{"entity": "journal", "iuid": "71ba9185361340249ba03f22c8c5191a", "timestamp": "2026-09-12T07:42:28.575Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/journal/New%20Phytol..json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/journal/New%20Phytol."}}, "title": "New Phytol.", "issn": "1469-8137", "issn-l": "0028-646X", "publications_count": 12, "publications": [{"entity": "publication", "iuid": "aa9f95b4639a44068ad80705aba1ec45", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/aa9f95b4639a44068ad80705aba1ec45.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/aa9f95b4639a44068ad80705aba1ec45"}}, "title": "The 'queen of the Andes' (Puya raimondii) is genetically fragile and fragmented: a consequence of long generation time and semelparity?", "authors": [{"family": "Liu", "given": "Lu", "initials": "L", "orcid": "0000-0001-7168-5017", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c659b1c306424989af636398dd57f975.json"}}, {"family": "James", "given": "Jennifer", "initials": "J", "orcid": "0000-0003-0518-6783", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4b807f7ab8f46f8a5e927e1b090d662.json"}}, {"family": "Zhang", "given": "Yu-Qu", "initials": "Y"}, {"family": "Wang", "given": "Zheng-Feng", "initials": "Z"}, {"family": "Arakaki", "given": "M\u00f3nica", "initials": "M", "orcid": "0000-0003-1081-2507", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b63566a5a85d4b75817fd1bb59b3f99a.json"}}, {"family": "Vadillo", "given": "Giovana", "initials": "G", "orcid": "0000-0002-0145-0367", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/29a2f91d2eab4066a098317b92075a8c.json"}}, {"family": "Zhou", "given": "Qiu-Jie", "initials": "Q", "orcid": "0000-0001-7351-2371", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/15244ffd4f4746ddb9ec39e4c038204e.json"}}, {"family": "Lascoux", "given": "Martin", "initials": "M", "orcid": "0000-0003-1699-9042", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0730d0f9c2524eb19383640612924701.json"}}, {"family": "Ge", "given": "Xue-Jun", "initials": "X", "orcid": "0000-0002-5008-9475", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ef81044779a4cf08dec7e2f062da88c.json"}}], "type": "journal article", "published": "2024-10-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "issn-l": "0028-646X", "volume": "244", "issue": "1", "pages": "277-291"}, "abstract": "Understanding how life history shapes genetic diversity is a fundamental issue in evolutionary biology, with important consequences for conservation. However, we still have an incomplete picture of the impact of life history on genome-wide patterns of diversity, especially in long-lived semelparous plants. Puya raimondii is a high-altitude semelparous species from the Andes that flowers at 40-100 years of age. We sequenced the whole genome and estimated the nucleotide diversity of 200 individuals sampled from nine populations. Coalescent-based approaches were then used to infer past population dynamics. Finally, these results were compared with results obtained for the iteroparous species, Puya macrura. The nine populations of P. raimondii were highly divergent, highly inbred, and carried an exceptionally high genetic load. They are genetically depauperate, although, locally in the genome, balancing selection contributed to the maintenance of genetic polymorphism. While both P. raimondii and P. macrura went through a severe bottleneck during the Pleistocene, P. raimondii did not recover from it and continuously declined, while P. macrura managed to bounce back. Our results demonstrate the importance of life history, in particular generation time and reproductive strategy, in affecting population dynamics and genomic variation, and illustrate the genetic fragility of long-lived semelparous plants.", "doi": "10.1111/nph.20036", "pmid": "39135394", "labels": {"Jennifer James": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2024-11-27T09:19:02.046Z", "modified": "2024-11-29T09:33:59.308Z"}, {"entity": "publication", "iuid": "7a6e3f3f8ec745eb8e1b8e3c2e5d43c7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7a6e3f3f8ec745eb8e1b8e3c2e5d43c7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7a6e3f3f8ec745eb8e1b8e3c2e5d43c7"}}, "title": "Genomic basis of the distinct biosynthesis of \u03b2-glucogallin, a biochemical marker for hydrolyzable tannin production, in three oak species.", "authors": [{"family": "Yang", "given": "Qinsong", "initials": "Q", "orcid": "0000-0002-9895-1917", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4841be2bec064e57ba36cd09dffbe2c6.json"}}, {"family": "Li", "given": "Jinjin", "initials": "J"}, {"family": "Wang", "given": "Yan", "initials": "Y", "orcid": "0009-0007-4804-6736", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7cce421866c47e994212de99e5d38c5.json"}}, {"family": "Wang", "given": "Zefu", "initials": "Z", "orcid": "0000-0002-5440-4188", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b6b75a1fa8cf49db8db7adb6d053e9f2.json"}}, {"family": "Pei", "given": "Ziqi", "initials": "Z"}, {"family": "Street", "given": "Nathaniel