{"entity": "journal", "iuid": "251e0a771d8a4f678c613ad3d3104b2e", "timestamp": "2026-08-15T13:45:19.451Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/journal/Evol%20Appl.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/journal/Evol%20Appl"}}, "title": "Evol Appl", "issn": "1752-4571", "issn-l": "1752-4571", "publications_count": 4, "publications": [{"entity": "publication", "iuid": "6aa338dc0cf745edaeac2562db318996", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6aa338dc0cf745edaeac2562db318996.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6aa338dc0cf745edaeac2562db318996"}}, "title": "Assessing the potential for assisted gene flow using past introduction of Norway spruce in southern Sweden: Local adaptation and genetic basis of quantitative traits in trees.", "authors": [{"family": "Milesi", "given": "Pascal", "initials": "P", "orcid": "0000-0001-8580-4291", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6025546b69354721b8a16fbe8124fa71.json"}}, {"family": "Berlin", "given": "Mats", "initials": "M"}, {"family": "Chen", "given": "Jun", "initials": "J"}, {"family": "Orsucci", "given": "Marion", "initials": "M", "orcid": "0000-0001-8516-1361", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/44bddb691cd349b19e8111c778f51402.json"}}, {"family": "Li", "given": "Lili", "initials": "L"}, {"family": "Jansson", "given": "Gunnar", "initials": "G"}, {"family": "Karlsson", "given": "Bo", "initials": "B"}, {"family": "Lascoux", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2019-12-00", "journal": {"title": "Evol Appl", "issn": "1752-4571", "issn-l": "1752-4571", "volume": "12", "issue": "10", "pages": "1946-1959"}, "abstract": "Norway spruce (Picea abies) is a dominant conifer species of major economic importance in northern Europe. Extensive breeding programs were established to improve phenotypic traits of economic interest. In southern Sweden, seeds used to create progeny tests were collected on about 3,000 trees of outstanding phenotype ('plus' trees) across the region. In a companion paper, we showed that some were of local origin but many were recent introductions from the rest of the natural range. The mixed origin of the trees together with partial sequencing of the exome of >1,500 of these trees and phenotypic data retrieved from the Swedish breeding program offered a unique opportunity to dissect the genetic basis of local adaptation of three quantitative traits (height, diameter and bud-burst) and assess the potential of assisted gene flow. Through a combination of multivariate analyses and genome-wide association studies, we showed that there was a very strong effect of geographical origin on growth (height and diameter) and phenology (bud-burst) with trees from southern origins outperforming local provenances. Association studies revealed that growth traits were highly polygenic and bud-burst somewhat less. Hence, our results suggest that assisted gene flow and genomic selection approaches could help to alleviate the effect of climate change on P. abies breeding programs in Sweden.", "doi": "10.1111/eva.12855", "pmid": "31700537", "labels": {"Pascal Milesi": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "EVA12855"}, {"db": "pmc", "key": "PMC6824079"}, {"db": "Dryad", "key": "10.5061/dryad.mr47gq3"}], "notes": [], "created": "2020-11-30T09:18:22.242Z", "modified": "2022-11-04T11:32:15.751Z"}, {"entity": "publication", "iuid": "9895de79493d43a5b50f03e5d1a8e6c3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9895de79493d43a5b50f03e5d1a8e6c3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9895de79493d43a5b50f03e5d1a8e6c3"}}, "title": "Genomic data provide new insights on the demographic history and the extent of recent material transfers in Norway spruce.", "authors": [{"family": "Chen", "given": "Jun", "initials": "J", "orcid": "0000-0003-3187-7668", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4eb977f0bb9d413486be3463b8a20d0c.json"}}, {"family": "Li", "given": "Lili", "initials": "L"}, {"family": "Milesi", "given": "Pascal", "initials": "P", "orcid": "0000-0001-8580-4291", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6025546b69354721b8a16fbe8124fa71.json"}}, {"family": "Jansson", "given": "Gunnar", "initials": "G"}, {"family": "Berlin", "given": "Mats", "initials": "M"}, {"family": "Karlsson", "given": "Bo", "initials": "B"}, {"family": "Aleksic", "given": "Jelena", "initials": "J"}, {"family": "Vendramin", "given": "Giovanni G", "initials": "GG"}, {"family": "Lascoux", "given": "Martin", "initials": "M", "orcid": "0000-0003-1699-9042", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0730d0f9c2524eb19383640612924701.json"}}], "type": "journal