A5054550293- Species Distribution and Climate Change
- Environmental DNA in Biodiversity Studies
- Genetic diversity and population structure
- Animal Ecology and Behavior Studies
- Wildlife Ecology and Conservation
- Genomics and Phylogenetic Studies
- Bat Biology and Ecology Studies
- Identification and Quantification in Food
- Microbial Community Ecology and Physiology
- Evolution and Paleontology Studies
- Research Data Management Practices
- Invertebrate Taxonomy and Ecology
- Mycorrhizal Fungi and Plant Interactions
- Rabbits: Nutrition, Reproduction, Health
- Helminth infection and control
- Coccidia and coccidiosis research
- Cancer Genomics and Diagnostics
- Fossil Insects in Amber
- Forest Ecology and Biodiversity Studies
- Plant and animal studies
- Fish Ecology and Management Studies
- Ecology and Vegetation Dynamics Studies
- Plant and Fungal Species Descriptions
- Plant Pathogens and Fungal Diseases
- Molecular Biology Techniques and Applications
European Bioinformatics Institute
2022-2025
Universidade do Porto
2015-2025
Centro de Investigação em Biodiversidade e Recursos Genéticos
2016-2024
Campo Arqueologico de Mertola
2024
Wellcome Trust
2022-2023
Elixir Medical (United States)
2023
Institute of Biodiversity and Ecosystem Research
2023
Pensoft Publishers (Bulgaria)
2023
Bulgarian Academy of Sciences
2023
University of Tartu Natural History Museum and Botanical Garden
2023
Abstract UNITE (https://unite.ut.ee) is a web-based database and sequence management environment for molecular identification of eukaryotes. It targets the nuclear ribosomal internal transcribed spacer (ITS) region offers nearly 10 million such sequences reference. These are clustered into ∼2.4M species hypotheses (SHs), each assigned unique digital object identifier (DOI) to promote unambiguous referencing across studies. users have contributed over 600 000 third-party annotations, which...
The European Nucleotide Archive (ENA; https://www.ebi.ac.uk/ena), maintained by the Molecular Biology Laboratory's Bioinformatics Institute (EMBL-EBI), offers those producing data an open and supported platform for management, archiving, publication, dissemination of data; to scientific community as a whole, it globally comprehensive set through host discovery retrieval tools. Here, we describe recent updates ENA's submission services well focused efforts improve connectivity, reusability,...
Abstract The European Nucleotide Archive (ENA; https://www.ebi.ac.uk/ena) is maintained by the Molecular Biology Laboratory's Bioinformatics Institute (EMBL-EBI). ENA one of three members International Sequence Database Collaboration (INSDC). It serves bioinformatics community worldwide via submission, processing, archiving and dissemination sequence data. supports data types ranging from raw reads, through alignments assemblies to functional annotation. enriched with contextual information...
Abstract Climate change and increasing habitat loss greatly impact species survival, requiring range shifts, phenotypic plasticity and/or evolutionary for long‐term persistence, which may not readily occur unaided in threatened species. Therefore, defining conservation actions requires a detailed assessment of factors. Existing genetic diversity needs to be thoroughly evaluated spatially mapped define units ( CU s ) an context, we address that here. We also propose multidisciplinary approach...
Genetic non-invasive sampling (gNIS) may provide valuable information for population monitoring, as it allows inferences of density and key behavioural traits such dispersal, kinship reproduction. Despite its enormous potential, gNIS has rarely been applied to small mammals, which live-trapping is still the most commonly used method. Here we evaluated applicability cost-effectiveness compared with live-trapping, monitor a metapopulation an Iberian endemic elusive rodent: Cabrera vole...
DNA metabarcoding can contribute to improving cost-effectiveness and accuracy of biological assessments aquatic ecosystems, but significant optimization standardization efforts are still required mainstream its application into biomonitoring programmes. In based on freshwater macroinvertebrates, a key challenge is that often extracted from cleaned, sorted homogenized bulk samples, which time-consuming may be incompatible with sample preservation requirements regulatory agencies. Here, we...
Species are generally described from morphological features, but there is growing recognition of sister forms that show substantial genetic differentiation without obvious variation and may therefore be considered ‘cryptic species’. Here, we investigate the field vole ( M icrotus agrestis ), a E urasian mammal with little apparent which, on basis previous sex‐linked nuclear mitochondrial DNA (mt ) analyses, subdivided into N orthern S outhern lineage, sufficiently divergent they represent...
Abstract Species identification through noninvasive sampling is increasingly used in animal conservation genetics, given that it obviates the need to handle free‐living individuals. Noninvasive particularly valuable for elusive and small species such as rodents. Although rodents are not usually assumed be most obvious target conservation, of 21 or near‐species present I beria, three considered endangered declining, while several others poorly studied. Here, we develop a genetic tool...
Cryptosporidium spp. and Giardia are important diarrhea-causing protozoan parasites worldwide that exhibit broad host ranges. Wild small mammals can harbor host-adapted potentially zoonotic species of both parasites. The aim this study was to investigate in wild rodents shrews Portugal, focusing on the protist's occurrence genetic diversity. Molecular screening by PCR at subunit (SSU) rRNA gene locus 290 fecal samples from wood mice (Apodemus sylvaticus), southwestern water voles (Arvicola...
