{"entity": "researcher", "timestamp": "2026-08-20T20:45:26.765Z", "family": "Klasson", "given": "Lisa", "initials": "L", "orcid": "0000-0002-5874-7153", "affiliations": ["Molecular Evolution, Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/acc68600f94643f49a02b2bcba1cdee5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/acc68600f94643f49a02b2bcba1cdee5"}}, "publications": [{"entity": "publication", "iuid": "25c17f6da0164c548fc5953c8b9742c8", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/25c17f6da0164c548fc5953c8b9742c8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/25c17f6da0164c548fc5953c8b9742c8"}}, "title": "A co-speciation dilemma and a lifestyle transition with genomic consequences in Wolbachia of Neotropical Drosophila", "authors": [{"family": "Papachristos", "given": "Konstantinos", "initials": "K", "orcid": "0000-0002-4777-9088", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/99e2607a5a3f4c32a3fb3e510b21f0f0.json"}}, {"family": "Miller", "given": "Wolfgang J", "initials": "WJ", "orcid": "0000-0002-5044-6276", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/03e245f4bec040808cd3764948906f33.json"}}, {"family": "Klasson", "given": "Lisa", "initials": "L", "orcid": "0000-0002-5874-7153", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/acc68600f94643f49a02b2bcba1cdee5.json"}}], "type": "posted-content", "published": "2025-04-20", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2025.04.16.649125", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T11:02:21.771Z", "modified": "2026-08-20T11:02:21.877Z"}, {"entity": "publication", "iuid": "93e1dbc98b954b649f76c1aa8754ba4f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/93e1dbc98b954b649f76c1aa8754ba4f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/93e1dbc98b954b649f76c1aa8754ba4f"}}, "title": "Saltational Episodes of Reticulate Evolution in the Drosophila saltans Species Group.", "authors": [{"family": "Prediger", "given": "Carolina", "initials": "C", "orcid": "0000-0002-8649-6400", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/735f44c95ce94e7fb41a91b285fccd38.json"}}, {"family": "Ferreira", "given": "Erina A", "initials": "EA", "orcid": "0000-0003-2069-1374", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/768492c763354f9d8123fa75ec3a3d26.json"}}, {"family": "Zorzato", "given": "Samara Videira", "initials": "SV", "orcid": "0000-0003-1107-2985", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ddf25b04b44349088cde06346dbe48c4.json"}}, {"family": "Hua-Van", "given": "Aur\u00e9lie", "initials": "A", "orcid": "0000-0001-7859-2788", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e1ccf47649a24eff8b8f046faf9f1221.json"}}, {"family": "Klasson", "given": "Lisa", "initials": "L", "orcid": "0000-0002-5874-7153", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/acc68600f94643f49a02b2bcba1cdee5.json"}}, {"family": "Miller", "given": "Wolfgang J", "initials": "WJ", "orcid": "0000-0002-5044-6276", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/03e245f4bec040808cd3764948906f33.json"}}, {"family": "Yassin", "given": "Amir", "initials": "A", "orcid": "0000-0002-2590-5434", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f61c80bfca8a4f5c839c8f5167a1ec6c.json"}}, {"family": "Madi-Ravazzi", "given": "Lilian", "initials": "L", "orcid": "0000-0002-6250-0794", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4bd17bc2354e416b91120355c558f542.json"}}], "type": "journal article", "published": "2024-12-06", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "volume": "41", "issue": "12", "issn-l": "0737-4038"}, "abstract": "Phylogenomics reveals reticulate evolution to be widespread across taxa, but whether reticulation is due to low statistical power or it is a true evolutionary pattern remains a field of study. Here, we investigate the phylogeny and quantify reticulation in the Drosophila saltans species group, a Neotropical clade of the subgenus Sophophora comprising 23 species whose relationships have long been problematic. Phylogenetic analyses revealed conflicting topologies between the X chromosome, autosomes and the mitochondria. We extended the ABBA-BABA