{"entity": "researcher", "timestamp": "2026-07-11T13:59:55.712Z", "family": "Lascoux", "given": "Martin", "initials": "M", "orcid": "0000-0003-1699-9042", "affiliations": ["Department of Ecology and Genetics, EBC, Uppsala University, 752 36 Uppsala, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/4ad3fadfb69448f397ad3bf55b2d2cb3.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/4ad3fadfb69448f397ad3bf55b2d2cb3"}}, "publications": [{"entity": "publication", "iuid": "ff4c4a6fe0524e3bb928418664c5a917", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ff4c4a6fe0524e3bb928418664c5a917.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ff4c4a6fe0524e3bb928418664c5a917"}}, "title": "Resilience of genetic diversity in forest trees over the Quaternary.", "authors": [{"family": "Milesi", "given": "Pascal", "initials": "P", "orcid": "0000-0001-8580-4291", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f59e048cc6a4159a1829885b370d978.json"}}, {"family": "Kastally", "given": "Chedly", "initials": "C", "orcid": "0000-0002-1820-4752", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d98c61ddd95447186180256d00410bd.json"}}, {"family": "Dauphin", "given": "Benjamin", "initials": "B", "orcid": "0000-0003-0982-4252", "researcher": {"href": "https://publications.scilifelab.se/researcher/8378e4ef12e34498b4f355a5ebcc0f0e.json"}}, {"family": "Cervantes", "given": "Sandra", "initials": "S", "orcid": "0000-0003-0793-5784", "researcher": {"href": "https://publications.scilifelab.se/researcher/9de980d11e35480e90f301e14b2e69df.json"}}, {"family": "Bagnoli", "given": "Francesca", "initials": "F", "orcid": "0000-0001-6909-0006", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc651aee75cf4447a747f642037e813d.json"}}, {"family": "Budde", "given": "Katharina B", "initials": "KB"}, {"family": "Cavers", "given": "Stephen", "initials": "S", "orcid": "0000-0003-2139-9236", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ab207ecaffd4f528dc5b4376ecc1c14.json"}}, {"family": "Fady", "given": "Bruno", "initials": "B"}, {"family": "Faivre-Rampant", "given": "Patricia", "initials": "P", "orcid": "0000-0003-0777-6621", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1ebde17a7204461b9c65dbb6b0fff56.json"}}, {"family": "Gonz\u00e1lez-Mart\u00ednez", "given": "Santiago C", "initials": "SC", "orcid": "0000-0002-4534-3766", "researcher": {"href": "https://publications.scilifelab.se/researcher/f6337448ae7f457fb17f11dabf6e48be.json"}}, {"family": "Grivet", "given": "Delphine", "initials": "D", "orcid": "0000-0001-8168-4456", "researcher": {"href": "https://publications.scilifelab.se/researcher/655a75d7756f41099d9fcbcb17fdb512.json"}}, {"family": "Gugerli", "given": "Felix", "initials": "F", "orcid": "0000-0003-3878-1845", "researcher": {"href": "https://publications.scilifelab.se/researcher/027bd6add3a340c6aaf002c02f464095.json"}}, {"family": "Jorge", "given": "V\u00e9ronique", "initials": "V", "orcid": "0000-0002-5016-3006", "researcher": {"href": "https://publications.scilifelab.se/researcher/34dd9cdd219940fcaf811cc98730e8e6.json"}}, {"family": "Lesur Kupin", "given": "Isabelle", "initials": "I"}, {"family": "Ojeda", "given": "Dario I", "initials": "DI"}, {"family": "Olsson", "given": "Sanna", "initials": "S", "orcid": "0000-0002-1199-4499", "researcher": {"href": "https://publications.scilifelab.se/researcher/a5a60a1a580d4634a6ca32dd1d4ba101.json"}}, {"family": "Opgenoorth", "given": "Lars", "initials": "L", "orcid": "0000-0003-0737-047X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b5ea2081d1341babd837bcfb8a4fd27.json"}}, {"family": "Pinosio", "given": "Sara", "initials": "S", "orcid": "0000-0002-1820-3637", "researcher": {"href": "https://publications.scilifelab.se/researcher/c691c7bb0181439ca1384d27061b59d9.json"}}, {"family": "Plomion", "given": "Christophe", "initials": "C"}, {"family": "Rellstab", "given": "Christian", "initials": "C", "orcid": "0000-0002-0221-5975", "researcher": {"href": "https://publications.scilifelab.se/researcher/d777277731b146da897676fb82ea4d7f.json"}}, {"family": "Rogier", "given": "Odile", "initials": "O", "orcid": "0000-0001-6879-364X", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d3148f27d7f4510a143eaf9eb3ceb1e.json"}}, {"family": "Scalabrin", "given": "Simone", "initials": "S", "orcid": "0000-0001-8686-8385", "researcher": {"href": "https://publications.scilifelab.se/researcher/06cae7b93e7e48c187df2bb95fd3031f.json"}}, {"family": "Scotti", "given": "Ivan", "initials": "I"}, {"family": "Vendramin", "given": "Giovanni