R", "initials": "NR", "orcid": "0000-0001-6031-005X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9fee0b9ea71c4a54abee68132840b274.json"}}, {"family": "Bhalerao", "given": "Rishikesh P", "initials": "RP", "orcid": "0000-0003-4384-7036", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ddd69add89849b7bdeac3959ab9cfa6.json"}}, {"family": "Yu", "given": "Zhaowei", "initials": "Z"}, {"family": "Gao", "given": "Yuhao", "initials": "Y"}, {"family": "Ni", "given": "Junbei", "initials": "J"}, {"family": "Jiao", "given": "Yang", "initials": "Y"}, {"family": "Sun", "given": "Minghui", "initials": "M"}, {"family": "Yang", "given": "Xiong", "initials": "X"}, {"family": "Chen", "given": "Yixin", "initials": "Y"}, {"family": "Liu", "given": "Puyuan", "initials": "P"}, {"family": "Wang", "given": "Jiaxi", "initials": "J"}, {"family": "Liu", "given": "Yong", "initials": "Y"}, {"family": "Li", "given": "Guolei", "initials": "G", "orcid": "0000-0002-2244-4716", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/822709e7c15f4714a6e682f5df09e609.json"}}], "type": "journal article", "published": "2024-06-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "volume": "242", "issue": "6", "pages": "2702-2718", "issn-l": "0028-646X"}, "abstract": "Hydrolyzable tannins (HTs), predominant polyphenols in oaks, are widely used in grape wine aging, feed additives, and human healthcare. However, the limited availability of a high-quality reference genome of oaks greatly hampered the recognition of the mechanism of HT biosynthesis. Here, high-quality reference genomes of three Asian oak species (Quercus variabilis, Quercus aliena, and Quercus dentata) that have different HT contents were generated. Multi-omics studies were carried out to identify key genes regulating HT biosynthesis. In vitro enzyme activity assay was also conducted. Dual-luciferase and yeast one-hybrid assays were used to reveal the transcriptional regulation. Our results revealed that \u03b2-glucogallin was a biochemical marker for HT production in the cupules of the three Asian oaks. UGT84A13 was confirmed as the key enzyme for \u03b2-glucogallin biosynthesis. The differential expression of UGT84A13, rather than enzyme activity, was the main reason for different \u03b2-glucogallin and HT accumulation. Notably, sequence variations in UGT84A13 promoters led to different trans-activating activities of WRKY32/59, explaining the different expression patterns of UGT84A13 among the three species. Our findings provide three high-quality new reference genomes for oak trees and give new insights into different transcriptional regulation for understanding \u03b2-glucogallin and HT biosynthesis in closely related oak species.", "doi": "10.1111/nph.19711", "pmid": "38515244", "labels": [], "xrefs": [{"db": "figshare", "key": "10.6084/m9.figshare.23910282"}, {"db": "figshare", "key": "10.6084/m9.figshare.23911602"}, {"db": "figshare", "key": "10.6084/m9.figshare.23911776"}], "notes": [], "created": "2026-08-20T11:19:05.670Z", "modified": "2026-08-20T11:19:05.925Z"}, {"entity": "publication", "iuid": "64bcdca9457b4025b3f6751bc6463e50", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/64bcdca9457b4025b3f6751bc6463e50.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/64bcdca9457b4025b3f6751bc6463e50"}}, "title": "Expression pattern of resynthesized allotetraploid Capsella is determined by hybridization, not whole-genome duplication.", "authors": [{"family": "Duan", "given": "Tianlin", "initials": "T", "orcid": "0000-0002-8719-7998", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3c891d186a1b477797a361d72494aaac.json"}}, {"family": "Sicard", "given": "Adrien", "initials": "A", "orcid": "0000-0002-4104-6844", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ecc0c606405c452f948b52544851b200.json"}}, {"family": "Gl\u00e9min", "given": "Sylvain", "initials": "S", "orcid": "0000-0001-7260-4573", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/29fc40d151df40ada3c5caf7ddc6049f.json"}}, {"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": "2023-01-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "volume": "237", "issue": "1", "pages": "339-353", "issn-l": "0028-646X"}, "abstract": "Polyploidization, the process leading to the increase in chromosome sets, is a major evolutionary transition in plants. Whole-genome duplication (WGD) within the same species gives rise to autopolyploids, whereas allopolyploids result from a compound process with two distinct components: WGD and interspecific hybridization. To dissect the instant effects of WGD and hybridization on gene expression and phenotype, we created a series of synthetic hybrid and polyploid Capsella plants, including diploid hybrids, autotetraploids of both parental species, and two kinds of resynthesized allotetraploids with different orders of WGD and hybridization. Hybridization played a major role in shaping the relative expression pattern of the neo-allopolyploids, whereas WGD had almost no immediate effect on relative gene expression pattern