test of asymmetry in phylogenetic discordance to cases where no \"true\" species tree could be inferred, and applied our new test (called 2A2B) to whole genome data and to individual loci. We used four strategies, two based on our new assemblies using either conserved genes or \u226550 kb-long syntenic blocks with conserved collinearity across Neotropical Sophophora, and two consisted of windows from pseudo-reference genomes aligned to either an ingroup or outgroup species. Evidence for reticulation varied among the strategies, being lowest in the synteny-based approach, where it did not exceed \u223c7% of the blocks in the most conflicting species quartets. High incidences of reticulation were restricted to three nodes on the tree that coincided with major paleogeographical events in South America. Our results identify possible technical biases in quantifying reticulate evolution and indicate that episodic rapid radiations have played a major role in the evolution of a largely understudied Neotropical clade.", "doi": "10.1093/molbev/msae250", "pmid": "39661651", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11662284"}, {"db": "pii", "key": "7921496"}, {"db": "BioProject", "key": "PRJNA1078835"}], "notes": [], "created": "2026-08-20T09:42:36.982Z", "modified": "2026-08-20T09:42:37.361Z"}, {"entity": "publication", "iuid": "3b6e62e4f9714c089c758998388780b2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3b6e62e4f9714c089c758998388780b2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3b6e62e4f9714c089c758998388780b2"}}, "title": "Saltational episodes of reticulate evolution in the Drosophila saltans species group", "authors": [{"family": "Prediger", "given": "Carolina", "initials": "C", "orcid": "0000-0002-8649-6400", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/735f44c95ce94e7fb41a91b285fccd38.json"}}, {"family": "Ferreira", "given": "Erina A", "initials": "EA", "orcid": "0000-0003-2069-1374", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/768492c763354f9d8123fa75ec3a3d26.json"}}, {"family": "Zorzato", "given": "Samara Videira", "initials": "SV", "orcid": "0000-0003-1107-2985", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ddf25b04b44349088cde06346dbe48c4.json"}}, {"family": "Hua-Van", "given": "Aur\u00e9lie", "initials": "A", "orcid": "0000-0001-7859-2788", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e1ccf47649a24eff8b8f046faf9f1221.json"}}, {"family": "Klasson", "given": "Lisa", "initials": "L", "orcid": "0000-0002-5874-7153", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/acc68600f94643f49a02b2bcba1cdee5.json"}}, {"family": "Miller", "given": "Wolfgang J", "initials": "WJ", "orcid": "0000-0002-5044-6276", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/03e245f4bec040808cd3764948906f33.json"}}, {"family": "Yassin", "given": "Amir", "initials": "A", "orcid": "0000-0002-2590-5434", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f61c80bfca8a4f5c839c8f5167a1ec6c.json"}}, {"family": "Madi-Ravazzi", "given": "Lilian", "initials": "L", "orcid": "0000-0002-6250-0794", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4bd17bc2354e416b91120355c558f542.json"}}], "type": "posted-content", "published": "2023-10-10", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2023.10.09.561511", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:48:24.225Z", "modified": "2026-08-20T10:48:24.319Z"}, {"entity": "publication", "iuid": "b35e73a61e4c4bbd8bcde36bcab6af66", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b35e73a61e4c4bbd8bcde36bcab6af66.