[{"intvolume":"       400","quality_controlled":"1","month":"04","type":"journal_article","das_tickbox":"1","title":"Context-dependent effects of livestock grazing on forest attributes and ecosystem multifunctionality in Nothofagus forests","status":"public","publisher":"Elsevier","publication_status":"published","OA_type":"closed access","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2026-04-15T00:00:00Z","date_created":"2026-01-25T23:01:38Z","_id":"21036","publication":"Agriculture, Ecosystems and Environment","day":"15","language":[{"iso":"eng"}],"supplementarymaterial":"yes","date_updated":"2026-07-27T11:01:30Z","author":[{"full_name":"Rodríguez, Paula","first_name":"Paula","last_name":"Rodríguez"},{"full_name":"Cruz Alonso, Verónica","last_name":"Cruz Alonso","first_name":"Verónica"},{"full_name":"Romano, Silvina","last_name":"Romano","first_name":"Silvina"},{"last_name":"Bustamante","first_name":"Gimena","full_name":"Bustamante, Gimena"},{"id":"9e668447-8c32-11ed-b0c7-8dc2d7b80803","last_name":"Soler Schaller","first_name":"Rosina Matilde","full_name":"Soler Schaller, Rosina Matilde"}],"fulldoi":"https://doi.org/10.1016/j.agee.2026.110219","oa_version":"None","researchdata_availability":"no","publication_identifier":{"issn":["0167-8809"]},"article_number":"110219","volume":400,"article_type":"original","department":[{"_id":"NiBa"}],"article_processing_charge":"No","citation":{"chicago":"Rodríguez, Paula, Verónica Cruz Alonso, Silvina Romano, Gimena Bustamante, and Rosina Matilde Soler Schaller. “Context-Dependent Effects of Livestock Grazing on Forest Attributes and Ecosystem Multifunctionality in Nothofagus Forests.” <i>Agriculture, Ecosystems and Environment</i>. Elsevier, 2026. <a href=\"https://doi.org/10.1016/j.agee.2026.110219\">https://doi.org/10.1016/j.agee.2026.110219</a>.","mla":"Rodríguez, Paula, et al. “Context-Dependent Effects of Livestock Grazing on Forest Attributes and Ecosystem Multifunctionality in Nothofagus Forests.” <i>Agriculture, Ecosystems and Environment</i>, vol. 400, 110219, Elsevier, 2026, doi:<a href=\"https://doi.org/10.1016/j.agee.2026.110219\">10.1016/j.agee.2026.110219</a>.","short":"P. Rodríguez, V. Cruz Alonso, S. Romano, G. Bustamante, R.M. Soler Schaller, Agriculture, Ecosystems and Environment 400 (2026).","ieee":"P. Rodríguez, V. Cruz Alonso, S. Romano, G. Bustamante, and R. M. Soler Schaller, “Context-dependent effects of livestock grazing on forest attributes and ecosystem multifunctionality in Nothofagus forests,” <i>Agriculture, Ecosystems and Environment</i>, vol. 400. Elsevier, 2026.","ama":"Rodríguez P, Cruz Alonso V, Romano S, Bustamante G, Soler Schaller RM. Context-dependent effects of livestock grazing on forest attributes and ecosystem multifunctionality in Nothofagus forests. <i>Agriculture, Ecosystems and Environment</i>. 2026;400. doi:<a href=\"https://doi.org/10.1016/j.agee.2026.110219\">10.1016/j.agee.2026.110219</a>","ista":"Rodríguez P, Cruz Alonso V, Romano S, Bustamante G, Soler Schaller RM. 2026. Context-dependent effects of livestock grazing on forest attributes and ecosystem multifunctionality in Nothofagus forests. Agriculture, Ecosystems and Environment. 400, 110219.","apa":"Rodríguez, P., Cruz Alonso, V., Romano, S., Bustamante, G., &#38; Soler Schaller, R. M. (2026). Context-dependent effects of livestock grazing on forest attributes and ecosystem multifunctionality in Nothofagus forests. <i>Agriculture, Ecosystems and Environment</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.agee.2026.110219\">https://doi.org/10.1016/j.agee.2026.110219</a>"},"acknowledgement":"We would like to thank Guillermo Ortiz (CADIC-CONICET) for his invaluable support in the field and lab work. We are extremely grateful to the ranchers for kindly allowing us access to their fields. Funding for this work was provided by the Argentine National Scientific and Technical Research Council (CONICET) and the National Agency for Scientific Promotion through project PICT 2019–675. PR was also granted the Mobility Scholarship Program 2025 between Andalusian and Ibero-American Universities (AUIP). VCA is co-supported by the Community of Madrid under the 2024 call for the ‘César Nombela’ research talent attraction programme (2024-T1/ECO-31335).","year":"2026","abstract":[{"lang":"eng","text":"Forests under livestock grazing sustain important ecosystem services but face potential trade-offs between production and ecological integrity. While the effects of grazing on individual forest attributes are well documented, their integrated consequences remain poorly understood, particularly in temperate forest ecosystems. We evaluated the combined influence of livestock grazing intensity and canopy cover on individual attributes and ecosystem multifunctionality in native Nothofagus forests of Tierra del Fuego, Argentina. Across eight ranches spanning two agroecological regions (Ecotone and Mountain Range), we quantified forest regeneration, understorey richness and biomass, and soil properties, integrating them into a multifunctionality index. Using generalized linear mixed models, we found strong context-dependence: in the Mountain Range, higher grazing intensity reduced seedling and sapling density, organic matter content, coarse woody debris, and overall multifunctionality. In the Ecotone, these effects of livestock use intensity were attenuated, and canopy cover diminished sapling density and multifunctionality, but moderate cover enhanced understorey. Our results extend multifunctionality research from grazed grasslands to grazed temperate forests and show that ecological responses and trade-offs vary across landscape units. We conclude that the Mountain Range is more vulnerable to grazing, requiring stricter management, whereas the Ecotone retains greater capacity to sustain multifunctionality under controlled livestock use intensity. These findings underscore the importance of region-specific silvopastoral strategies that reconcile food production with forest conservation in southern Patagonia and comparable temperate forest landscapes worldwide."}],"scopus_import":"1","dataavailabilitystatement":"The authors do not have permission to share data.","doi":"10.1016/j.agee.2026.110219"},{"citation":{"short":"D. Bradley, L. Boell, D. Richardson, L. Copsey, A. Whibley, T. Xu, Y. Zhang, Y. Xue, D. Field, E. Coen, Science Advances 12 (2026) 1–11.","mla":"Bradley, Desmond, et al. “Shaping of Developmental Gradients through Selection on Multiple Loci in Antirrhinum.” <i>Science Advances</i>, vol. 12, no. 29, AAAS, 2026, pp. 1–11, doi:<a href=\"https://doi.org/10.1126/sciadv.adx2011\">10.1126/sciadv.adx2011</a>.","chicago":"Bradley, Desmond, Louis Boell, Daniel Richardson, Lucy Copsey, Annabel Whibley, Ting Xu, Yu’E Zhang, Yongbiao Xue, David Field, and Enrico Coen. “Shaping of Developmental Gradients through Selection on Multiple Loci in Antirrhinum.” <i>Science Advances</i>. AAAS, 2026. <a href=\"https://doi.org/10.1126/sciadv.adx2011\">https://doi.org/10.1126/sciadv.adx2011</a>.","apa":"Bradley, D., Boell, L., Richardson, D., Copsey, L., Whibley, A., Xu, T., … Coen, E. (2026). Shaping of developmental gradients through selection on multiple loci in Antirrhinum. <i>Science Advances</i>. AAAS. <a href=\"https://doi.org/10.1126/sciadv.adx2011\">https://doi.org/10.1126/sciadv.adx2011</a>","ama":"Bradley D, Boell L, Richardson D, et al. Shaping of developmental gradients through selection on multiple loci in Antirrhinum. <i>Science Advances</i>. 