but, nonetheless, still affected phenotypes. No transposable element-mediated genomic shock scenario was observed in either neo-hybrids or neo-polyploids. Finally, WGD and hybridization interacted and the distorting effects of WGD were less strong in hybrids. Whole-genome duplication may even improve hybrid fertility. In summary, while the initial relative gene expression pattern in neo-allotetraploids was almost entirely determined by hybridization, WGD only had trivial effects on relative expression patterns, both processes interacted and had a strong impact on physical attributes and meiotic behaviors.", "doi": "10.1111/nph.18542", "pmid": "36254103", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10099941"}], "notes": [], "created": "2026-08-21T12:21:23.289Z", "modified": "2026-08-21T12:21:23.400Z"}, {"entity": "publication", "iuid": "90c27eb89d2a439581c0692c040853aa", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/90c27eb89d2a439581c0692c040853aa.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/90c27eb89d2a439581c0692c040853aa"}}, "title": "Teasing apart the joint effect of demography and natural selection in the birth of a contact zone.", "authors": [{"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": "Tiret", "given": "Mathieu", "initials": "M", "orcid": "0000-0001-5389-4886", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2f84d6608d1b46ed8a7aceabee030230.json"}}, {"family": "Chen", "given": "Jun", "initials": "J", "orcid": "0000-0003-3187-7668", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4eb977f0bb9d413486be3463b8a20d0c.json"}}, {"family": "Sendrowski", "given": "Janek", "initials": "J"}, {"family": "Baison", "given": "John", "initials": "J"}, {"family": "Chen", "given": "Zhi-Qiang", "initials": "ZQ", "orcid": "0000-0001-9725-8929", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e8935d36e8274be3bf02f7404d85f4fc.json"}}, {"family": "Zhou", "given": "Linghua", "initials": "L"}, {"family": "Karlsson", "given": "Bo", "initials": "B"}, {"family": "Berlin", "given": "Mats", "initials": "M", "orcid": "0000-0002-7099-3322", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d439f229eb9e424e81a93ba5255ecd79.json"}}, {"family": "Westin", "given": "Johan", "initials": "J"}, {"family": "Garcia-Gil", "given": "Maria Rosario", "initials": "MR", "orcid": "0000-0002-6834-6708", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6c915e7cb6af4bb98bc08ecd5c12a930.json"}}, {"family": "Wu", "given": "Harry X", "initials": "HX", "orcid": "0000-0002-7072-4704", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d09d9cea430d4bf7907374fd9fc44b18.json"}}, {"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": "2022-12-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "volume": "236", "issue": "5", "pages": "1976-1987", "issn-l": "0028-646X"}, "abstract": "Vast population movements induced by recurrent climatic cycles have shaped the genetic structure of plant species. During glacial periods species were confined to low-latitude refugia from which they recolonized higher latitudes as the climate improved. This multipronged recolonization led to many lineages that later met and formed large contact zones. We utilize genomic data from 5000 Picea abies trees to test for the presence of natural selection during recolonization and establishment of a contact zone in Scandinavia. Scandinavian P. abies is today made up of a southern genetic cluster originating from the Baltics, and a northern one originating from Northern Russia. The contact zone delineating them closely matches the limit between two major climatic regions. We show that natural selection contributed to its establishment and maintenance. First, an isolation-with-migration model with genome-wide linked selection fits the data better than a purely neutral one. Second, many loci show signatures of selection or are associated with environmental variables. These loci, regrouped in clusters on chromosomes, are often related to phenology. Altogether, our results illustrate how climatic cycles, recolonization and selection can establish strong local adaptation along contact zones and affect the genetic architecture of adaptive traits.", "doi": "10.1111/nph.18480", "pmid": "36093739", "labels": {"Pascal Milesi": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "RefSeq", "key": "PRJNA511374"}, {"db": "RefSeq", "key": "PRJNA731384"}], "notes": [], "created": "2022-12-05T11:41:48.115Z", "modified": "2022-12-05T11:41:48.272Z"}, {"entity": "publication", "iuid": "e2e00852af6d4402b419bbb2fc4b3041", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e2e00852af6d4402b419bbb2fc4b3041.