G", "initials": "GG", "orcid": "0000-0001-9921-7872", "researcher": {"href": "https://publications.scilifelab.se/researcher/e70f1198e7b4482fabb1a5167eab3c0f.json"}}, {"family": "Westergren", "given": "Marjana", "initials": "M", "orcid": "0000-0002-4204-0161", "researcher": {"href": "https://publications.scilifelab.se/researcher/d082e25234e7480382aa7c068f65ed49.json"}}, {"family": "Lascoux", "given": "Martin", "initials": "M", "orcid": "0000-0003-1699-9042", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ad3fadfb69448f397ad3bf55b2d2cb3.json"}}, {"family": "Pyh\u00e4j\u00e4rvi", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6958-5172", "researcher": {"href": "https://publications.scilifelab.se/researcher/87ba3d35a88442848f22835c85fadbce.json"}}, {"family": "GenTree Consortium", "given": "", "initials": ""}], "type": "journal article", "published": "2024-10-14", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "8538", "issn-l": "2041-1723"}, "abstract": "The effect of past environmental changes on the demography and genetic diversity of natural populations remains a contentious issue and has rarely been investigated across multiple, phylogenetically distant species. Here, we perform comparative population genomic analyses and demographic inferences for seven widely distributed and ecologically contrasting European forest tree species based on concerted sampling of 164 populations across their natural ranges. For all seven species, the effective population size, Ne, increased or remained stable over many glacial cycles and up to 15 million years in the most extreme cases. Surprisingly, the drastic environmental changes associated with the Pleistocene glacial cycles have had little impact on the level of genetic diversity of dominant forest tree species, despite major shifts in their geographic ranges. Based on their trajectories of Ne over time, the seven tree species can be divided into three major groups, highlighting the importance of life history and range size in determining synchronous variation in genetic diversity over time. Altogether, our results indicate that forest trees have been able to retain their evolutionary potential over very long periods of time despite strong environmental changes.", "doi": "10.1038/s41467-024-52612-y", "pmid": "39402024", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11473659"}, {"db": "pii", "key": "10.1038/s41467-024-52612-y"}], "notes": [], "created": "2024-11-25T10:18:08.923Z", "modified": "2024-11-25T10:18:09.656Z"}, {"entity": "publication", "iuid": "8b0ca8d9347d4e589bbd155951bd924a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8b0ca8d9347d4e589bbd155951bd924a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8b0ca8d9347d4e589bbd155951bd924a"}}, "title": "Dominance between self-incompatibility alleles determines the mating system of Capsella allopolyploids.", "authors": [{"family": "Duan", "given": "Tianlin", "initials": "T"}, {"family": "Zhang", "given": "Zebin", "initials": "Z"}, {"family": "Genete", "given": "Mathieu", "initials": "M"}, {"family": "Poux", "given": "C\u00e9line", "initials": "C"}, {"family": "Sicard", "given": "Adrien", "initials": "A", "orcid": "0000-0002-4104-6844", "researcher": {"href": "https://publications.scilifelab.se/researcher/559469d6cd9a4435beffc526f2655c5c.json"}}, {"family": "Lascoux", "given": "Martin", "initials": "M", "orcid": "0000-0003-1699-9042", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ad3fadfb69448f397ad3bf55b2d2cb3.json"}}, {"family": "Castric", "given": "Vincent", "initials": "V"}, {"family": "Vekemans", "given": "Xavier", "initials": "X"}], "type": "journal article", "published": "2024-08-00", "journal": {"issn": "2056-3744", "title": "Evolution Letters", "volume": "8", "issue": "4", "pages": "550-560", "issn-l": "2056-3744"}, "abstract": "The shift from outcrossing to self-fertilization is one of the main evolutionary transitions in plants and has broad effects on evolutionary trajectories. In Brassicaceae, the ability to inhibit self-fertilization is controlled by 2 genes, SCR and SRK, tightly linked within the S-locus. A series of small non-coding RNAs also encoded within the S-locus regulates the transcriptional activity of SCR alleles, resulting in a linear dominance hierarchy between them. In Brassicaceae, natural allopolyploid species are often