{"entity": "researcher", "timestamp": "2026-09-23T15:20:37.426Z", "family": "Pinto", "given": "M Alice", "initials": "MA", "orcid": "0000-0001-9663-8399", "affiliations": ["Mountain Research Centre (CIMO) Polytechnic Institute of Bragan\u00e7a Bragan\u00e7a Portugal."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/53da6ce1d57d42b0a280ee68a1d26938.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/53da6ce1d57d42b0a280ee68a1d26938"}}, "publications": [{"entity": "publication", "iuid": "3c30f7b9488048389e6efd3921633650", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3c30f7b9488048389e6efd3921633650.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3c30f7b9488048389e6efd3921633650"}}, "title": "The honeybee (Apis mellifera) developmental state shapes the genetic composition of the deformed wing virus-A quasispecies during serial transmission.", "authors": [{"family": "Ya\u00f1ez", "given": "Orlando", "initials": "O", "orcid": "0000-0001-8493-2726", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/845aaeb4172842e4b47404f2876a617c.json"}}, {"family": "Ch\u00e1vez-Galarza", "given": "Julio", "initials": "J"}, {"family": "Tellgren-Roth", "given": "Christian", "initials": "C", "orcid": "0000-0003-0502-3693", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8f4ddcd6923469e9d72fa98557ea196.json"}}, {"family": "Pinto", "given": "M Alice", "initials": "MA", "orcid": "0000-0001-9663-8399", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/53da6ce1d57d42b0a280ee68a1d26938.json"}}, {"family": "Neumann", "given": "Peter", "initials": "P"}, {"family": "de Miranda", "given": "Joachim R", "initials": "JR", "orcid": "0000-0002-0335-0386", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/57fc43785bcb40af8d8e6379b39664b0.json"}}], "type": "journal article", "published": "2020-04-06", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "5956", "issn-l": "2045-2322"}, "abstract": "The main biological threat to the western honeybee (Apis mellifera) is the parasitic mite Varroa destructor, largely because it vectors lethal epidemics of honeybee viruses that, in the absence of this mite, are relatively innocuous. The severe pathology is a direct consequence of excessive virus titres caused by this novel transmission route. However, little is known about how the virus adapts genetically during transmission and whether this influences the pathology. Here, we show that upon injection into honeybee pupae, the deformed wing virus type-A (DWV-A) quasispecies undergoes a rapid, extensive expansion of its sequence space, followed by strong negative selection towards a uniform, common shape by the time the pupae have completed their development, with no difference between symptomatic and asymptomatic adults in either DWV titre or genetic composition. This suggests that the physiological and molecular environment during pupal development has a strong, conservative influence on shaping the DWV-A quasispecies in emerging adults. There was furthermore no evidence of any progressive adaptation of the DWV-A quasispecies to serial intra-abdominal injection, simulating mite transmission, despite the generation of ample variation immediately following each transmission, suggesting that the virus either had already adapted to transmission by injection, or was unaffected by it.", "doi": "10.1038/s41598-020-62673-w", "pmid": "32249797", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC7136270"}, {"db": "pii", "key": "10.1038/s41598-020-62673-w"}], "notes": [], "created": "2026-09-23T09:57:45.128Z", "modified": "2026-09-23T10:33:27.127Z"}, {"entity": "publication", "iuid": "892ec2042f18469a88fd21991e7d3d97", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/892ec2042f18469a88fd21991e7d3d97.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/892ec2042f18469a88fd21991e7d3d97"}}, "title": "Developing reduced SNP assays from whole-genome sequence data to estimate introgression in an organism with complex genetic patterns, the Iberian honeybee (Apis mellifera iberiensis).", "authors": [{"family": "Henriques", "given": "Dora", "initials": "D"}, {"family": "Parejo", "given": "Melanie", "initials": "M"}, {"family": "Vignal", "given": "Alain", "initials": "A"}, {"family": "Wragg", "given": "David", "initials": "D"}, {"family": "Wallberg", "given": "Andreas", "initials": "A"}, {"family": "Webster", "given": "Matthew T", "initials": "MT"}, {"family": "Pinto", "given": "M Alice", "initials": "MA", "orcid": "0000-0001-9663-8399", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/53da6ce1d57d42b0a280ee68a1d26938.json"}}], "type": "journal article", "published": "2018-09-00", "journal": {"title": "Evol Appl", "issn": "1752-4571", "volume": "11", "issue": "8", "pages": "1270-1282", "issn-l": "1752-4571"}, "abstract": "The most important managed pollinator, the honeybee (Apis mellifera L.), has been subject