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e2e00852af6d4402b419bbb2fc4b3041"}}, "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-affiliated.scilifelab.se/researcher/12a87b7eb74b4f9889755dd7c54670fe.json"}}, {"family": "Kryvokhyzha", "given": "Dmytro", "initials": "D", "orcid": "0000-0001-6498-1977", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a652c836aef945e08076f3ddc88debf2.json"}}, {"family": "Orsucci", "given": "Marion", "initials": "M", "orcid": "0000-0001-8516-1361", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/44bddb691cd349b19e8111c778f51402.json"}}, {"family": "Gl\u00e9min", "given": "Sylvain", "initials": "S", "orcid": "0000-0001-7260-4573", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/29fc40d151df40ada3c5caf7ddc6049f.json"}}, {"family": "Milesi", "given": "Pascal", "initials": "P", "orcid": "0000-0001-8580-4291", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6025546b69354721b8a16fbe8124fa71.json"}}, {"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": "2022-12-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "volume": "236", "issue": "6", "pages": "2344-2357", "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": {"Pascal Milesi": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2022-12-05T11:42:07.190Z", "modified": "2022-12-05T11:42:07.262Z"}, {"entity": "publication", "iuid": "3278c59c61e340e486c23565f6981adb", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3278c59c61e340e486c23565f6981adb.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3278c59c61e340e486c23565f6981adb"}}, "title": "Elevation and plant species identity jointly shape a diverse arbuscular mycorrhizal fungal community in the High Arctic.", "authors": [{"family": "Rasmussen", "given": "Pil U", "initials": "PU", "orcid": "0000-0003-0607-4230", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/80035ea7380843aa9d2c58a3ebfa3d4b.json"}}, {"family": "Abrego", "given": "Nerea", "initials": "N", "orcid": "0000-0001-6347-6127", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/224552896bb04ea6a2cf695729ea94f7.json"}}, {"family": "Roslin", "given": "Tomas", "initials": "T", "orcid": "0000-0002-2957-4791", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4b6e491ae382479b8e92eda9a11cabae.json"}}, {"family": "\u00d6pik", "given": "Maarja", "initials": "M", "orcid": "0000-0001-8025-7460", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d4aa2839065c4a0f86a008d9c6a8bb57.json"}}, {"family": "Sepp", "given": "Siim-Kaarel", "initials": "SK", "orcid": "0000-0003-2906-4609", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/76351ce330da4f2eaf2c12948882dfbb.json"}}, {"family": "Blanchet", "given": "F Guillaume", "initials": "FG", "orcid": "0000-0001-5149-2488", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5332dbed91464890b63acd68c6770254.json"}}, {"family": "Huotari", "given": "Tea", "initials": "T"}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW", "orcid": "0000-0001-5432-1764", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/246ed7b405dd4c3f9ec5e7ff9f1d3ade.json"}}, {"family": "Tack", "given": "Ayco J M", "initials": "AJM", "orcid": "0000-0002-3550-1070", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/20531f32048b4cd498311138500cc6bc.json"}}], "type": "journal article", "published": "2022-10-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "volume": "236", "issue": "2", "pages": "671-683", "issn-l": "0028-646X"}, "abstract": "Knowledge about the distribution and local diversity patterns of arbuscular mycorrhizal (AM) fungi are limited for extreme environments such as the Arctic, where most studies have focused on spore morphology or root colonization. We here studied the joint effects of plant species identity and elevation on AM fungal distribution and diversity. We sampled roots of 19 plant species in 18 locations in Northeast Greenland, using next generation sequencing to identify AM fungi. We studied the joint effect of plant species, elevation and selected abiotic conditions on AM fungal presence, richness and composition. We identified 29 AM fungal virtual taxa (VT), of which six represent putatively new VT. Arbuscular mycorrhizal fungal presence increased with elevation, and as vegetation cover and the active soil layer decreased. Arbuscular mycorrhizal fungal composition was shaped jointly by elevation and plant species identity. We demonstrate that the Arctic harbours a relatively species-rich and nonrandomly distributed diversity of AM fungi. Given the high diversity and general lack of knowledge exposed herein, we encourage further research into the diversity, drivers and functional role of AM fungi in the Arctic. Such insight is urgently needed for an area with some of the globally highest rates of climate change.", "doi": "10.1111/nph.18342", "pmid": "35751540", "labels": {"DDLS Fellow": null, "Luisa Hugerth": null}, "xrefs": [{"db": "pmc", "key": "PMC9796444"}, {"db": "RefSeq", "key": "PRJEB40490"}], "notes": [], "created": "2023-05-12T13:20:04.309Z", "modified": "2023-05-12T13:20:04.514Z"}, {"entity": "publication", "iuid": "0a189134d99242de9cb1f624dcb1ae7c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0a189134d99242de9cb1f624dcb1ae7c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0a189134d99242de9cb1f624dcb1ae7c"}}, "title": "Genomic insights on the contribution of balancing selection and local adaptation to the long-term survival of a widespread living fossil tree, Cercidiphyllum