self-compatible (SC) even when one of the progenitor species is self-incompatible, but the reason why polyploid lineages tend to lose self-incompatibility (SI) and the timing of the loss of SI (immediately after ancestral hybridization between the progenitor species, or at a later stage after the formation of allopolyploid lineages) have generally remained elusive. We used a series of synthetic diploid and tetraploid hybrids obtained between self-fertilizing Capsella orientalis and outcrossing Capsella grandiflora to test whether the breakdown of SI could be observed immediately after hybridization, and whether the occurrence of SC phenotypes could be explained by the dominance interactions between S-haplotypes inherited from the parental lineages. We used RNA-sequencing data from young inflorescences to measure allele-specific expression of the SCR gene and infer dominance interactions in the synthetic hybrids. We then evaluated the seed set from autonomous self-pollination in the synthetic hybrids. Our results demonstrate that self-compatibility of the hybrids depends on the relative dominance between S-alleles inherited from the parental species, confirming that SI can be lost instantaneously upon formation of the ancestral allopolyploid lineage. They also confirm that the epigenetic regulation that controls dominance interactions between S-alleles can function between subgenomes in allopolyploids. Together, our results illustrate how a detailed knowledge of the mechanisms controlling SI can illuminate our understanding of the patterns of co-variation between the mating system and changes in ploidy.", "doi": "10.1093/evlett/qrae011", "pmid": "39100231", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11291619"}, {"db": "pii", "key": "qrae011"}, {"db": "figshare", "key": "10.6084/m9.figshare.22567558.v2"}], "notes": [], "created": "2024-05-16T06:32:00.828Z", "modified": "2025-02-28T14:17:25.871Z"}, {"entity": "publication", "iuid": "d392ed58887449ec845d08831ec8b3c2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d392ed58887449ec845d08831ec8b3c2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d392ed58887449ec845d08831ec8b3c2"}}, "title": "Complex Polyploids: Origins, Genomic Composition, and Role of Introgressed Alleles.", "authors": [{"family": "Leal", "given": "J Luis", "initials": "JL", "orcid": "0000-0003-0731-7329", "researcher": {"href": "https://publications.scilifelab.se/researcher/22b1c077dfa040d0b65494d9b944cf7d.json"}}, {"family": "Milesi", "given": "Pascal", "initials": "P"}, {"family": "Hodkov\u00e1", "given": "Eva", "initials": "E"}, {"family": "Zhou", "given": "Qiujie", "initials": "Q"}, {"family": "James", "given": "Jennifer", "initials": "J", "orcid": "0000-0003-0518-6783", "researcher": {"href": "https://publications.scilifelab.se/researcher/627b7b16c94a440b9f5ba11b6aee12fc.json"}}, {"family": "Eklund", "given": "D Magnus", "initials": "DM"}, {"family": "Pyh\u00e4j\u00e4rvi", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6958-5172", "researcher": {"href": "https://publications.scilifelab.se/researcher/87ba3d35a88442848f22835c85fadbce.json"}}, {"family": "Saloj\u00e4rvi", "given": "Jarkko", "initials": "J"}, {"family": "Lascoux", "given": "Martin", "initials": "M", "orcid": "0000-0003-1699-9042", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ad3fadfb69448f397ad3bf55b2d2cb3.json"}}], "type": "journal article", "published": "2024-07-27", "journal": {"title": "Syst. Biol.", "issn": "1076-836X", "volume": "73", "issue": "2", "pages": "392-418", "issn-l": "1063-5157"}, "abstract": "Introgression allows polyploid species to acquire new genomic content from diploid progenitors or from other unrelated diploid or polyploid lineages, contributing to genetic diversity and facilitating adaptive allele discovery. In some cases, high levels of introgression elicit the replacement of large numbers of alleles inherited from the polyploid's ancestral species, profoundly reshaping the polyploid's genomic composition. In such complex polyploids, it is often difficult to determine which taxa were the progenitor species and which taxa provided additional introgressive blocks through subsequent hybridization. Here, we use population-level genomic data to reconstruct the phylogenetic history of Betula pubescens (downy birch), a tetraploid species often assumed to be of allopolyploid origin and which is known to hybridize with at least four