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b35e73a61e4c4bbd8bcde36bcab6af66"}}, "title": "Genomic Changes During the Evolution of the Coxiella Genus Along the Parasitism-Mutualism Continuum", "authors": [{"family": "Santos-Garcia", "given": "Diego", "initials": "D", "orcid": "0000-0002-3401-2662", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/46e4929af55346b98c85516c541b8360.json"}}, {"family": "Morel", "given": "Olivier", "initials": "O"}, {"family": "Henri", "given": "H\u00e9l\u00e8ne", "initials": "H", "orcid": "0000-0001-9609-1952", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c59baa9fd86f4e91b4f4fa1162d2e660.json"}}, {"family": "Filali", "given": "Adil El", "initials": "AE", "orcid": "0000-0001-5183-0010", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/80dec81de1ca4021b3584a0bd3e32dfe.json"}}, {"family": "Buysse", "given": "Marie", "initials": "M", "orcid": "0000-0002-8160-2470", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/701e89947562493f9bcaf12d88ad3c59.json"}}, {"family": "No\u00ebl", "given": "Val\u00e9rie", "initials": "V", "orcid": "0000-0002-4305-0046", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c934eb7a346c42b9822e6ab98b3c8bd8.json"}}, {"family": "McCoy", "given": "Karen D", "initials": "KD", "orcid": "0000-0002-8972-3808", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f4afe92050744383bc6f9e3a088cdd59.json"}}, {"family": "Gottlieb", "given": "Yuval", "initials": "Y", "orcid": "0000-0002-2028-7438", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e11b9aad0c314757b83a196efee3fb94.json"}}, {"family": "Klasson", "given": "Lisa", "initials": "L", "orcid": "0000-0002-5874-7153", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/acc68600f94643f49a02b2bcba1cdee5.json"}}, {"family": "Zenner", "given": "Lionel", "initials": "L", "orcid": "0000-0001-5637-8799", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b7855f157d7f4a2d878ff47183812785.json"}}, {"family": "Duron", "given": "Olivier", "initials": "O", "orcid": "0000-0002-7426-782X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c22059db60c4b81b44c636fd16324ad.json"}}, {"family": "Vavre", "given": "Fabrice", "initials": "F", "orcid": "0000-0003-0909-2936", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/89608a38ca38456d8251ef9a23a9dcab.json"}}], "type": "posted-content", "published": "2022-10-26", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.10.26.513839", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:41:58.335Z", "modified": "2026-08-20T10:41:58.744Z"}, {"entity": "publication", "iuid": "fd34a50c7d9844d68f23f4df2d4c3914", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/fd34a50c7d9844d68f23f4df2d4c3914.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/fd34a50c7d9844d68f23f4df2d4c3914"}}, "title": "Comparative genome sequencing reveals insights into the dynamics of Wolbachia in native and invasive cherry fruit flies.", "authors": [{"family": "Wolfe", "given": "Thomas M", "initials": "TM", "orcid": "0000-0002-1509-0147", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0a6c33800c2c43d7a1b843a6c6fd4f00.json"}}, {"family": "Bruzzese", "given": "Daniel J", "initials": "DJ", "orcid": "0000-0002-3115-6599", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2beebd02d7d248d1b2cbcf6b663e1b80.json"}}, {"family": "Klasson", "given": "Lisa", "initials": "L", "orcid": "0000-0002-5874-7153", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/acc68600f94643f49a02b2bcba1cdee5.json"}}, {"family": "Corretto", "given": "Erika", "initials": "E", "orcid": "0000-0002-7767-5191", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d58b6fc272e94c9db3291307384a80fb.json"}}, {"family": "Le\u010di\u0107", "given": "Sonja", "initials": "S", "orcid": "0000-0001-8865-3230", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a71059def3c540b29c996f3c2345123c.json"}}, {"family": "Stauffer", "given": "Christian", "initials": "C", "orcid": "0000-0002-2985-8911", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/96e6cf5ba3994dd2bcdae1d5fea96507.json"}}, {"family": "Feder", "given": "Jeffrey L", "initials": "JL", "orcid": "0000-0002-8797-980X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7eee75d63ac4143a4bcb0603bff88f8.json"}}, {"family": "Schuler", "given": "Hannes", "initials": "H", "orcid": "0000-0001-8307-9831", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/acb539353a60475d9701c9d88865f175.json"}}], "type": "journal article", "published": "2021-12-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "30", "issue": "23", "pages": "6259-6272", "issn-l": "0962-1083"}, "abstract": "Wolbachia is a maternally inherited obligate endosymbiont that can induce a wide spectrum of effects in its host, ranging from mutualism