japonicum.", "authors": [{"family": "Zhu", "given": "Shanshan", "initials": "S", "orcid": "0000-0003-1582-1007", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/09d08db787a6483ba964dd7b66890a9c.json"}}, {"family": "Chen", "given": "Jun", "initials": "J", "orcid": "0000-0003-3187-7668", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4eb977f0bb9d413486be3463b8a20d0c.json"}}, {"family": "Zhao", "given": "Jing", "initials": "J", "orcid": "0000-0002-7449-124X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fd83c98d466e4546b6e8cedd6f4e35b7.json"}}, {"family": "Comes", "given": "Hans Peter", "initials": "HP", "orcid": "0000-0002-2659-8069", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/94264a07aad244cc914b8e0e035996d8.json"}}, {"family": "Li", "given": "Pan", "initials": "P", "orcid": "0000-0002-9407-7740", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/62c92136024f421fae0eddf188df2a76.json"}}, {"family": "Fu", "given": "Chengxin", "initials": "C"}, {"family": "Xie", "given": "Xiao", "initials": "X", "orcid": "0000-0002-5241-6900", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d0e443a71da04aef80848c1ac58ba6e4.json"}}, {"family": "Lu", "given": "Ruisen", "initials": "R"}, {"family": "Xu", "given": "Wuqin", "initials": "W"}, {"family": "Feng", "given": "Yu", "initials": "Y"}, {"family": "Ye", "given": "Wenqing", "initials": "W"}, {"family": "Sakaguchi", "given": "Shota", "initials": "S", "orcid": "0000-0002-6180-1747", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b78b1248c2c64f708cb6b732d90c0992.json"}}, {"family": "Isagi", "given": "Yuji", "initials": "Y", "orcid": "0000-0002-9777-076X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0d507e1dd66c4dbf9db72fc07ca57482.json"}}, {"family": "Li", "given": "Linfeng", "initials": "L", "orcid": "0000-0003-2820-3187", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9c4dd020c3474725813cf0bf08bf2775.json"}}, {"family": "Lascoux", "given": "Martin", "initials": "M", "orcid": "0000-0003-1699-9042", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0730d0f9c2524eb19383640612924701.json"}}, {"family": "Qiu", "given": "Yingxiong", "initials": "Y", "orcid": "0000-0002-4982-4997", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5e8f0e4c9a92486e817b430b6224bfb8.json"}}], "type": "journal article", "published": "2020-12-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "volume": "228", "issue": "5", "pages": "1674-1689", "issn-l": "0028-646X"}, "abstract": "'Living fossils' are testimonies of long-term sustained ecological success, but how demographic history and natural selection contributed to their survival, resilience, and persistence in the face of Quaternary climate fluctuations remains unclear. To better understand the interplay between demographic history and selection in shaping genomic diversity and evolution of such organisms, we assembled the whole genome of Cercidiphyllum japonicum, a widespread East Asian Tertiary relict tree, and resequenced 99 individuals of C. japonicum and its sister species, Cercidiphyllum magnificum (Central Japan). We dated this speciation event to the mid-Miocene, and the intraspecific lineage divergence of C. japonicum (China vs Japan) to the Early Pliocene. Throughout climatic upheavals of the late Tertiary/Quaternary, population bottlenecks greatly reduced the genetic diversity of C. japonicum. However, this polymorphism loss was likely counteracted by, first, long-term balancing selection at multiple chromosomal and heterozygous gene regions, potentially reflecting overdominance, and, second, selective sweeps at stress response and growth-related genes likely involved in local adaptation. Our findings contribute to a better understanding of how living fossils have survived climatic upheaval and maintained an extensive geographic range; that is, both types of selection could be major factors contributing to the species' survival, resilience, and persistence.", "doi": "10.1111/nph.16798", "pmid": "32643803", "labels": [], "xrefs": [], "notes": [], "created": "2026-08-21T12:21:20.741Z", "modified": "2026-08-21T12:21:21.134Z"}, {"entity": "publication", "iuid": "02f35a0abcd44e3cb1b058abe77c3636", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/02f35a0abcd44e3cb1b058abe77c3636.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/02f35a0abcd44e3cb1b058abe77c3636"}}, "title": "What do tropical cryptogams reveal? Strong genetic structure in Amazonian bryophytes.", "authors": [{"family": "Ledent", "given": "Alice", "initials": "A", "orcid": "0000-0003-3024-8720", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7447f53e3d694feb9af9adf61b28bb07.json"}}, {"family": "Gauthier", "given": "J\u00e9r\u00e9my", "initials": "J", "orcid": "0000-0001-6666-1002", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/898f2cf0568c48379a3e80ba9bd84dbe.json"}}, {"family": "Pereira", "given": "Martinha", "initials": "M"}, {"family": "Overson", "given": "Rick", "initials": "R"}, {"family": "Laenen", "given": "Benjamin", "initials": "B"}, {"family": "Mardulyn", "given": "Patrick", "initials": "P", "orcid": "0000-0003-2154-5256", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e5e8455b0bc46d1b4f1f80ce8323cd6.json"}}, {"family": "Gradstein", "given": "S