other birch species. This was achieved by modeling polyploidization and introgression events under the multispecies coalescent and then using an approximate Bayesian computation rejection algorithm to evaluate and compare competing polyploidization models. We provide evidence that B. pubescens is the outcome of an autoploid genome doubling event in the common ancestor of B. pendula and its extant sister species, B. platyphylla, that took place approximately 178,000-188,000 generations ago. Extensive hybridization with B. pendula, B. nana, and B. humilis followed in the aftermath of autopolyploidization, with the relative contribution of each of these species to the B. pubescens genome varying markedly across the species' range. Functional analysis of B. pubescens loci containing alleles introgressed from B. nana identified multiple genes involved in climate adaptation, while loci containing alleles derived from B. humilis revealed several genes involved in the regulation of meiotic stability and pollen viability in plant species.", "doi": "10.1093/sysbio/syae012", "pmid": "38613229", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11282369"}, {"db": "pii", "key": "7645150"}], "notes": [], "created": "2024-11-25T10:25:56.877Z", "modified": "2025-02-28T14:19:27.018Z"}, {"entity": "publication", "iuid": "98e4505a97e8498295f664d0b66ace12", "links": {"self": {"href": "https://publications.scilifelab.se/publication/98e4505a97e8498295f664d0b66ace12.json"}, "display": {"href": "https://publications.scilifelab.se/publication/98e4505a97e8498295f664d0b66ace12"}}, "title": "Separating phases of allopolyploid evolution with resynthesized and natural Capsella bursa-pastoris.", "authors": [{"family": "Duan", "given": "Tianlin", "initials": "T", "orcid": "0000-0002-8719-7998", "researcher": {"href": "https://publications.scilifelab.se/researcher/78c1a5d458814388bbcbbe6a020944d6.json"}}, {"family": "Sicard", "given": "Adrien", "initials": "A"}, {"family": "Gl\u00e9min", "given": "Sylvain", "initials": "S", "orcid": "0000-0001-7260-4573", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ce5a8d7ac9a490eb2e261aeb75088d4.json"}}, {"family": "Lascoux", "given": "Martin", "initials": "M", "orcid": "0000-0003-1699-9042", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ad3fadfb69448f397ad3bf55b2d2cb3.json"}}], "type": "journal article", "published": "2024-01-08", "journal": {"title": "Elife", "issn": "2050-084X", "volume": "12", "issn-l": "2050-084X"}, "abstract": "Allopolyploidization is a frequent evolutionary transition in plants that combines whole-genome duplication (WGD) and interspecific hybridization. The genome of an allopolyploid species results from initial interactions between parental genomes and long-term evolution. Distinguishing the contributions of these two phases is essential to understanding the evolutionary trajectory of allopolyploid species. Here, we compared phenotypic and transcriptomic changes in natural and resynthesized Capsella allotetraploids with their diploid parental species. We focused on phenotypic traits associated with the selfing syndrome and on transcription-level phenomena such as expression-level dominance (ELD), transgressive expression (TRE), and homoeolog expression bias (HEB). We found that selfing syndrome, high pollen, and seed quality in natural allotetraploids likely resulted from long-term evolution. Similarly, TRE and most down-regulated ELD were only found in natural allopolyploids. Natural allotetraploids also had more ELD toward the self-fertilizing parental species than resynthesized allotetraploids, mirroring the establishment of the selfing syndrome. However, short-term changes mattered, and 40% of the cases of ELD in natural allotetraploids were already observed in resynthesized allotetraploids. Resynthesized allotetraploids showed striking variation of HEB among chromosomes and individuals. Homoeologous synapsis was its primary source and may still be a source of genetic variation in natural allotetraploids. In conclusion, both short- and long-term mechanisms contributed to transcriptomic and phenotypic changes in natural allotetraploids. However, the initial gene expression changes were largely reshaped during long-term evolution leading to further morphological