2026;12(29):1-11. doi:<a href=\"https://doi.org/10.1126/sciadv.adx2011\">10.1126/sciadv.adx2011</a>","ista":"Bradley D, Boell L, Richardson D, Copsey L, Whibley A, Xu T, Zhang Y, Xue Y, Field D, Coen E. 2026. Shaping of developmental gradients through selection on multiple loci in Antirrhinum. Science Advances. 12(29), 1–11.","ieee":"D. Bradley <i>et al.</i>, “Shaping of developmental gradients through selection on multiple loci in Antirrhinum,” <i>Science Advances</i>, vol. 12, no. 29. AAAS, pp. 1–11, 2026."},"year":"2026","acknowledgement":"We thank C. Taylor for plant care, N. Barton for sharing SNP data and useful comments, H. Tavares for useful discussions and bioinformatics, M. Couchman for field and data archiving, T. Li for help with photography and phenotyping, J. Chan for help with ImageJ analyses, and X. Rebocho for organization of field experiments. This work was supported by Biotechnology and Biological Sciences Research Council grants BB/S009256/1 (to E.C.), BB/G009325/1 (to E.C.), BBS/E/JI/230002C (to E.C.), and BBS/E/J/000PR9773 (to E.C.); Biotechnology Biological Sciences Research Council Norwich Research Park Biosciences Doctoral Training Partnership grant BB/M011216/1 (to D.R.); and Natural Science Foundation of China grant 32030007 (to Y.X.)","abstract":[{"lang":"eng","text":"Development depends on precise shaping of molecular gradients, but how natural selection acts to establish precision is unknown. Here, we analyze genes that control differences in the gradient of yellow flower color between two varieties of snapdragon (Antirrhinum). We show that these differences depend, in part, on cis-regulatory variation in the pigment biosynthetic gene, FLAVIA (FLA). FLA interacts multiplicatively with three other loci, one of which is a trans-acting regulator of FLA, to further shape the yellow gradient. All the loci exhibit clines at a hybrid zone, with widths that correlate with phenotypic effect, showing how selection can hone gradient shape with remarkable precision by acting on cis and trans variation at multiple loci."}],"scopus_import":"1","doi":"10.1126/sciadv.adx2011","ddc":["570"],"dataavailabilitystatement":"All data and code needed to evaluate and reproduce the results in the paper are present in the paper and/or the Supplementary Materials. All materials generated in this study are described in Materials and Methods and are available on request from E.C. (enrico.coen@jic.ac.uk).","article_type":"original","volume":12,"department":[{"_id":"NiBa"}],"issue":"29","article_processing_charge":"Yes","oa_version":"Published Version","fulldoi":"https://doi.org/10.1126/sciadv.adx2011","researchdata_availability":"no","corr_author":"1","file":[{"file_name":"2026_ScienceAdv_Bradley.pdf","file_id":"22635","content_type":"application/pdf","access_level":"open_access","creator":"dernst","checksum":"f9155dc2d9273e43c0caf78dffa96864","file_size":916329,"date_created":"2026-08-03T09:44:40Z","date_updated":"2026-08-03T09:44:40Z","relation":"main_file","success":1}],"publication_identifier":{"eissn":["2375-2548"]},"pmid":1,"oa":1,"PlanS_conform":"1","DOAJ_listed":"1","language":[{"iso":"eng"}],"supplementarymaterial":"yes","author":[{"full_name":"Bradley, Desmond","last_name":"Bradley","first_name":"Desmond"},{"full_name":"Boell, Louis","last_name":"Boell","first_name":"Louis"},{"first_name":"Daniel","last_name":"Richardson","full_name":"Richardson, Daniel"},{"full_name":"Copsey, Lucy","last_name":"Copsey","first_name":"Lucy"},{"full_name":"Whibley, Annabel","first_name":"Annabel","last_name":"Whibley"},{"full_name":"Xu, Ting","first_name":"Ting","last_name":"Xu"},{"last_name":"Zhang","first_name":"Yu’E","full_name":"Zhang, Yu’E"},{"full_name":"Xue, Yongbiao","first_name":"Yongbiao","last_name":"Xue"},{"orcid":"0000-0002-4014-8478","full_name":"Field, David","first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Enrico","last_name":"Coen","full_name":"Coen, Enrico"}],"date_updated":"2026-08-03T09:52:37Z","OA_place":"publisher","_id":"22620","publication":"Science Advances","day":"17","page":"1-11","publisher":"AAAS","publication_status":"published","OA_type":"gold","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2026-07-17T00:00:00Z","date_created":"2026-08-02T22:01:53Z","quality_controlled":"1","month":"07","das_tickbox":"1","type":"journal_article","file_date_updated":"2026-08-03T09:44:40Z","title":"Shaping of developmental gradients through selection on multiple loci in Antirrhinum","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":"        12","external_id":{"pmid":["42467783"]},"has_accepted_license":"1"},{"PlanS_conform":"1","oa":1,"pmid":1,"date_updated":"2026-08-11T07:55:22Z","author":[{"first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","orcid":"0000-0002-4014-8478","full_name":"Field, David"},{"id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","first_name":"Sean","full_name":"Stankowski, Sean"},{"last_name":"Reiter","first_name":"Taylor","full_name":"Reiter, Taylor"},{"full_name":"Polechova, Jitka","last_name":"Polechova","first_name":"Jitka"},{"full_name":"Bradley, Desmond","first_name":"Desmond","last_name":"Bradley"},{"first_name":"Daniel M.","last_name":"Richardson","full_name":"Richardson, Daniel M."},{"last_name":"Whibley","first_name":"Annabel","full_name":"Whibley, Annabel"},{"first_name":"Arka","last_name":"Pal","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","full_name":"Pal, Arka","orcid":"0000-0002-4530-8469"},{"orcid":"0000-0002-1145-9226","full_name":"Shipilina, Daria","id":"428A94B0-F248-11E8-B48F-1D18A9856A87","last_name":"Shipilina","first_name":"Daria"},{"first_name":"Louis","last_name":"Boell","full_name":"Boell, Louis"},{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","last_name":"Pickup","first_name":"Melinda","orcid":"0000-0001-6118-0541","full_name":"Pickup, Melinda"},{"first_name":"Yongbiao","last_name":"Xue","full_name":"Xue, Yongbiao"},{"full_name":"Coen, Enrico","first_name":"Enrico","last_name":"Coen"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"}],"supplementarymaterial":"yes","language":[{"iso":"eng"}],"DOAJ_listed":"1","corr_author":"1","fulldoi":"https://doi.org/10.1371/journal.pgen.1012173","oa_version":"Published Version","researchdata_availability":"yes","article_number":"e1012173","publication_identifier":{"eissn":["1553-7404"]},"file":[{"success":1,"relation":"main_file","access_level":"open_access","date_created":"2026-08-11T07:53:14Z","date_updated":"2026-08-11T07:53:14Z","checksum":"3e2d3acc179f4672c49217ae4a6e237c","creator":"dernst","file_size":2462781,"content_type":"application/pdf","file_id":"22683","file_name":"2026_PloSGenetics_Field.pdf"}],"department":[{"_id":"NiBa"}],"project":[{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","grant_number":"101055327","name":"Understanding