Robbert", "initials": "SR", "orcid": "0000-0002-3849-6457", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3fddb42fe1154a2a80d7d20c90b1c340.json"}}, {"family": "de Haan", "given": "Myriam", "initials": "M"}, {"family": "Ballings", "given": "Petra", "initials": "P"}, {"family": "Van der Beeten", "given": "Iris", "initials": "I"}, {"family": "Zartman", "given": "Charles E", "initials": "CE", "orcid": "0000-0001-8481-9782", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f55972ce6543411c90c95ec56c592236.json"}}, {"family": "Vanderpoorten", "given": "Alain", "initials": "A", "orcid": "0000-0002-5918-7709", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0cc85719e73049c190b20fb347b64520.json"}}], "type": "journal article", "published": "2020-10-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "volume": "228", "issue": "2", "pages": "640-650", "issn-l": "0028-646X"}, "abstract": "Lowland tropical bryophytes have been perceived as excellent dispersers. In such groups, the inverse isolation hypothesis proposes that spatial genetic structure is erased beyond the limits of short-distance dispersal. Here, we determine the influence of environmental variation and geographic barriers on the spatial genetic structure of a widely dispersed and phylogenetically independent sample of Amazonian bryophytes. Single nucleotide polymorphism data were produced from a restriction site-associated DNA sequencing protocol for 10 species and analyzed through F-statistics and Mantel tests. Neither isolation-by-environment nor the impact of geographic barriers were recovered from the analyses. However, significant isolation-by-distance patterns were observed for 8 out of the 10 investigated species beyond the scale of short-distance dispersal (> 1 km), offering evidence contrary to the inverse isolation hypothesis. Despite a cadre of life-history traits and distributional patterns suggesting that tropical bryophytes are highly vagile, our analyses reveal spatial genetic structures comparable to those documented for angiosperms, whose diaspores are orders of magnitude larger. Dispersal limitation for tropical bryophytes flies in the face of traditional assumptions regarding their dispersal potential, and suggests that the plight of this component of cryptic biodiversity is more dire than previously considered in light of accelerated forest fragmentation in the Amazon.", "doi": "10.1111/nph.16720", "pmid": "32488881", "labels": [], "xrefs": [], "notes": [], "created": "2026-08-21T12:21:18.322Z", "modified": "2026-08-21T12:21:18.564Z"}, {"entity": "publication", "iuid": "2cb0f75d45124bbf8e1529be8f2e3d48", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2cb0f75d45124bbf8e1529be8f2e3d48.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2cb0f75d45124bbf8e1529be8f2e3d48"}}, "title": "Genetic basis and timing of a major mating system shift in Capsella.", "authors": [{"family": "Bachmann", "given": "J\u00f6rg A", "initials": "JA"}, {"family": "Tedder", "given": "Andrew", "initials": "A", "orcid": "0000-0002-7378-4673", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/26d7d583cedd47efb92edee2599ca453.json"}}, {"family": "Laenen", "given": "Benjamin", "initials": "B"}, {"family": "Fracassetti", "given": "Marco", "initials": "M", "orcid": "0000-0002-2962-2669", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1bb64f4233d54d12838eb245a146e8b9.json"}}, {"family": "D\u00e9samor\u00e9", "given": "Aur\u00e9lie", "initials": "A", "orcid": "0000-0003-1922-3557", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2f26bdff84c0472b85999586f46dbed7.json"}}, {"family": "Lafon-Placette", "given": "Cl\u00e9ment", "initials": "C", "orcid": "0000-0001-6634-8104", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e34c34eedadd48d495d746d7f7e1a62c.json"}}, {"family": "Steige", "given": "Kim A", "initials": "KA"}, {"family": "Callot", "given": "Caroline", "initials": "C"}, {"family": "Marande", "given": "William", "initials": "W"}, {"family": "Neuffer", "given": "Barbara", "initials": "B"}, {"family": "Berg\u00e8s", "given": "H\u00e9l\u00e8ne", "initials": "H", "orcid": "0000-0002-5492-1062", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fa1461a80bd742f6b325d74806a3e3b6.json"}}, {"family": "K\u00f6hler", "given": "Claudia", "initials": "C", "orcid": "0000-0002-2619-4857", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/115f27abd45a4a8d96cf0b0d0de6c049.json"}}, {"family": "Castric", "given": "Vincent", "initials": "V", "orcid": "0000-0002-4461-4915", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/daea86709e354edeb28c3e68b91cc7bc.json"}}, {"family": "Slotte", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6020-5102", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3daf6b63a930473b9a609949a3882b06.json"}}], "type": "journal article", "published": "2019-10-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "issn-l": "0028-646X", "volume": "224", "issue": "1", "pages": "505-517"}, "abstract": "A