy) consisted primarily of previously common species, such as cuckoo (Cuculus canorus). Our results show that focusing purely on changes in spatial beta–diversity over time may obscure important information about how changes in the occupancy patterns of individual species contribute to homogenization and heterogenization.
- Flower Visitation through the Lens: Exploring the Foraging Behaviour of Bombus terrestris with a Computer Vision-Based ApplicationPublication . Varga-Szilay, Zsófia; Szövényi, Gergely; Pozsgai, GaborTo understand the processes behind pollinator declines and for the conservation of pollination services, we need to understand fundamental drivers influencing pollinator behaviour. Here, we aimed to elucidate how wild bumblebees interact with three plant species and investigated their foraging behaviour with varying flower densities. We video-recorded Bombus terrestris in 60 × 60 cm quadrats of Lotus creticus, Persicaria capitata, and Trifolium pratense in urban areas of Terceira (Azores, Portugal). For the automated bumblebee detection and counting, we created deep learning-based computer vision models with custom datasets. We achieved high model accuracy of 0.88 for Lotus and Persicaria and 0.95 for Trifolium, indicating accurate bumblebee detection. In our study, flower cover was the only factor that influenced the attractiveness of flower patches, and plant species did not have an effect. We detected a significant positive effect of flower cover on the attractiveness of flower patches for flower-visiting bumblebees. The time spent per unit of inflorescence surface area was longer on the Trifolium than those on the Lotus and Persicaria. However, our result did not indicate significant differences in the time bumblebees spent on inflorescences among the three plant species. Here, we also justify computer vision-based analysis as a reliable tool for studying pollinator behavioural ecology.
- The role of sheltered habitats in biodiversity conservation of species sensitive to drought: a case study using ground beetles (Coleoptera, Carabidae) in the Gorongosa National ParkPublication . Baptista, Martim; Carvalho, Rui; Boieiro, Mário; Bartz, M. L. C.; Mendes, Sara; Timóteo, Sérgio; Azevedo-Pereira, Henrique M.V.S.; Alves, Joana; Alves Da Silva, António; Briones, Maria J.I.; Serrano, Artur; Sousa, José Paulo; Martins da Silva, PedroIn the aftermath of 2019’ tropical cyclones Idai and Kenneth, we assessed ground beetle communities of the Gorongosa National Park (GNP) in Mozambique. The influence of habitat shelters, namely the buffering role of closed microhabitat conditions on Alpha diversity and community trait values during a long period of drought, was evaluated across the main habitat types of the park: miombo forests, mixed forests, transitional forests, and grasslands (open savannas). These habitat types comprised a distance gradient in relation to lake Urema, in the center of GNP. Miombo forests were farther from the lake while grasslands and transitional forests were in the floodplain area. Ground beetle communities were sampled using pitfall traps set up at 25 sites of each habitat type along an environmental gradient of tree canopy cover during the last twenty days of the dry season. Higher species richness of ground beetles was found in closed habitat shelters along the distance gradient to lake Urema. A higher functional diversity was also found along the canopy gradient, with larger sized and wingless species being more abundant in closed habitats than in open areas. This result highlights the crucial role of habitat closedness in the protection of sensitive ground beetles. In particular, the buffer effect of tree canopy and the protection of the understory plants and the litter layer was critical for the survival of hygrophilous species and will be key in conservation strategies to face climate aridification and habitat fragmentation.
- Prey consumption and conversion efficiency in females of two feral populations of Macrolophus pygmaeus, a biocontrol agent of Tuta absolutaPublication . Borges, Isabel; Oliveira, Luísa; Barbosa, Francisco; Figueiredo, Elisabete; Franco, José Carlos; Durão, Ana; Soares, António O.Macrolophus pygmaeus (Rambur, 1839) (Hemiptera: Miridae) is a polyphagous predator used in programs of biological control and integrated pest management as a natural enemy against small arthropod pests including whiteflies, thrips, spider mites and aphid. This mirid is also successfully mass reared under factitious prey for commercial purposes. In the present study we assessed and compared the prey consumption, weight gain and conversion efficiency in females of two populations of M. pygmaeus, from mainland Portugal and the Azores, fed on single prey diets of Ephestia kuehniella Zeller (Lepidoptera: Pyralidae) eggs, or Tuta absoluta (Meyrick) (Lepidoptera: Gelechiidae) eggs. We found that female’s prey consumption on eggs of T. absoluta was higher than that of E. kuehniella, presumably due to the comparative size/amount of biomass of the eggs. Translating prey consumption in biomass ingested, we only found a significant difference for consumption on E. kuehniella eggs by M. pygmaeus from the Azores. Despite the smaller size of females from the Azores, they were able to consume more prey and ultimately reaching a similar body weight and conversion efficiency compared with females from mainland, independently of the prey provided. Our results are in line with a previous study, showing differences in the life-history traits of M. pygmaeus from mainland Portugal and Azorean populations fed on alternative prey. From an applied perspective, our results are a contribution to the decision-making on the use of the most effective biocontrol agents for different prey and/or agroecosystem contexts.