the evolution of continuous genomes"}],"article_type":"original","volume":22,"article_processing_charge":"Yes","issue":"7","citation":{"chicago":"Field, David, Sean Stankowski, Taylor Reiter, Jitka Polechova, Desmond Bradley, Daniel M. Richardson, Annabel Whibley, et al. “Genome-Wide Cline Analysis Identifies New Locus Contributing to a Barrier to Gene Flow across an Antirrhinum Hybrid Zone.” <i>PLOS Genetics</i>. Public Library of Science, 2026. <a href=\"https://doi.org/10.1371/journal.pgen.1012173\">https://doi.org/10.1371/journal.pgen.1012173</a>.","mla":"Field, David, et al. “Genome-Wide Cline Analysis Identifies New Locus Contributing to a Barrier to Gene Flow across an Antirrhinum Hybrid Zone.” <i>PLOS Genetics</i>, vol. 22, no. 7, e1012173, Public Library of Science, 2026, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1012173\">10.1371/journal.pgen.1012173</a>.","short":"D. Field, S. Stankowski, T. Reiter, J. Polechova, D. Bradley, D.M. Richardson, A. Whibley, A. Pal, D. Shipilina, L. Boell, M. Pickup, Y. Xue, E. Coen, N.H. Barton, PLOS Genetics 22 (2026).","ieee":"D. Field <i>et al.</i>, “Genome-wide cline analysis identifies new locus contributing to a barrier to gene flow across an Antirrhinum hybrid zone,” <i>PLOS Genetics</i>, vol. 22, no. 7. Public Library of Science, 2026.","ista":"Field D, Stankowski S, Reiter T, Polechova J, Bradley D, Richardson DM, Whibley A, Pal A, Shipilina D, Boell L, Pickup M, Xue Y, Coen E, Barton NH. 2026. Genome-wide cline analysis identifies new locus contributing to a barrier to gene flow across an Antirrhinum hybrid zone. PLOS Genetics. 22(7), e1012173.","ama":"Field D, Stankowski S, Reiter T, et al. Genome-wide cline analysis identifies new locus contributing to a barrier to gene flow across an Antirrhinum hybrid zone. <i>PLOS Genetics</i>. 2026;22(7). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1012173\">10.1371/journal.pgen.1012173</a>","apa":"Field, D., Stankowski, S., Reiter, T., Polechova, J., Bradley, D., Richardson, D. M., … Barton, N. H. (2026). Genome-wide cline analysis identifies new locus contributing to a barrier to gene flow across an Antirrhinum hybrid zone. <i>PLOS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1012173\">https://doi.org/10.1371/journal.pgen.1012173</a>"},"doi":"10.1371/journal.pgen.1012173","dataavailabilitystatement":"The raw DNA poolSeq data and RNA data have been uploaded to SRA under accession number PRJNA1232105. The A. m. m. var. pseudo majus assembly and GFF annotations have been uploaded to NCBI WGS under accession number PRJNA1232105. The A. majus reference genome V3.0 is available at the NGDC Genome Warehouse under accession number GWHBJVT00000000. The SNP KASP data and flower colour phenotyping is available on Dryad at DOI: https://doi.org/10.5061/dryad.3bk3j9kx2. The FastClines script is available at https://github.com/dfield007/fastClines, slidingWindow genome scans at https://github.com/dfield007/slidingWindows, and all other scripts for analyses and generating figures available at https://github.com/dfield007/genome_wide_clines].","ddc":["570"],"scopus_import":"1","abstract":[{"lang":"eng","text":"Identification of the genomic regions that contribute to reproductive isolation and how\r\nthey interact is a major goal of evolutionary genetics. Much effort has focused on\r\nlocating candidate genes and potential barrier loci by scanning genomes for regions\r\nof excess differentiation (FST). An alternative, and perhaps more robust approach, is\r\nto scan for genomic regions exhibiting steep clines in allele frequency across a hybrid\r\nzone. We develop a computationally efficient method for approximating cline parameters\r\nfor large number of loci, and apply it to genomic data from across a hybrid zone\r\nbetween flower colour varieties of Antirrhinum majus (A. m. m var. pseudomajus and\r\nA. m. m var. striatum). Most steep clines are clustered in seven genomic regions,\r\nonly four of which were present from FST scans between all pair-wise comparisons.\r\nSix of these regions carry previously identified loci that influence flower colour in the\r\nhybrid zone. The seventh region harbours a novel locus, RUBIA, modifying magenta\r\nintensity. Clines at RUBIA approached fixation on the magenta side of the hybrid\r\nzone, whilst remaining polymorphic on the yellow side. This polymorphism on the\r\nyellow side may reflect a smaller phenotypic effect of RUBIA in yellow compared\r\nto magenta genetic backgrounds. Our findings illustrate how whole-genome cline\r\nscans in hybrid zones can robustly detect genomic regions contributing to phenotypic\r\ndifferences and highlight how different reproductive barrier loci interact across the\r\ngenome."}],"year":"2026","acknowledgement":"This work was supported by the Biotechnology and Biological Sciences Research Council (https://www.ukri.org/councils/bbsrc/) (grants BB/S009256/1, BB/G009325/1, BBS/E/JI/230002C, and BBS/E/J/000PR9773 to EC, and Norwich Research Park Biosciences Doctoral Training Partnership grant (https://www.jic.ac.uk/training-careers/postgraduate-opportunities/nrp-doctoral-training-partnership/) (BB/M011216/1 to DR) and European Research Council (https://erc.europa.eu/homepage) ERC Advanced Grant HaplotypeStructure (101055327 to NB). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. We are grateful to Monique Burrus, Christophe Andalo, Tom Ellis, Parvathy Surendranadh and members of the Barton group for interesting discussion. We are also grateful for numerous undergraduate volunteers who assisted with collecting of flowers and leaf samples in the field. Melinda Pickup passed away before the submission of the final version of this manuscript. David L Field accepts responsibility for the integrity and validity of the data collected and analyzed.","intvolume":"        22","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"biorxivid":["10.1101/2025.02.17.638607"],"pmid":["42441626"]},"has_accepted_license":"1","quality_controlled":"1","month":"07","biorxivid":1,"status":"public","title":"Genome-wide cline analysis identifies new locus contributing to a barrier to gene flow across an Antirrhinum hybrid zone","type":"journal_article","file_date_updated":"2026-08-11T07:53:14Z","das_tickbox":"1","publication_status":"published","publisher":"Public Library of Science","date_created":"2026-08-11T06:19:05Z","date_published":"2026-07-13T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"gold","publication":"PLOS Genetics","_id":"22674","OA_place":"publisher","day":"13"},{"OA_type":"hybrid","date_published":"2026-06-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2026-04-26T22:01:46Z","publisher":"Elsevier","publication_status":"published","day":"01","OA_place":"publisher","_id":"21759","publication":"Current Opinion in Genetics & Development","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":"        98","type":"journal_article","das_tickbox":"1","file_date_updated":"2026-07-27T13:39:59Z","title":"Long-term evolution of regulatory DNA sequences. Part 2: Theory and future challenges","status":"public","quality_controlled":"1","month":"06","article_processing_charge":"Yes (via OA deal)","article_type":"review","volume":98,"project":[{"name":"Understanding the evolution of continuous genomes","grant_number":"101055327","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00"}],"department":[{"_id":"GaTk"},{"_id":"NiBa"}],"acknowledgement":"We thank Calin Guet and Santiago Herrera-Álvarez for essential contributions to this manuscript.