crucial step in the transition from outcrossing to self-fertilization is the loss of genetic self-incompatibility (SI). In the Brassicaceae, SI involves the interaction of female and male specificity components, encoded by the genes SRK and SCR at the self-incompatibility locus (S-locus). Theory predicts that S-linked mutations, and especially dominant mutations in SCR, are likely to contribute to loss of SI. However, few studies have investigated the contribution of dominant mutations to loss of SI in wild plant species. Here, we investigate the genetic basis of loss of SI in the self-fertilizing crucifer species Capsella orientalis, by combining genetic mapping, long-read sequencing of complete S-haplotypes, gene expression analyses and controlled crosses. We show that loss of SI in C. orientalis occurred < 2.6 Mya and maps as a dominant trait to the S-locus. We identify a fixed frameshift deletion in the male specificity gene SCR and confirm loss of male SI specificity. We further identify an S-linked small RNA that is predicted to cause dominance of self-compatibility. Our results agree with predictions on the contribution of dominant S-linked mutations to loss of SI, and thus provide new insights into the molecular basis of mating system transitions.", "doi": "10.1111/nph.16035", "pmid": "31254395", "labels": {"Tanja Slotte": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "GENBANK", "key": "PRJEB32122"}, {"db": "GENBANK", "key": "KJ772374.1"}], "notes": [], "created": "2020-10-09T13:58:31.926Z", "modified": "2022-11-04T11:32:15.928Z"}, {"entity": "publication", "iuid": "83ee2300b9a74f8e9d22ba7c8dcdfb49", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/83ee2300b9a74f8e9d22ba7c8dcdfb49.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/83ee2300b9a74f8e9d22ba7c8dcdfb49"}}, "title": "Multiscale patterns and drivers of arbuscular mycorrhizal fungal communities in the roots and root-associated soil of a wild perennial herb.", "authors": [{"family": "Rasmussen", "given": "Pil U", "initials": "PU", "orcid": "0000-0003-0607-4230", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/80035ea7380843aa9d2c58a3ebfa3d4b.json"}}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW"}, {"family": "Blanchet", "given": "F Guillaume", "initials": "FG"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Lindahl", "given": "Bj\u00f6rn D", "initials": "BD"}, {"family": "Tack", "given": "Ayco J M", "initials": "AJM", "orcid": "0000-0002-3550-1070", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/20531f32048b4cd498311138500cc6bc.json"}}], "type": "journal article", "published": "2018-12-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "volume": "220", "issue": "4", "pages": "1248-1261", "issn-l": "0028-646X"}, "abstract": "Arbuscular mycorrhizal (AM) fungi form diverse communities and are known to influence above-ground community dynamics and biodiversity. However, the multiscale patterns and drivers of AM fungal composition and diversity are still poorly understood. We sequenced DNA markers from roots and root-associated soil from Plantago lanceolata plants collected across multiple spatial scales to allow comparison of AM fungal communities among neighbouring plants, plant subpopulations, nearby plant populations, and regions. We also measured soil nutrients, temperature, humidity, and community composition of neighbouring plants and nonAM root-associated fungi. AM fungal communities were already highly dissimilar among neighbouring plants (c. 30 cm apart), albeit with a high variation in the degree of similarity at this small spatial scale. AM fungal communities were increasingly, and more consistently, dissimilar at larger spatial scales. Spatial structure and environmental drivers explained a similar percentage of the variation, from 7% to 25%. A large fraction of the variation remained unexplained, which may be a result of unmeasured environmental variables, species interactions and stochastic processes. We conclude that AM fungal communities are highly variable among nearby plants. AM fungi may therefore play a major role in maintaining small-scale variation in community dynamics and biodiversity.", "doi": "10.1111/nph.15088", "pmid": "29573431", "labels": {"Luisa Hugerth": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC6282561"}], "notes": [], "created": "2022-11-08T07:01:18.958Z", "modified": "2023-10-27T09:34:00.549Z"}, {"entity": "publication", "iuid": "74bb636c0550454184cd8981776c1b24", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/74bb636c0550454184cd8981776c1b24.