<title>Abstract</title> Background The field vole, an abundant and widespread microtine rodent, is a complex comprising three cryptic species. short-tailed vole (<italic>Microtus agrestis</italic>) present over much of Eurasia, the Mediterranean lavernedii</italic>) in southern Europe, Portuguese rozianus</italic>) limited to western Spain Portugal. Previous research has shown high genomic differentiation these lineages; however, details process underlying their divergence remain unknown....
Metabarcoding is invaluable for understanding trophic interactions, enabling high-resolution and rapid dietary assessments. However, it requires a robust DNA barcode reference library accurate taxa identification. This dataset has been generated in the framework of InBIO Barcoding Initiative (IBI) Agrivole project. The integration these two projects was crucial, as aimed to investigate niche small mammals Trás-os-Montes Region through metabarcoding, which required reliable plant this same...
Abstract Glacial refugia protected and promoted biodiversity during the Pleistocene, not only at a broader scale, but also for many endemics that contracted expanded their ranges within refugial areas. Understanding evolutionary history of is especially important in case endangered species to recognize origins genetic structure thus produce better informed conservation practices. The Iberian Peninsula an European glacial refugium, rich concern, including small mammals, such as Cabrera vole (...
The paper summarises many years of discussions and experience biodiversity publishers, organisations, research projects individual researchers, proposes recommendations for implementation persistent identifiers article metadata, structural elements (sections, subsections, figures, tables, references, supplementary materials others) data specific to (taxonomic treatments, treatment citations, taxon names, material gene sequences, specimens, scientific collections) in taxonomy publishing. best...
BiCIKL ( Bi odiversity C ommunity I ntegrated K nowledge L ibrary) is a European Union (EU) Horizon 2020 project (2021–2024) building new community of research infrastructures (RIs), researchers and other stakeholders, through improved access to interlinked, open FAIR F indable, A ccessible, nteroperable, R eusable) biodiversity data along the cycle (specimens, sequences, taxon names, publications) (Penev et al. 2022). The project’s 14 partners developed or substantially 16 tools services...
Abstract Freshwater ecosystems are among the most threatened in world, and downstream reaches of stream networks often affected by multiple anthropogenic stressors. In these circumstances, many species currently restricted to headwaters may represent remnants once larger populations, though this is generally difficult ascertain due limited historical data. Here, we document a case range contraction into globally Pyrenean desman Galemys pyrenaicus , endemic South‐western Europe, from surveys...
The InBIO Barcoding Initiative (IBI) Diptera 02 dataset contains records of 412 crane fly specimens belonging to the families: Limoniidae, Pediciidae and Tipulidae. This is second release by IBI on it greatly increases knowledge DNA barcodes distribution flies from Portugal. All were collected in Portugal, including six Azores Madeira archipelagos. Sampling took place 2003 2019. Specimens have been morphologically identified species level taxonomists belong 83 total. species, represented...
Understanding how small mammals (SM) are associated with environmental characteristics in olive groves is important to identify potential threats agriculture and assess the overall conservation value functioning of agro-ecosystems. Here, we provide first insights on this topic applied traditional northeast (NE) Portugal by assessing landscape attributes that determine SM occurrence, focusing one species concern (Microtus cabrerae Thomas 1906) often perceived as a pest olives lusitanicus...
Abstract Virus monitoring in small mammals is central to the design of epidemiological control strategies for rodent-borne zoonotic viruses. Synanthropic are versatile and may be potential carriers several microbial agents. In present work, a total 330 fecal samples were collected at two sites North Portugal screened hepatitis E virus (HEV, species Paslahepevirus balayani ). mammal ( n = 40) city park Porto belonged Algerian mouse Mus spretus ) 26) greater white-toothed shrew Crocidura...
The InBIO Barcoding Initiative (IBI) Dataset - DS-IBILP08 contains records of 2350 specimens moths (Lepidoptera species that do not belong to the superfamily Papilionoidea). All have been morphologically identified or subspecies level and represent 1158 in total. this dataset correspond about 42% mainland Portuguese Lepidoptera species. were collected Portugal between 2001 2022. DNA extracts over 96% are deposited IBI collection at CIBIO, Research Center Biodiversity Genetic Resources.
This study outlines the procedures used for collecting, processing, and categorizing data on 16 new mammal species mainland Portugal, belonging to four taxonomic groups: Eulipotyphla (1), Chiroptera (4), Rodentia (2), Cetacea (9). Data collection processing encompassed field lab work bibliographic compilation. categorization involves, whenever possible, assessment of approximate number mature individuals in populations, extent occurrence, area occupancy. The approach employed led...
Context. The wild rabbit (Oryctolagus cuniculus) is a keystone species from the Iberian Peninsula that has suffered strong decline in Spain during past decades. Data on historical and current population trends Portugal are virtually non-existent. Aims. To investigate changes abundance at national level so as to inform conservation status assessments, evaluate usefulness of hunting bags index. Methods. Field surveys based latrine counts linear transects were performed two periods (1995 2002)...