to reproductive parasitism. At the genomic level, recombination within and between strains, transposable elements, and horizontal transfer of strains between host species make Wolbachia an evolutionarily dynamic bacterial system. The invasive cherry fruit fly Rhagoletis cingulata arrived in Europe from North America ~40 years ago, where it now co-occurs with the native cherry pest R. cerasi. This shared distribution has been proposed to have led to the horizontal transfer of different Wolbachia strains between the two species. To better understand transmission dynamics, we performed a comparative genome study of the strain wCin2 in its native United States and invasive European populations of R. cingulata with wCer2 in European R. cerasi. Previous multilocus sequence genotyping (MLST) of six genes implied that the source of wCer2 in R. cerasi was wCin2 from R. cingulata. However, we report genomic evidence discounting the recent horizontal transfer hypothesis for the origin of wCer2. Despite near identical sequences for the MLST markers, substantial sequence differences for other loci were found between wCer2 and wCin2, as well as structural rearrangements, and differences in prophage, repetitive element, gene content, and cytoplasmic incompatibility inducing genes. Our study highlights the need for whole-genome sequencing rather than relying on MLST markers for resolving Wolbachia strains and assessing their evolutionary dynamics.", "doi": "10.1111/mec.15923", "pmid": "33882628", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9290052"}, {"db": "GENBANK", "key": "CP072012"}, {"db": "GENBANK", "key": "JX073687.1"}, {"db": "GENBANK", "key": "KJ546857.1"}, {"db": "GENBANK", "key": "JX073689.1"}, {"db": "GENBANK", "key": "KJ546853.1"}, {"db": "GENBANK", "key": "JX073685.1"}, {"db": "GENBANK", "key": "KJ546849.1"}, {"db": "GENBANK", "key": "JX073691.1"}, {"db": "GENBANK", "key": "KJ546845.1"}, {"db": "GENBANK", "key": "JX073683.1"}, {"db": "GENBANK", "key": "KJ546841.1"}, {"db": "GENBANK", "key": "JX073681.1"}, {"db": "GENBANK", "key": "AF418557.1"}], "notes": [], "created": "2026-08-20T11:18:59.705Z", "modified": "2026-08-20T11:19:00.161Z"}, {"entity": "publication", "iuid": "d5a15b1c9273491bb550b1abfcad32c9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d5a15b1c9273491bb550b1abfcad32c9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d5a15b1c9273491bb550b1abfcad32c9"}}, "title": "Comparative genomics reveals factors associated with phenotypic expression of Wolbachia", "authors": [{"family": "Bai\u00e3o", "given": "Guilherme Costa", "initials": "GC"}, {"family": "Janice", "given": "Jessin", "initials": "J"}, {"family": "Galinou", "given": "Maria", "initials": "M"}, {"family": "Klasson", "given": "Lisa", "initials": "L", "orcid": "0000-0002-5874-7153", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/acc68600f94643f49a02b2bcba1cdee5.json"}}], "type": "posted-content", "published": "2021-01-29", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2021.01.29.428792", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:02:22.852Z", "modified": "2026-08-20T10:02:22.907Z"}, {"entity": "publication", "iuid": "47d890e341dd4409aa9cba23ba5c3303", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/47d890e341dd4409aa9cba23ba5c3303.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/47d890e341dd4409aa9cba23ba5c3303"}}, "title": "Multiple introgressions shape mitochondrial evolutionary history in Drosophila paulistorum and the Drosophila willistoni group", "authors": [{"family": "Bai\u00e3o", "given": "Guilherme C", "initials": "GC"}, {"family": "Schneider", "given": "Daniela I", "initials": "DI"}, {"family": "Miller", "given": "Wolfgang J", "initials": "WJ"}, {"family": "Klasson", "given": "Lisa", "initials": "L", "orcid": "0000-0002-5874-7153", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/acc68600f94643f49a02b2bcba1cdee5.json"}}], "type": "posted-content", "published": "2020-09-18", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2020.09.17.301572", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T09:59:12.165Z", "modified": "2026-08-20T09:59:12.180Z"}]}