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/74bb636c0550454184cd8981776c1b24"}}, "title": "Homeologue-specific expression divergence in the recently formed tetraploid Capsella bursa-pastoris (Brassicaceae).", "authors": [{"family": "Huang", "given": "Hui-Run", "initials": "HR"}, {"family": "Liu", "given": "Jia-Jia", "initials": "JJ"}, {"family": "Xu", "given": "Yong", "initials": "Y"}, {"family": "Lascoux", "given": "Martin", "initials": "M"}, {"family": "Ge", "given": "Xue-Jun", "initials": "XJ"}, {"family": "Wright", "given": "Stephen I", "initials": "SI"}], "type": "journal article", "published": "2018-10-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "volume": "220", "issue": "2", "pages": "624-635", "issn-l": "0028-646X"}, "abstract": "Following allopolyploid formation, extensive genome evolution occurs, with the eventual loss of many homeologous gene copies. Although this process of diploidization has occurred many times independently, the evolutionary forces determining the probability and rate of gene loss remain poorly understood. Here, we conduct genome and transcriptome sequencing in a broad sample of Chinese accessions of Capsella bursa-pastoris, a recently formed allotetraploid. Our whole genome data reveal three groups of these accessions: an Eastern group from low-altitude regions, a Western group from high-altitude regions, and a much more differentiated Northwestern group. Population differentiation in total expression was limited among closely related populations; by contrast, the relative expression of the two homeologous copies closely mirrors the genome-wide SNP divergence. Consistent with this, we observe a negative correlation between expression changes in the two homeologues. However, genes showing population genomic evidence for adaptive evolution do not show an enrichment for expression divergence between homeologues, providing no clear evidence for adaptive shifts in relative gene expression. Overall, these patterns suggest that neutral drift may contribute to the population differentiation in the expression of the homeologues, and drive eventual gene loss over longer periods of time.", "doi": "10.1111/nph.15299", "pmid": "30028022", "labels": [], "xrefs": [{"db": "GENBANK", "key": "SRR6179226"}, {"db": "GENBANK", "key": "SRR6179253"}, {"db": "GENBANK", "key": "SRR6214506"}, {"db": "GENBANK", "key": "SRR6214532"}, {"db": "GENBANK", "key": "SRR6227293"}, {"db": "GENBANK", "key": "SRR6227300"}], "notes": [], "created": "2026-08-21T12:21:16.252Z", "modified": "2026-08-21T12:21:16.266Z"}, {"entity": "publication", "iuid": "ef7655473ce548d6a4f0ce8be06d13da", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ef7655473ce548d6a4f0ce8be06d13da.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ef7655473ce548d6a4f0ce8be06d13da"}}, "title": "Increased diversification rates follow shifts to bisexuality in liverworts.", "authors": [{"family": "Laenen", "given": "Benjamin", "initials": "B"}, {"family": "Machac", "given": "Antonin", "initials": "A"}, {"family": "Gradstein", "given": "S Robbert", "initials": "SR"}, {"family": "Shaw", "given": "Blanka", "initials": "B"}, {"family": "Pati\u00f1o", "given": "Jairo", "initials": "J"}, {"family": "D\u00e9samor\u00e9", "given": "Aur\u00e9lie", "initials": "A"}, {"family": "Goffinet", "given": "Bernard", "initials": "B"}, {"family": "Cox", "given": "Cymon J", "initials": "CJ"}, {"family": "Shaw", "given": "A Jonathan", "initials": "AJ"}, {"family": "Vanderpoorten", "given": "Alain", "initials": "A"}], "type": "journal article", "published": "2016-05-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "volume": "210", "issue": "3", "pages": "1121-1129", "issn-l": "0028-646X"}, "abstract": "Shifts in sexual systems are one of the key drivers of species diversification. In contrast to angiosperms, unisexuality prevails in bryophytes. Here, we test the hypotheses that bisexuality evolved from an ancestral unisexual condition and is a key innovation in liverworts. We investigate whether shifts in sexual systems influence diversification using hidden state speciation and extinction analysis (HiSSE). This new method compares the effects of the variable of interest to the best-fitting latent variable, yielding robust and conservative tests. We find that the transitions in sexual systems are significantly biased toward unisexuality, even though bisexuality is coupled with increased diversification. Sexual systems are strongly conserved deep within the liverwort tree but become much more labile toward the present. Bisexuality appears to be a key innovation in liverworts. Its effects on diversification are presumably mediated by the interplay of high fertilization rates, massive spore production and long-distance dispersal, which may separately or together have facilitated liverwort speciation, suppressed their extinction, or both. Importantly, shifts in liverwort sexual systems have the opposite effect when compared to angiosperms, leading to contrasting diversification patterns between the two groups. The high prevalence of unisexuality among liverworts suggests, however, a strong selection for sexual dimorphism.", "doi": "10.1111/nph.13835", "pmid": "27074401", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "GENBANK", "key": "15950"}], "notes": [], "created": "2018-12-05T11:46:52.769Z", "modified": "2018-12-05T11:46:52.798Z"}], "created": "2018-12-05T11:46:52.782Z", "modified": "2020-11-27T13:12:54.092Z"}