\r\nE.M. acknowledges support from the APART-USA fellowship, jointly funded by the Austrian Academy of Sciences (ÖAW) and the Institute of Science and Technology Austria (ISTA). N.B. acknowledges funding from the ERC Advanced Grant 101055327 “HaplotypeStructure”.\r\nThis study was also supported by the European Molecular Biology Laboratory (N.O.B., J.C.).","year":"2026","abstract":[{"text":"Promoters and enhancers are cis-regulatory elements (CREs), DNA sequences that bind transcription factor (TF) proteins to up- or down-regulate target genes. Decades-long efforts yielded TF-DNA interaction models that predict how strongly an individual TF binds arbitrary DNA sequences and how individual binding events on the CRE combine to affect gene expression. These insights can be synthesized into a global, biophysically realistic, and quantitative genotype-phenotype (GP) map for gene regulation, a ‘holy grail’ for the application of evolutionary theory. A global map provides a rare opportunity to simulate the long-term evolution of regulatory sequences and pose several fundamental questions: How long does it take to evolve CREs de novo? How many non-trivial regulatory functions exist in sequence space? How connected are they? For which regulatory architecture is CRE evolution most rapid and evolvable? In this article, the second of a two-part series, we review the application of evolutionary concepts — epistasis, robustness, evolvability, tunability, plasticity, and bet-hedging — to the evolution of gene regulatory sequences. We then evaluate the potential for a unifying theory for the evolution of regulatory sequences and identify key open challenges.","lang":"eng"}],"scopus_import":"1","ddc":["570"],"doi":"10.1016/j.gde.2026.102472","dataavailabilitystatement":"No data were used for the research described in the article.","citation":{"mla":"Mascolo, Elia, et al. “Long-Term Evolution of Regulatory DNA Sequences. Part 2: Theory and Future Challenges.” <i>Current Opinion in Genetics &#38; Development</i>, vol. 98, 102472, Elsevier, 2026, doi:<a href=\"https://doi.org/10.1016/j.gde.2026.102472\">10.1016/j.gde.2026.102472</a>.","short":"E. Mascolo, R.E. Körei, N.O. Borst, N.H. Barton, J. Crocker, G. Tkačik, Current Opinion in Genetics &#38; Development 98 (2026).","chicago":"Mascolo, Elia, Reka E Körei, Noa O. Borst, Nicholas H Barton, Justin Crocker, and Gašper Tkačik. “Long-Term Evolution of Regulatory DNA Sequences. Part 2: Theory and Future Challenges.” <i>Current Opinion in Genetics &#38; Development</i>. Elsevier, 2026. <a href=\"https://doi.org/10.1016/j.gde.2026.102472\">https://doi.org/10.1016/j.gde.2026.102472</a>.","ista":"Mascolo E, Körei RE, Borst NO, Barton NH, Crocker J, Tkačik G. 2026. Long-term evolution of regulatory DNA sequences. Part 2: Theory and future challenges. Current Opinion in Genetics &#38; Development. 98, 102472.","ama":"Mascolo E, Körei RE, Borst NO, Barton NH, Crocker J, Tkačik G. Long-term evolution of regulatory DNA sequences. Part 2: Theory and future challenges. <i>Current Opinion in Genetics &#38; Development</i>. 2026;98. doi:<a href=\"https://doi.org/10.1016/j.gde.2026.102472\">10.1016/j.gde.2026.102472</a>","apa":"Mascolo, E., Körei, R. E., Borst, N. O., Barton, N. H., Crocker, J., &#38; Tkačik, G. (2026). Long-term evolution of regulatory DNA sequences. Part 2: Theory and future challenges. <i>Current Opinion in Genetics &#38; Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.gde.2026.102472\">https://doi.org/10.1016/j.gde.2026.102472</a>","ieee":"E. Mascolo, R. E. Körei, N. O. Borst, N. H. Barton, J. Crocker, and G. Tkačik, “Long-term evolution of regulatory DNA sequences. Part 2: Theory and future challenges,” <i>Current Opinion in Genetics &#38; Development</i>, vol. 98. Elsevier, 2026."},"language":[{"iso":"eng"}],"supplementarymaterial":"no","author":[{"orcid":"0000-0003-2977-7844","full_name":"Mascolo, Elia","first_name":"Elia","id":"776a6ed0-a053-11f0-8635-80b95e0e0d53","last_name":"Mascolo"},{"full_name":"Körei, Reka E","first_name":"Reka E","id":"50FDE43E-AA30-11E9-A72B-8A12E6697425","last_name":"Körei"},{"full_name":"Borst, Noa O.","first_name":"Noa O.","last_name":"Borst"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Crocker","first_name":"Justin","full_name":"Crocker, Justin"},{"first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"}],"date_updated":"2026-08-12T09:56:02Z","PlanS_conform":"1","oa":1,"file":[{"success":1,"relation":"main_file","date_updated":"2026-07-27T13:39:59Z","file_size":3190001,"access_level":"open_access","creator":"dernst","checksum":"ac8bbee61717bfe7116e312cc6825259","date_created":"2026-07-27T13:39:59Z","file_name":"2026_CurrentOpinionGeneticsDev_Mascolo.pdf","file_id":"22590","content_type":"application/pdf"}],"article_number":"102472","publication_identifier":{"issn":["0959-437X"],"eissn":["1879-0380"]},"researchdata_availability":"no","fulldoi":"https://doi.org/10.1016/j.gde.2026.102472","corr_author":"1","oa_version":"Published Version"},{"citation":{"ista":"Vijatovic D, Toma FA, Ignatyev Y, Harrington ZP, Sommer CM, Hauschild R, Smits MG, Dalla Vecchia M, Trevisan AJ, Chapman P, Julseth M, Brenner-Morton S, Gabitto MI, Dasen JS, Bikoff JB, Sweeney LB. 2026. Multifold increase in spinal inhibitory cell types with emergence of limb movement. Cell Reports. 45(4), 117227.","ama":"Vijatovic D, Toma FA, Ignatyev Y, et al. Multifold increase in spinal inhibitory cell types with emergence of limb movement. <i>Cell Reports</i>. 2026;45(4). doi:<a href=\"https://doi.org/10.1016/j.celrep.2026.117227\">10.1016/j.celrep.2026.117227</a>","apa":"Vijatovic, D., Toma, F. A., Ignatyev, Y., Harrington, Z. P., Sommer, C. M., Hauschild, R., … Sweeney, L. B. (2026). Multifold increase in spinal inhibitory cell types with emergence of limb movement. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2026.117227\">https://doi.org/10.1016/j.celrep.2026.117227</a>","ieee":"D. Vijatovic <i>et al.