to a growing number of threats. In western Europe, one such threat is large-scale introductions of commercial strains (C-lineage ancestry), which is leading to introgressive hybridization and even the local extinction of native honeybee populations (M-lineage ancestry). Here, we developed reduced assays of highly informative SNPs from 176 whole genomes to estimate C-lineage introgression in the most diverse and evolutionarily complex subspecies in Europe, the Iberian honeybee (Apis mellifera iberiensis). We started by evaluating the effects of sample size and sampling a geographically restricted area on the number of highly informative SNPs. We demonstrated that a bias in the number of fixed SNPs (FST = 1) is introduced when the sample size is small (N \u2264 10) and when sampling only captures a small fraction of a population's genetic diversity. These results underscore the importance of having a representative sample when developing reliable reduced SNP assays for organisms with complex genetic patterns. We used a training data set to design four independent SNP assays selected from pairwise FST between the Iberian and C-lineage honeybees. The designed assays, which were validated in holdout and simulated hybrid data sets, proved to be highly accurate and can be readily used for monitoring populations not only in the native range of A. m. iberiensis in Iberia but also in the introduced range in the Balearic islands, Macaronesia and South America, in a time- and cost-effective manner. While our approach used the Iberian honeybee as model system, it has a high value in a wide range of scenarios for the monitoring and conservation of potentially hybridized domestic and wildlife populations.", "doi": "10.1111/eva.12623", "pmid": "30151039", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC6099811"}, {"db": "pii", "key": "EVA12623"}, {"db": "Dryad", "key": "10.5061/dryad.v8cp134"}], "notes": [], "created": "2019-01-17T13:59:22.234Z", "modified": "2026-09-23T08:41:35.689Z"}, {"entity": "publication", "iuid": "4314cd89b9b443da9aa9e8f7b36cfb6d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4314cd89b9b443da9aa9e8f7b36cfb6d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4314cd89b9b443da9aa9e8f7b36cfb6d"}}, "title": "Whole genome SNP-associated signatures of local adaptation in honeybees of the Iberian Peninsula.", "authors": [{"family": "Henriques", "given": "Dora", "initials": "D"}, {"family": "Wallberg", "given": "Andreas", "initials": "A", "orcid": "0000-0002-9081-9663", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/612978d6845d4e70949078f2bbf1cc62.json"}}, {"family": "Ch\u00e1vez-Galarza", "given": "Julio", "initials": "J"}, {"family": "Johnston", "given": "J Spencer", "initials": "JS"}, {"family": "Webster", "given": "Matthew T", "initials": "MT"}, {"family": "Pinto", "given": "M Alice", "initials": "MA", "orcid": "0000-0001-9663-8399", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/53da6ce1d57d42b0a280ee68a1d26938.json"}}], "type": "journal article", "published": "2018-07-24", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "8", "issue": "1", "pages": "11145", "issn-l": "2045-2322"}, "abstract": "The availability of powerful high-throughput genomic tools, combined with genome scans, has helped identifying genes and genetic changes responsible for environmental adaptation in many organisms, including the honeybee. Here, we resequenced 87 whole genomes of the honeybee native to Iberia and used conceptually different selection methods (Sam\u03b2ada, LFMM, PCAdapt, iHs) together with in sillico protein modelling to search for selection footprints along environmental gradients. We found 670 outlier SNPs, most of which associated with precipitation, longitude and latitude. Over 88.7% SNPs laid outside exons and there was a significant enrichment in regions adjacent to exons and UTRs. Enrichment was also detected in exonic regions. Furthermore, in silico protein modelling suggests that several non-synonymous SNPs are likely direct targets of selection, as they lead to amino acid replacements in functionally important sites of proteins. We identified genomic signatures of local adaptation in 140 genes, many of which are putatively implicated in fitness-related functions such as reproduction, immunity, olfaction, lipid biosynthesis and circadian clock. Our genome scan suggests that local adaptation in the Iberian honeybee involves variations in regions that might alter patterns of gene expression and in protein-coding genes, which are promising candidates to underpin adaptive change in the honeybee.", "doi": "10.1038/s41598-018-29469-5", "pmid": "30042407", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC6057950"}, {"db": "pii", "key": "10.1038/s41598-018-29469-5"}], "notes": [], "created": "2019-01-17T13:55:33.882Z", "modified": "2026-09-23T10:21:46.470Z"}]}