{"entity": "researcher", "timestamp": "2026-07-22T17:48:33.563Z", "family": "Pyh\u00e4j\u00e4rvi", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6958-5172", "affiliations": ["Department of Forest Sciences, University of Helsinki, Helsinki, Finland. tanja.pyhajarvi@helsinki.fi.", "Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland. tanja.pyhajarvi@helsinki.fi."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/87ba3d35a88442848f22835c85fadbce.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/87ba3d35a88442848f22835c85fadbce"}}, "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": "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"}]}