</i>, “Multifold increase in spinal inhibitory cell types with emergence of limb movement,” <i>Cell Reports</i>, vol. 45, no. 4. Elsevier, 2026.","mla":"Vijatovic, David, et al. “Multifold Increase in Spinal Inhibitory Cell Types with Emergence of Limb Movement.” <i>Cell Reports</i>, vol. 45, no. 4, 117227, Elsevier, 2026, doi:<a href=\"https://doi.org/10.1016/j.celrep.2026.117227\">10.1016/j.celrep.2026.117227</a>.","short":"D. Vijatovic, F.A. Toma, Y. Ignatyev, Z.P. Harrington, C.M. Sommer, R. Hauschild, M.G. Smits, M. Dalla Vecchia, A.J. Trevisan, P. Chapman, M. Julseth, S. Brenner-Morton, M.I. Gabitto, J.S. Dasen, J.B. Bikoff, L.B. Sweeney, Cell Reports 45 (2026).","chicago":"Vijatovic, David, Florina Alexandra  Toma, Y Ignatyev, Zoe P Harrington, Christoph M Sommer, Robert Hauschild, Matthijs Geert Smits, et al. “Multifold Increase in Spinal Inhibitory Cell Types with Emergence of Limb Movement.” <i>Cell Reports</i>. Elsevier, 2026. <a href=\"https://doi.org/10.1016/j.celrep.2026.117227\">https://doi.org/10.1016/j.celrep.2026.117227</a>."},"scopus_import":"1","abstract":[{"lang":"eng","text":"As vertebrates transitioned from water to land, locomotion shifted from undulatory swimming to limb-based movement. How spinal circuits and their cell types evolved to support this transition remains unclear. We leverage frog metamorphosis, which recapitulates this transition within a single organism, to define how spinal circuits generate aquatic versus terrestrial motor patterns. At swim stages, spinal architecture is uniform, with a transcriptionally and anatomically homogeneous motor and interneurons. As limbs develop and their movement complexifies, spinal circuits expand in neuron number and subtype diversity. This expansion is most pronounced for V1 inhibitory neurons, which increase ∼70-fold and diversify into transcriptionally distinct subtypes. Disrupting transcription factors defining emerging motor and V1 populations reveals molecular segregation between swim and limb circuits, highlighting the role of subtype diversity in motor coordination. A multifold increase in inhibitory neuron diversity thus underlies the tail-to-limb locomotor transition, providing a framework for spinal circuit adaptation during vertebrate evolution."}],"year":"2026","acknowledgement":"We would like to thank the members of the Sweeney Lab, Mario de Bono, Michael Forsthofer, Katharina Lust, and Meital Oren, for comments on the manuscript. We are also grateful to Tom Jessell and Chris Kintner for their scientific insight and mentorship during the conception of this project. It would also have not been possible without the technical support of the Aquatics and Imaging and Optics Facility support teams (ISTA). We thank Martin Estermann for preparing the initial draft of the graphical abstract and Niki Barolini for the final version. In addition, we thank our funding sources for providing the resources to do these experiments: GFF NÖ FTI Strategy Lower Austria dissertation grant FT121-D-046 (to D.V.), Horizon Europe ERC starting grant 101041551 (to Y.I., L.B.S., F.A.T., and D.V.), Special Research Program (SFB) of the Austrian Science Fund (FWF) project F7814-B (to L.B.S.), Austrian Science Fund (FWF) 10.55776/COE16 (to Y.I. and L.B.S.), NINDS 5R35NS116858 (to J.S.D.), CZI grant DAF2020-225401 (DOI) 10.37921/120055ratwvi (to R.H.), NIH grant R01NS123116 (to J.B.B.), American Lebanese Syrian Associated Charities (ALSAC) (to J.B.B.), German Academic Exchange Service (DAAD) IFI grant 57515251-91853472 (to Z.H.), and Project A.L.S. (to S.B.-M.).","doi":"10.1016/j.celrep.2026.117227","ddc":["570"],"project":[{"grant_number":"101041551","_id":"ebb66355-77a9-11ec-83b8-b8ac210a4dae","name":"Development and Evolution of Tetrapod Motor Circuits"},{"_id":"8da85f50-16d5-11f0-9cad-eab8b0ff6c9e","grant_number":"F7814","name":"Stem Cell Modulation in Neural Development and Regeneration/ P14-Swim-to-limb transition: cell type to connection diversity"},{"name":"Tools for automation and feedback microscopy","_id":"c08e9ad1-5a5b-11eb-8a69-9d1cf3b07473","grant_number":"CZI01"},{"name":"Development of V1 interneuron diversity during swim-to-walk transition of Xenopus metamorphosis","grant_number":"FTI21-D-046","_id":"bd73af52-d553-11ed-ba76-912049f0ac7a"},{"_id":"cf428362-b037-11f1-b015-8277a8a2f63d","grant_number":"COE16","name":"Neuronal circuits in health and disease (Sweeney)"}],"article_type":"original","volume":45,"department":[{"_id":"LoSw"},{"_id":"GradSch"},{"_id":"TiVo"},{"_id":"Bio"},{"_id":"NiBa"}],"issue":"4","article_processing_charge":"Yes","fulldoi":"https://doi.org/10.1016/j.celrep.2026.117227","oa_version":"Published Version","corr_author":"1","file":[{"date_created":"2026-05-04T12:20:10Z","date_updated":"2026-05-04T12:20:10Z","checksum":"0d26cdb5b8d8dec3a911d8261a65cdef","file_size":14925958,"creator":"dernst","access_level":"open_access","content_type":"application/pdf","file_id":"21795","file_name":"2026_CellReports_Vijatovic.pdf","success":1,"relation":"main_file"}],"article_number":"117227","publication_identifier":{"eissn":["2211-1247"],"issn":["2639-1856"]},"pmid":1,"PlanS_conform":"1","oa":1,"language":[{"iso":"eng"}],"DOAJ_listed":"1","date_updated":"2026-09-16T07:33:54Z","author":[{"first_name":"David","last_name":"Vijatovic","id":"cf391e77-ec3c-11ea-a124-d69323410b58","full_name":"Vijatovic, David","orcid":"0000-0002-5494-0941"},{"full_name":"Toma, Florina Alexandra ","id":"2f73f876-f128-11eb-9611-b96b5a30cb0e","last_name":"Toma","first_name":"Florina Alexandra "},{"full_name":"Ignatyev, Y","first_name":"Y","last_name":"Ignatyev"},{"id":"a8144562-32c9-11ee-b5ce-d9800628bda2","last_name":"Harrington","first_name":"Zoe P","full_name":"Harrington, Zoe P","orcid":"0009-0008-0158-4032"},{"first_name":"Christoph M","last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M"},{"first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert"},{"first_name":"Matthijs Geert","id":"7a231d52-e216-11ee-a0bb-8acd55f8f1f0","last_name":"Smits","full_name":"Smits, Matthijs Geert"},{"first_name":"Marco","last_name":"Dalla Vecchia","id":"02a7a869-ff06-11ed-a87f-86649d6077e5","full_name":"Dalla Vecchia, Marco"},{"full_name":"Trevisan, Alexandra J.","last_name":"Trevisan","first_name":"Alexandra J."},{"full_name":"Chapman, Phillip","last_name":"Chapman","first_name":"Phillip"},{"first_name":"Mara","id":"1cf464b2-dc7d-11ea-9b2f-f9b1aa9417d1","last_name":"Julseth","full_name":"Julseth, Mara"},{"full_name":"Brenner-Morton, Susan","first_name":"Susan","last_name":"Brenner-Morton"},{"full_name":"Gabitto, Mariano I.","first_name":"Mariano I.","last_name":"Gabitto"},{"last_name":"Dasen","first_name":"Jeremy S.","full_name":"Dasen, Jeremy S."