changes.", "doi": "10.7554/eLife.88398", "pmid": "38189348", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10945474"}, {"db": "pii", "key": "88398"}], "notes": [], "created": "2024-03-21T13:55:14.769Z", "modified": "2024-11-25T10:34:07.268Z"}, {"entity": "publication", "iuid": "73903819e7d04c8080b1d59bc8404916", "links": {"self": {"href": "https://publications.scilifelab.se/publication/73903819e7d04c8080b1d59bc8404916.json"}, "display": {"href": "https://publications.scilifelab.se/publication/73903819e7d04c8080b1d59bc8404916"}}, "title": "How broad is the selfing syndrome? Insights from convergent evolution of gene expression across species and tissues in the Capsella genus.", "authors": [{"family": "Zhang", "given": "Zebin", "initials": "Z", "orcid": "0000-0002-9828-4245", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ff9ac7ea672401eafa52c91fd57173d.json"}}, {"family": "Kryvokhyzha", "given": "Dmytro", "initials": "D", "orcid": "0000-0001-6498-1977", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3ca1c441506436282871ecd40f7be35.json"}}, {"family": "Orsucci", "given": "Marion", "initials": "M", "orcid": "0000-0001-8516-1361", "researcher": {"href": "https://publications.scilifelab.se/researcher/386ae7a5a09640ff850a8bc62a31202c.json"}}, {"family": "Gl\u00e9min", "given": "Sylvain", "initials": "S", "orcid": "0000-0001-7260-4573", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ce5a8d7ac9a490eb2e261aeb75088d4.json"}}, {"family": "Milesi", "given": "Pascal", "initials": "P", "orcid": "0000-0001-8580-4291", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f59e048cc6a4159a1829885b370d978.json"}}, {"family": "Lascoux", "given": "Martin", "initials": "M", "orcid": "0000-0003-1699-9042", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ad3fadfb69448f397ad3bf55b2d2cb3.json"}}], "type": "journal article", "published": "2022-09-12", "journal": {"title": "New Phytol.", "issn": "1469-8137", "issn-l": "0028-646X"}, "abstract": "The shift from outcrossing to selfing is one of the main evolutionary transitions in plants. It is accompanied by profound effects on reproductive traits, the so-called selfing syndrome. Because the transition to selfing also implies deep genomic and ecological changes, one also expects to observe a genomic selfing syndrome. We took advantage of the three independent transitions from outcrossing to selfing in the Capsella genus to characterize the overall impact of mating system change on RNA expression, in flowers but also in leaves and roots. We quantified the extent of both selfing and genomic syndromes, and tested whether changes in expression corresponded to adaptation to selfing or to relaxed selection on traits that were constrained in outcrossers. Mating system change affected gene expression in all three tissues but more so in flowers than in roots and leaves. Gene expression in selfing species tended to converge in flowers but diverged in the two other tissues. Hence, convergent adaptation to selfing dominates in flowers, whereas genetic drift plays a more important role in leaves and roots. The effect of mating system transition is not limited to reproductive tissues and corresponds to both adaptation to selfing and relaxed selection on previously constrained traits.", "doi": "10.1111/nph.18477", "pmid": "36089898", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2022-11-09T15:46:32.614Z", "modified": "2024-01-16T13:48:35.027Z"}, {"entity": "publication", "iuid": "903a0d4b47c0422abb32f266006c4d51", "links": {"self": {"href": "https://publications.scilifelab.se/publication/903a0d4b47c0422abb32f266006c4d51.json"}, "display": {"href": "https://publications.scilifelab.se/publication/903a0d4b47c0422abb32f266006c4d51"}}, "title": "Allorecognition genes drive reproductive isolation in Podospora anserina.", "authors": [{"family": "Ament-Vel\u00e1squez", "given": "S Lorena", "initials": "SL", "orcid": "0000-0003-3371-9292", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d54ef94f91c4c1c85d5dc3a846023e5.json"}}, {"family": "Vogan", "given": "Aaron A", "initials": "AA", "orcid": "0000-0003-2013-7445", "researcher": {"href": "https://publications.scilifelab.se/researcher/71c6d460e3b44712a1a9dc19066211a4.json"}}, {"family": "Granger-Farbos", "given": "Alexandra", "initials": "A"}, {"family": "Bastiaans", "given": "Eric", "initials": "E", "orcid": "0000-0003-1502-0947", "researcher": {"href": "https://publications.scilifelab.se/researcher/870bd6035e54489187ef1d5131d14108.json"}}, {"family": "Martinossi-Allibert", "given": "Ivain", "initials": "I"}, {"family": "Saupe", "given": "Sven