article", "published": "2019-09-00", "journal": {"title": "Evol Appl", "issn": "1752-4571", "issn-l": "1752-4571", "volume": "12", "issue": "8", "pages": "1539-1551"}, "abstract": "Primeval forests are today exceedingly rare in Europe, and transfer of forest reproductive material for afforestation and improvement has been very common, especially over the last two centuries. This can be a serious impediment when inferring past population movements in response to past climate changes such as the last glacial maximum (LGM), some 18,000 years ago. In the present study, we genotyped 1,672 individuals from three Picea species (P. abies, P. obovata, and P. omorika) at 400K SNPs using exome capture to infer the past demographic history of Norway spruce (P. abies) and estimate the amount of recent introduction used to establish the Norway spruce breeding program in southern Sweden. Most of these trees belong to P. abies and originate from the base populations of the Swedish breeding program. Others originate from populations across the natural ranges of the three species. Of the 1,499 individuals stemming from the breeding program, a large proportion corresponds to recent introductions from mainland Europe. The split of P. omorika occurred 23 million years ago (mya), while the divergence between P. obovata and P. abies began 17.6 mya. Demographic inferences retrieved the same main clusters within P. abies than previous studies, that is, a vast northern domain ranging from Norway to central Russia, where the species is progressively replaced by Siberian spruce (P. obovata) and two smaller domains, an Alpine domain and a Carpathian one, but also revealed further subdivision and gene flow among clusters. The three main domains divergence was ancient (15 mya), and all three went through a bottleneck corresponding to the LGM. Approximately 17% of P. abies Nordic domain migrated from P. obovata ~103K years ago, when both species had much larger effective population sizes. Our analysis of genomewide polymorphism data thus revealed the complex demographic history of Picea genus in Western Europe and highlighted the importance of material transfer in Swedish breeding program.", "doi": "10.1111/eva.12801", "pmid": "31462913", "labels": {"Pascal Milesi": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "EVA12801"}, {"db": "pmc", "key": "PMC6708423"}], "notes": [], "created": "2020-11-30T09:18:21.105Z", "modified": "2022-11-04T11:32:16.042Z"}, {"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 (\n            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"}], "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 (\n            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\u00a0=\u00a01) is introduced when the sample size is small (N\u00a0\u2264\u00a010) 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.\u00a0m.\u00a0iberiensis 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": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "EVA12623"}, {"db": "pmc", "key": "PMC6099811"}, {"db": "Dryad", "key": "10.5061/dryad.v8cp134"}], "notes": [], "created": "2019-01-17T13:59:22.234Z", "modified": "2019-01-17T13:59:22.253Z"}, {"entity": "publication", "iuid": "d7b2c32b16fd4a5f89fc626f7a23fbec", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d7b2c32b16fd4a5f89fc626f7a23fbec.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d7b2c32b16fd4a5f89fc626f7a23fbec"}}, "title": "Crop-to-wild gene flow and its fitness consequences for a wild fruit tree: Towards a comprehensive conservation strategy of the wild apple in Europe.", "authors": [{"family": "Feurtey", "given": "Alice", "initials": "A"}, {"family": "Cornille", "given": "Amandine", "initials": "A"}, {"family": "Shykoff", "given": "Jacqui A", "initials": "JA"}, {"family": "Snirc", "given": "Alodie", "initials": "A"}, {"family": "Giraud", "given": "Tatiana", "initials": "T"}], "type": "journal article", "published": "2017-02-00", "journal": {"title": "Evol Appl", "issn": "1752-4571", "volume": "10", "issue": "2", "pages": "180-188", "issn-l": "1752-4571"}, "abstract": "Crop-to-wild gene flow can reduce the fitness and genetic integrity of wild species. ", "doi": "10.1111/eva.12441", "pmid": "28127394", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "EVA12441"}, {"db": "pmc", "key": "PMC5253423"}], "notes": [], "created": "2018-12-05T12:32:06.305Z", "modified": "2018-12-05T12:32:06.335Z"}], "created": "2018-12-05T12:32:06.317Z", "modified": "2020-11-27T13:12:56.868Z"}