},{"full_name":"Bikoff, Jay B.","first_name":"Jay B.","last_name":"Bikoff"},{"full_name":"Sweeney, Lora Beatrice Jaeger","orcid":"0000-0001-9242-5601","last_name":"Sweeney","id":"56BE8254-C4F0-11E9-8E45-0B23E6697425","first_name":"Lora Beatrice Jaeger"}],"OA_place":"publisher","publication":"Cell Reports","_id":"21746","day":"28","related_material":{"record":[{"id":"22667","status":"public","relation":"dissertation_contains"}]},"publication_status":"published","publisher":"Elsevier","OA_type":"gold","date_created":"2026-04-19T22:07:43Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2026-04-28T00:00:00Z","quality_controlled":"1","month":"04","title":"Multifold increase in spinal inhibitory cell types with emergence of limb movement","type":"journal_article","file_date_updated":"2026-05-04T12:20:10Z","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":"        45","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"has_accepted_license":"1","external_id":{"pmid":["41964955 "]}},{"language":[{"iso":"eng"}],"date_updated":"2025-12-29T11:29:16Z","author":[{"full_name":"Berg, Jeremy J.","first_name":"Jeremy J.","last_name":"Berg"},{"full_name":"Li, Xinyi","first_name":"Xinyi","last_name":"Li"},{"last_name":"Riall","first_name":"Kellen","full_name":"Riall, Kellen"},{"full_name":"Hayward, Laura","first_name":"Laura","last_name":"Hayward","id":"fc885ee5-24bf-11eb-ad7b-bcc5104c0c1b"},{"full_name":"Sella, Guy","first_name":"Guy","last_name":"Sella"}],"pmid":1,"oa":1,"file":[{"file_size":1182339,"checksum":"b02eb6b78028b8bef435edc8435a8468","date_created":"2025-12-29T11:27:51Z","date_updated":"2025-12-29T11:27:51Z","creator":"dernst","access_level":"open_access","file_id":"20863","file_name":"2025_Genetics_Berg.pdf","content_type":"application/pdf","success":1,"relation":"main_file"}],"publication_identifier":{"eissn":["1943-2631"],"issn":["0016-6731"]},"article_number":"iyaf220","oa_version":"Published Version","fulldoi":"https://doi.org/10.1093/genetics/iyaf220","issue":"4","article_processing_charge":"Yes (in subscription journal)","article_type":"original","volume":231,"department":[{"_id":"NiBa"}],"scopus_import":"1","acknowledgement":"We thank Nick Barton, Magnus Nordborg, John Novembre, Molly Przeworski, and Himani Sachdeva for many helpful discussions and for comments on the manuscript, and we thank Joshua Schraiber and 2 anonymous reviewers for comments on the manuscript. We also thank members of the Sella, Przeworski and Andolfatto labs at Columbia University, and the Berg, Novembre and Steinrücken labs at the University of Chicago, for feedback on the work at various stages. This work was completed in part with resources provided by the University of Chicago's Research Computing Center. This work was supported by National Institutes of Health F32 grant GM126787 and R35 grant GM151257 to J.J.B. and National Institutes of Health R01 grant GM115889 to G.S.","abstract":[{"lang":"eng","text":"Genetic variation that influences complex disease susceptibility is introduced into the population by mutation and removed by natural selection and genetic drift. This mutation–selection–drift balance (MSDB) shapes the prevalence of a disease and its genetic architecture. To date, however, MSDB has been modeled only for monogenic (Mendelian) diseases. Here, we develop an MSDB model for complex disease susceptibility: we assume that genotype relates to disease risk according to the canonical liability threshold model and that the selection on variants affecting risk stems from the fitness cost of the disease. We focus on diseases that are highly polygenic, entail a substantial fitness cost, and are neither extremely common in the population nor exceedingly rare. The comparison of model predictions with genome-wide association studies and other observations in humans indicates that common genetic variation affecting complex disease susceptibility is little affected by directional selection and instead shaped by pleiotropic stabilizing selection on other traits. In turn, directional selection may exert a more substantial effect on rare, large-effect variants. Our results also suggest that current estimates of disease heritability are likely biased. The model thus provides a better understanding of the evolutionary processes that shape the architecture and prevalence of complex diseases."}],"year":"2025","doi":"10.1093/genetics/iyaf220","ddc":["570"],"citation":{"chicago":"Berg, Jeremy J., Xinyi Li, Kellen Riall, Laura Hayward, and Guy Sella. “Mutation–Selection–Drift Balance Models of Complex Diseases.” <i>Genetics</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/genetics/iyaf220\">https://doi.org/10.1093/genetics/iyaf220</a>.","mla":"Berg, Jeremy J., et al. “Mutation–Selection–Drift Balance Models of Complex Diseases.” <i>Genetics</i>, vol. 231, no. 4, iyaf220, Oxford University Press, 2025, doi:<a href=\"https://doi.org/10.1093/genetics/iyaf220\">10.1093/genetics/iyaf220</a>.","short":"J.J. Berg, X. Li, K. Riall, L. Hayward, G. Sella, Genetics 231 (2025).","ieee":"J. J. Berg, X. Li, K. Riall, L. Hayward, and G. Sella, “Mutation–selection–drift balance models of complex diseases,” <i>Genetics</i>, vol. 231, no. 4. Oxford University Press, 2025.","ama":"Berg JJ, Li X, Riall K, Hayward L, Sella G. Mutation–selection–drift balance models of complex diseases. <i>Genetics</i>. 2025;231(4). doi:<a href=\"https://doi.org/10.1093/genetics/iyaf220\">10.1093/genetics/iyaf220</a>","ista":"Berg JJ, Li X, Riall K, Hayward L, Sella G. 2025. Mutation–selection–drift balance models of complex diseases. Genetics. 231(4), iyaf220.","apa":"Berg, J. J., Li, X., Riall, K., Hayward, L., &#38; Sella, G. (2025). Mutation–selection–drift balance models of complex diseases. <i>Genetics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/genetics/iyaf220\">https://doi.org/10.1093/genetics/iyaf220</a>"},"external_id":{"pmid":["41073879"]},"has_accepted_license":"1","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"intvolume":"       231","title":"Mutation–selection–drift balance models of complex diseases","file_date_updated":"2025-12-29T11:27:51Z","type":"journal_article","status":"public","quality_controlled":"1","month":"12","OA_type":"hybrid","date_created":"2025-12-21T23:01:34Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2025-12-01T00:00:00Z","publication_status":"published","publisher":"Oxford University Press","day":"01","OA_place":"publisher","publication":"Genetics","_id":"20848"},{"publisher":"Wiley","publication_status":"published","OA_type":"closed access","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2025-12-01T00:00:00Z","date_created":"2025-12-29T12:14:26Z","_id":"20869","publication":"American Journal of Botany","related_material":{"link":[{"relation":"software","url":"https://github.com/Alex-Fuster/hybrids_drought"}]},"day":"01","intvolume":"       112","external_id":{"pmid":["41327576 "]},"month":"12","quality_controlled":"1","type":"journal_article","title":"Reduced fitness under drought stress in F1 hybrids of Antirrhinum majus varieties with divergent flower colors","status":"public","volume":112,"article_type":"original","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"department":[{"_id":"NiBa"}],"issue":"12","article_processing_charge":"No","citation":{"mla":"Fuster‐Calvo, Alexandre, et al. “Reduced Fitness under Drought Stress in F1 Hybrids of Antirrhinum Majus Varieties with Divergent Flower Colors.” <i>American Journal of Botany</i>, vol. 112, no. 12, e70129, Wiley, 2025, doi:<a href=\"https://doi.org/10.1002/ajb2.70129\">10.1002/ajb2.70129</a>.","short":"A. Fuster‐Calvo, C.C. Jaworski, T. Ellis, C. Baskett, American Journal of Botany 112 (2025).","chicago":"Fuster‐Calvo, Alexandre, Coline C. Jaworski, Thomas Ellis, and Carina Baskett. “Reduced Fitness under Drought Stress in F1 Hybrids of Antirrhinum Majus Varieties with Divergent Flower Colors.” <i>American Journal of Botany</i>. Wiley, 2025. <a href=\"https://doi.org/10.1002/ajb2.70129\">https://doi.org/10.1002/ajb2.70129</a>.","ista":"Fuster‐Calvo A, Jaworski CC, Ellis T, Baskett C. 2025. Reduced fitness under drought stress in F1 hybrids of Antirrhinum majus varieties with divergent flower colors. American Journal of Botany. 