- Insect conservation on islandsPublication . Gerlach, Justin; Borges, Paulo A. V.; Fattorini, Simone; Porch, Nick; Wilkins, Vicky
- Microsatellites reveal high levels of genetic admixture in the natural populations of Laurus azorica, LauraceaePublication . Rego, Rúben; Vieira, Ângela F.; Silva, Luís; Elias, Rui B.; Silva, Carlos; Resendes, Roberto; Moura, MónicaLaurus (Lauraceae) species are currently restricted to isolated refugia in the southern Black Sea, Mediterranean Basin, southern Morocco, and Macaronesian archipelagos. One to three species of Laurus has been recognized: the Azorean endemic Laurus azorica, L. nobilis from the Mediterranean, and L. novocanariensis from Madeira and the Canary Islands. This study aims to determine the population structure, genetic diversity, and associated patterns of gene flow within and between Azorean populations, using eight existing SSR markers. We also included plant material from L. nobilis populations found in the Azores, for comparison. Amplification was performed in 212 samples of L. azorica and in 30 samples of L. nobilis. For L. azorica, 78 alleles were amplified (average 9.75 alleles per loci). Bayesian analysis with STRUCTURE unveiled five genetic groups for the Azorean accessions, with high level of genetic admixture. Genetic diversity was generally high, with moderate levels of genetic differentiation among L. azorica populations. Moreover, high gene flow levels, likely mediated by past human translocations and naturally, by birds, might have contributed to the high level of genetic admixture observed possibly reflecting hybridization events between L. nobilis and L. azorica. Conservation measures should be applied to some populations of São Miguel, Santa Maria, and Flores Islands, based on the number of private alleles, and further, ad hoc translocation events should be avoided. Conservation in situ and the preservation of laurel forest remains are recommended. The study of this species’ taxonomy, genetics, and population dynamics in the Macaronesian region should be continued.
- First record of the great barracuda, Sphyraena barracuda (Perciformes, Sphyraenidae), in the Azores, north‐east AtlanticPublication . Barcelos, Luis M. D.; Barreiros, João B.; Barreiros, João P.One individual of Sphyraena barracuda was collected on August 5, 2023, in the northern coast of Terceira Island, Azores, Portugal, by spearfishing. In this note, we report this first record and discuss the occurrence, which represents the northernmost one in the north-east Atlantic.
- Land-use change interacts with island biogeography to alter bird community assemblyPublication . Zhao, Yuhao; Mendenhall, Chase D.; Matthews, Thomas J.; Wang, Duorun; Li, Wande; Liu, Xiangxu; Tang, Shupei; Han, Peng; Wei, Guangpeng; Kang, Yi; Wu, Chenxiao; Wang, Rui; Zeng, Di; Frishkoff, Luke O.; Si, XingfengAnthropogenic activities have reshaped biodiversity on islands worldwide. However, it remains unclear how island attributes and land-use change interactively shape multiple facets of island biodiversity through community assembly processes. To answer this, we conducted bird surveys in various land-use types (mainly forest and farmland) using transects on 34 oceanic land-bridge islands in the largest archipelago of China. We found that bird species richness increased with island area and decreased with isolation, regardless of the intensity of land-use change. However, forest-dominated habitats exhibited lower richness than farmland-dominated habitats. Island bird assemblages generally comprised species that share more similar traits or evolutionary histories (i.e. functional and/or phylogenetic clustering) than expected if assemblages were randomly assembled. Contrary to our expectations, we observed that bird assemblages in forest-dominated habitats were more clustered on large and close islands, whereas assemblages in farmland-dominated habitats were more clustered on small islands. These contrasting results indicate that land-use change interacts with island biogeography to alter the community assembly of birds on inhabited islands. Our findings emphasize the importance of incorporating human-modified habitats when examining the community assembly of island biota, and further suggest that agricultural landscapes on large islands may play essential roles in protecting countryside island biodiversity.
- The MOVECLIM – AZORES project: Bryophytes from Terceira Island along an elevation gradientPublication . Gabriel, Rosalina; Morgado, Leila; Henriques, Debora; Coelho, Márcia; Hernández-Hernández, Raquel; Borges, Paulo A. V.Systematic studies on the biodiversity of bryophytes along elevational gradients have been conductuted within the native vegetation of the Azores, using the MOVECLIM framework. The primary objective of this study was to inventory the bryophytes present within preserved areas of native vegetation in Terceira Island (Azores). From 25 to 28 September 2012, an inventory of the bryoflora was carried out along an elevational gradient, starting near Serreta lighthouse (38.76658 Latitude; -27.37539 Longitude; 40 m a.s.l.) and culminating on the top of Santa Bárbara Mountain (38.73064 Latitude; -27.32164 Longitude; 1000 m a.s.l.). The study followed the adapted MOVECLIM standardised protocol, as follows: i) six sites were selected along an elevational transect, each site spaced at 200 m elevation intervals; ii) within each site, two 10 m x 10 m plots were established in close proximity from each other (10-15 m); iii) within these plots, three 2 m x 2 m quadrats were randomly selected and sampled for bryophytes. The following substrates were surveyed in each quadrat: rock, soil, humus, organic matter, tree bark at three different heights and leaves/fronds. For each available and bryophyte-colonised substrate, three replicate microplots of 10 cm x 5 cm were collected, resulting in a maximum of 24 microplots per quadrat. New information Nearly three-quarters of the maximum expected number of microplots (636 out of 864; eventID) were found across the six sites on Terceira Island, resulting in a total of 3677 records (occurrenceID). A high proportion of the specimens could be identified to the species rank (n = 3661; 99.6%), representing 38 families, 60 genera and 92 species, including 58 species of liverworts (Marchantiophyta) and 34 species of mosses (Bryophyta). The inventory included several endemic species: two liverwort species endemic to the Azores, five species endemic to Macaronesia (three mosses and two liverworts) and 11 European endemic species (three mosses and eight liverworts). The elevations with the highest species richness, the highest number of endemic species and the highest number of conservation concern species, spanned between 600 and 1000 m a.s.l. above sea level, coinciding with the best preserved forest vegetation. Overall, tree-dwelling and ground-dwelling substrates showed similar levels of bryophyte occupation (75% vs. 72%). However, the 636 events were unevenly distributed across substrates: leaves and rocks had the fewest replicates (n = 54; 50.0%), while humus and the lowest tree height had the highest values (n = 106; 98.1% and n = 98; 90.7%, respectively).