J", "initials": "SJ"}, {"family": "de Groot", "given": "Suzette", "initials": "S"}, {"family": "Lascoux", "given": "Martin", "initials": "M", "orcid": "0000-0003-1699-9042", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ad3fadfb69448f397ad3bf55b2d2cb3.json"}}, {"family": "Debets", "given": "Alfons J M", "initials": "AJM", "orcid": "0000-0002-1799-4617", "researcher": {"href": "https://publications.scilifelab.se/researcher/b95b282c02d44a1a9f4d3d2aa7578b8a.json"}}, {"family": "Clav\u00e9", "given": "Corinne", "initials": "C"}, {"family": "Johannesson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6359-9856", "researcher": {"href": "https://publications.scilifelab.se/researcher/36e8fe278e01470e8cddaaccc5dad596.json"}}], "type": "journal article", "published": "2022-07-00", "journal": {"title": "Nat Ecol Evol", "issn": "2397-334X", "issn-l": "2397-334X", "volume": "6", "issue": "7", "pages": "910-923"}, "abstract": "Allorecognition, the capacity to discriminate self from conspecific non-self, is a ubiquitous organismal feature typically governed by genes evolving under balancing selection. Here, we show that in the fungus Podospora anserina, allorecognition loci controlling vegetative incompatibility (het genes), define two reproductively isolated groups through pleiotropic effects on sexual compatibility. These two groups emerge from the antagonistic interactions of the unlinked loci het-r (encoding a NOD-like receptor) and het-v (encoding a methyltransferase and an MLKL/HeLo domain protein). Using a combination of genetic and ecological data, supported by simulations, we provide a concrete and molecularly defined example whereby the origin and coexistence of reproductively isolated groups in sympatry is driven by pleiotropic genes under balancing selection.", "doi": "10.1038/s41559-022-01734-x", "pmid": "35551248", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41559-022-01734-x"}, {"db": "pmc", "key": "PMC9262711"}], "notes": [], "created": "2022-11-09T15:43:47.396Z", "modified": "2024-01-16T13:48:36.025Z"}, {"entity": "publication", "iuid": "f2783eb01fdf456e80223bff259edce4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f2783eb01fdf456e80223bff259edce4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f2783eb01fdf456e80223bff259edce4"}}, "title": "Competitive ability depends on mating system and ploidy level across Capsella species.", "authors": [{"family": "Orsucci", "given": "Marion", "initials": "M"}, {"family": "Yang", "given": "Xuyue", "initials": "X"}, {"family": "Vanikiotis", "given": "Theofilos", "initials": "T"}, {"family": "Guerrina", "given": "Maria", "initials": "M"}, {"family": "Duan", "given": "Tianlin", "initials": "T"}, {"family": "Lascoux", "given": "Martin", "initials": "M", "orcid": "0000-0003-1699-9042", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ad3fadfb69448f397ad3bf55b2d2cb3.json"}}, {"family": "Gl\u00e9min", "given": "Sylvain", "initials": "S"}], "type": "journal article", "published": "2022-05-12", "journal": {"title": "Ann. Bot.", "issn": "1095-8290", "volume": "129", "issue": "6", "pages": "697-708", "issn-l": "0305-7364"}, "abstract": "Self-fertilization is often associated with ecological traits corresponding to the ruderal strategy, and selfers are expected to be less competitive than outcrossers, either because of a colonization/competition trade-off or because of the deleterious genetic effects of selfing. Range expansion could reduce further competitive ability while polyploidy could mitigate the effects of selfing. If pollinators are not limited, individual fitness is thus expected to be higher in outcrossers than in selfers and, within selfers, in polyploids than in diploids. Although often proposed in the botanical literature and also suggested by meta-analyses, these predictions have not been directly tested yet.\n\nIn order to compare fitness and the competitive ability of four Capsella species with a different mating system and ploidy level, we combined two complementary experiments. First, we carried out an experiment outdoors in north-west Greece, i.e. within the range of the obligate outcrossing species, C. grandiflora, where several life history traits were measured under two different disturbance treatments, weeded plots vs. unweeded plots. To better control competition and to remove potential effects of local adaptation of the outcrosser, we also performed a similar competition experiment but under growth chamber conditions.