112(12), e70129.","ama":"Fuster‐Calvo A, Jaworski CC, Ellis T, Baskett C. Reduced fitness under drought stress in F1 hybrids of Antirrhinum majus varieties with divergent flower colors. <i>American Journal of Botany</i>. 2025;112(12). doi:<a href=\"https://doi.org/10.1002/ajb2.70129\">10.1002/ajb2.70129</a>","apa":"Fuster‐Calvo, A., Jaworski, C. C., Ellis, T., &#38; Baskett, C. (2025). Reduced fitness under drought stress in F1 hybrids of Antirrhinum majus varieties with divergent flower colors. <i>American Journal of Botany</i>. Wiley. <a href=\"https://doi.org/10.1002/ajb2.70129\">https://doi.org/10.1002/ajb2.70129</a>","ieee":"A. Fuster‐Calvo, C. C. Jaworski, T. Ellis, and C. Baskett, “Reduced fitness under drought stress in F1 hybrids of Antirrhinum majus varieties with divergent flower colors,” <i>American Journal of Botany</i>, vol. 112, no. 12. Wiley, 2025."},"year":"2025","abstract":[{"text":"Premise: What maintains trait divergence in the face of gene flow? Two varieties of wild snapdragon (Antirrhinum majus) characterized by divergent flower color hybridize in their native range. Selection on flower color genes is indicated by sharp clines, but the selective agents have not been demonstrated. Although previous work has focused on pollinators, pigmentation genes can also contribute to abiotic stress tolerance. We hypothesized that pigmentation in A. majus mediates stress tolerance, which could contribute to hybrid zone maintenance through parental niche divergence or hybrid maladaptation. Specifically, we tested whether morphotype mediates drought tolerance in an experiment comparing magenta-flowered var. pseudomajus, yellow-flowered var. striatum, and their pink-flowered hybrid cross.\r\nMethods: We experimentally compared drought tolerance of each morphotype from allopatric crosses within and between varieties using three greenhouse treatments. Control plants were watered as needed, while drought-treated plants were watered half as often, either from the transplant stage (“early” drought), or from flowering onset (“late” drought).\r\nResults: Parental morphotypes responded identically to drought in fitness and most phenotypic traits. However, hybrids had lower survival (14%) under late drought stress than parental morphotypes (70%). All hybrids that flowered in the late drought treatment died, compared to ~20% of flowering parental morphotypes.\r\nConclusions: Hybrid maladaptation to abiotic stress could potentially contribute to flower color divergence in the face of gene flow in A. majus. Further research should test the relevance of our results to field conditions and explicitly probe the role of flower color genes in drought tolerance.","lang":"eng"}],"acknowledgement":"Thank you to Doug Schemske and Nick Barton forcritically reviewing the manuscript, Beatriz Pablo Car-mona for assisting with data collection, Melinda Pickupand Eva Cereghetti for seedlings, and Louise Arathoon,Ksenia Khudiakova, Georg Rieckh, Daria Shiplina, andAnja Westram for help with experimental maintenance.We sincerely thank the Associate Editor Brenda Grewelland two anonymous reviewers for their thoughtfulcomments and suggestions, which substantially improved the clarity and quality of our manuscript. C.B. receivedfunding from the European Union's Horizon 2020 researchand innovation programme under the Marie Skłodowska‐Curie Grant Agreement No. 754411","scopus_import":"1","doi":"10.1002/ajb2.70129","pmid":1,"language":[{"iso":"eng"}],"date_updated":"2026-01-05T11:56:22Z","author":[{"first_name":"Alexandre","last_name":"Fuster‐Calvo","full_name":"Fuster‐Calvo, Alexandre"},{"full_name":"Jaworski, Coline C.","last_name":"Jaworski","first_name":"Coline C."},{"orcid":"0000-0002-8511-0254","full_name":"Ellis, Thomas","first_name":"Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","last_name":"Ellis"},{"id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","last_name":"Baskett","first_name":"Carina","full_name":"Baskett, Carina","orcid":"0000-0002-7354-8574"}],"fulldoi":"https://doi.org/10.1002/ajb2.70129","oa_version":"None","ec_funded":1,"article_number":"e70129","publication_identifier":{"issn":["0002-9122"],"eissn":["1537-2197"]}},{"citation":{"ieee":"O. O. Olusanya, K. Khudiakova, and H. Sachdeva, “Genetic load, eco-evolutionary feedback, and extinction in metapopulations,” <i>The American Naturalist</i>, vol. 205, no. 6. University of Chicago Press, pp. 617–636, 2025.","apa":"Olusanya, O. O., Khudiakova, K., &#38; Sachdeva, H. (2025). Genetic load, eco-evolutionary feedback, and extinction in metapopulations. <i>The American Naturalist</i>. University of Chicago Press. <a href=\"https://doi.org/10.1086/735562\">https://doi.org/10.1086/735562</a>","ama":"Olusanya OO, Khudiakova K, Sachdeva H. Genetic load, eco-evolutionary feedback, and extinction in metapopulations. <i>The American Naturalist</i>. 2025;205(6):617-636. doi:<a href=\"https://doi.org/10.1086/735562\">10.1086/735562</a>","ista":"Olusanya OO, Khudiakova K, Sachdeva H. 2025. Genetic load, eco-evolutionary feedback, and extinction in metapopulations. The American Naturalist. 205(6), 617–636.","chicago":"Olusanya, Oluwafunmilola O, Kseniia Khudiakova, and Himani Sachdeva. “Genetic Load, Eco-Evolutionary Feedback, and Extinction in Metapopulations.” <i>The American Naturalist</i>. University of Chicago Press, 2025. <a href=\"https://doi.org/10.1086/735562\">https://doi.org/10.1086/735562</a>.","short":"O.O. Olusanya, K. Khudiakova, H. Sachdeva, The American Naturalist 205 (2025) 617–636.","mla":"Olusanya, Oluwafunmilola O., et al. “Genetic Load, Eco-Evolutionary Feedback, and Extinction in Metapopulations.” <i>The American Naturalist</i>, vol. 205, no. 6, University of Chicago Press, 2025, pp. 617–36, doi:<a href=\"https://doi.org/10.1086/735562\">10.1086/735562</a>."