\n\nIn the outdoor experiment, disturbance of the environment did not affect the phenotype in any of the four species. For most traits, the obligate outcrossing species performed better than all selfing species. In contrast, polyploids did not survive or reproduce better than diploids. Under controlled conditions, as in the field experiment, the outcrosser had a higher fitness than selfing species and was less affected by competition. Finally, contrary to the outdoor experiment where the two behaved identically, polyploid selfers were less affected by competition than diploid selfes.\n\nIn the Capsella genus, selfing induces lower fitness than outcrossing and can also reduce competitive ability. The effect of polyploidy is, however, unclear. These results highlight the possible roles of ecological context in the evolution of selfing species.", "doi": "10.1093/aob/mcac044", "pmid": "35325927", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "6553953"}, {"db": "pmc", "key": "PMC9113120"}], "notes": [], "created": "2022-11-09T15:40:07.480Z", "modified": "2024-01-16T13:48:36.532Z"}, {"entity": "publication", "iuid": "86f05d7bca134d87b5dd15cffe3d55dd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/86f05d7bca134d87b5dd15cffe3d55dd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/86f05d7bca134d87b5dd15cffe3d55dd"}}, "title": "An introgressed gene causes meiotic drive in Neurospora sitophila.", "authors": [{"family": "Svedberg", "given": "Jesper", "initials": "J", "orcid": "0000-0002-0951-3019", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d35216730c841d197a958bfa00a06a0.json"}}, {"family": "Vogan", "given": "Aaron A", "initials": "AA"}, {"family": "Rhoades", "given": "Nicholas A", "initials": "NA"}, {"family": "Sarmarajeewa", "given": "Dilini", "initials": "D"}, {"family": "Jacobson", "given": "David J", "initials": "DJ"}, {"family": "Lascoux", "given": "Martin", "initials": "M", "orcid": "0000-0003-1699-9042", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ad3fadfb69448f397ad3bf55b2d2cb3.json"}}, {"family": "Hammond", "given": "Thomas M", "initials": "TM", "orcid": "0000-0002-0812-4759", "researcher": {"href": "https://publications.scilifelab.se/researcher/cdc694cc4c4749ca821feadf727fe77b.json"}}, {"family": "Johannesson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6359-9856", "researcher": {"href": "https://publications.scilifelab.se/researcher/36e8fe278e01470e8cddaaccc5dad596.json"}}], "type": "journal article", "published": "2021-04-27", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "118", "issue": "17", "pages": "e2026605118", "issn-l": "0027-8424"}, "abstract": "Meiotic drive elements cause their own preferential transmission following meiosis. In fungi, this phenomenon takes the shape of spore killing, and in the filamentous ascomycete Neurospora sitophila, the Sk-1 spore killer element is found in many natural populations. In this study, we identify the gene responsible for spore killing in Sk-1 by generating both long- and short-read genomic data and by using these data to perform a genome-wide association test. We name this gene Spk-1 Through molecular dissection, we show that a single 405-nt-long open reading frame generates a product that both acts as a poison capable of killing sibling spores and as an antidote that rescues spores that produce it. By phylogenetic analysis, we demonstrate that the gene has likely been introgressed from the closely related species Neurospora hispaniola, and we identify three subclades of N. sitophila, one where Sk-1 is fixed, another where Sk-1 is absent, and a third where both killer and sensitive strain are found. Finally, we show that spore killing can be suppressed through an RNA interference-based genome defense pathway known as meiotic silencing by unpaired DNA. Spk-1 is not related to other known meiotic drive genes, and similar sequences are only found within Neurospora These results shed light on the diversity of genes capable of causing meiotic drive, their origin and evolution, and their interaction with the host genome.", "doi": "10.1073/pnas.2026605118", "pmid": "33875604", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "2026605118"}, {"db": "pmc", "key": "PMC8092558"}, {"db": "figshare", "key": "10.6084/m9.figshare.c.5093585.v1"}], "notes": [], "created": "2021-06-01T20:57:22.667Z", "modified": "2024-01-16T13:48:39.983Z"}]}