},"doi":"10.1086/735562","abstract":[{"text":"Habitat fragmentation poses a significant risk to population survival, causing both demographic stochasticity and genetic drift within local populations to increase, thereby increasing genetic load. Higher load causes population numbers to decline, which reduces the efficiency of selection and further increases load, resulting in a positive feedback that may drive entire populations to extinction. Here, we investigate this eco-evolutionary feedback in a metapopulation consisting of local demes connected via migration, with individuals subject to deleterious mutation at a large number of loci. We first analyze the determinants of load under soft selection, where population sizes are fixed, and then build on this to understand hard selection, where population sizes and load coevolve. We show that under soft selection, very little gene flow (less than one migrant per generation) is enough to prevent fixation of deleterious alleles. By contrast, much higher levels of migration are required to mitigate load and prevent extinction when selection is hard, with critical migration thresholds for metapopulation persistence increasing sharply as the genome-wide deleterious mutation rate becomes comparable to the baseline population growth rate. Moreover, critical migration thresholds are highest if deleterious mutations have intermediate selection coefficients but lower if alleles are predominantly recessive rather than additive (due to more efficient purging of recessive load within local populations). Our analysis is based on a combination of analytical approximations and simulations, allowing for a more comprehensive understanding of the factors influencing load and extinction in fragmented populations.","lang":"eng"}],"acknowledgement":"This research was partially funded by the Austrian Science Fund (FWF P-32896B) and DOC Fellowships of the Austrian Academy of Sciences: grants 26380 (O.O.) and 26293 (K.K.). We thank Nick Barton for useful comments on the chapter in O.O.’s thesis that led to this article.","year":"2025","scopus_import":"1","department":[{"_id":"JaMa"},{"_id":"NiBa"}],"article_type":"original","project":[{"name":"Causes and consequences of population fragmentation","grant_number":"P32896","_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8"},{"_id":"34c872fe-11ca-11ed-8bc3-8534b82131e6","grant_number":"26380","name":"Polygenic Adaptation in a Metapopulation"},{"name":"The impact of deleterious mutations on small populations","_id":"34d33d68-11ca-11ed-8bc3-ec13763c0ca8","grant_number":"26293"}],"volume":205,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2023.12.02.569702"}],"article_processing_charge":"No","issue":"6","fulldoi":"https://doi.org/10.1086/735562","oa_version":"Preprint","corr_author":"1","publication_identifier":{"eissn":["1537-5323"],"issn":["0003-0147"]},"oa":1,"pmid":1,"author":[{"last_name":"Olusanya","id":"41AD96DC-F248-11E8-B48F-1D18A9856A87","first_name":"Oluwafunmilola O","full_name":"Olusanya, Oluwafunmilola O","orcid":"0000-0003-1971-8314"},{"orcid":"0000-0002-6246-1465","full_name":"Khudiakova, Kseniia","first_name":"Kseniia","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","last_name":"Khudiakova"},{"full_name":"Sachdeva, Himani","first_name":"Himani","last_name":"Sachdeva","id":"42377A0A-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2026-04-07T08:45:14Z","language":[{"iso":"eng"}],"_id":"21322","publication":"The American Naturalist","OA_place":"repository","related_material":{"record":[{"relation":"earlier_version","id":"14732","status":"public"}]},"day":"01","page":"617-636","publisher":"University of Chicago Press","publication_status":"published","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2025-06-01T00:00:00Z","date_created":"2026-02-18T10:47:18Z","OA_type":"green","quality_controlled":"1","month":"06","status":"public","type":"journal_article","title":"Genetic load, eco-evolutionary feedback, and extinction in metapopulations","intvolume":"       205","external_id":{"pmid":["40446297 "]}},{"date_updated":"2025-12-30T08:44:12Z","author":[{"full_name":"Surendranadh, Parvathy","orcid":"0000-0001-6395-386X","id":"455235B8-F248-11E8-B48F-1D18A9856A87","last_name":"Surendranadh","first_name":"Parvathy"},{"full_name":"Sachdeva, Himani","last_name":"Sachdeva","first_name":"Himani"}],"has_accepted_license":"1","oa":1,"acknowledged_ssus":[{"_id":"ScienComp"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","title":"Mathematica notebook and Fortran code for 'Effect of assortative mating and sexual selection on polygenic barriers to gene flow'","file":[{"file_id":"18722","file_name":"Codes.zip","content_type":"application/zip","date_updated":"2025-01-02T12:30:27Z","file_size":326835,"date_created":"2025-01-02T12:30:27Z","checksum":"9c5f91876014706990a0728c3675cd2a","access_level":"open_access","creator":"psurendr","relation":"main_file","success":1},{"success":1,"relation":"main_file","date_created":"2025-01-02T12:30:39Z","creator":"psurendr","date_updated":"2025-01-02T12:30:39Z","checksum":"47fe98b7cc526e634e42de58f5eae288","file_size":620,"access_level":"open_access","content_type":"text/plain","file_name":"ReadMe.txt","file_id":"18723"}],"type":"research_data","file_date_updated":"2025-01-02T12:30:39Z","corr_author":"1","fulldoi":"https://doi.org/10.15479/AT:ISTA:17344","oa_version":"Published Version","month":"01","date_created":"2025-01-01T15:28:27Z","article_processing_charge":"No","user_id":"9947682f-b9fa-11ee-9c4a-b3ffaafe6614","date_published":"2025-01-07T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","ddc":["576"],"day":"07","doi":"10.15479/AT:ISTA:17344","related_material":{"record":[{"relation":"used_in_publication","id":"19876","status":"public"}]},"year":"2025","abstract":[{"lang":"eng","text":"This file contains the code associated with the manuscript 'Effect of assortative mating and sexual selection on polygenic barriers to gene flow'. "}],"_id":"18712","citation":{"mla":"Surendranadh, Parvathy, and Himani Sachdeva. <i>Mathematica Notebook and Fortran Code for “Effect of Assortative Mating and Sexual Selection on Polygenic Barriers to Gene Flow.”</i> Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:17344\">10.15479/AT:ISTA:17344</a>.","short":"P. Surendranadh, H. Sachdeva, (2025).","chicago":"Surendranadh, Parvathy, and Himani Sachdeva. “Mathematica Notebook and Fortran Code for ‘Effect of Assortative Mating and Sexual Selection on Polygenic Barriers to Gene Flow.’” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT:ISTA:17344\">https://doi.org/10.15479/AT:ISTA:17344</a>.","ista":"Surendranadh P, Sachdeva H. 2025. Mathematica notebook and Fortran code for ‘Effect of assortative mating and sexual selection on polygenic barriers to gene flow’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:17344\">10.15479/AT:ISTA:17344</a>.","ama":"Surendranadh P, Sachdeva H. Mathematica notebook and Fortran code for “Effect of assortative mating and sexual selection on polygenic barriers to gene flow.” 2025. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:17344\">10.15479/AT:ISTA:17344</a>","apa":"Surendranadh, P., &#38; Sachdeva, H. (2025). Mathematica notebook and Fortran code for “Effect of assortative mating and sexual selection on polygenic barriers to gene flow.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:17344\">https://doi.org/10.15479/AT:ISTA:17344</a>","ieee":"P. Surendranadh and H. Sachdeva, “Mathematica notebook and Fortran code for ‘Effect of assortative mating and sexual selection on polygenic barriers to gene flow.’” Institute of Science and Technology Austria, 2025."}},{"day":"01","page":"367-378","_id":"19438","publication":"Journal of Evolutionary Biology","OA_place":"publisher","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2025-03-01T00:00:00Z","date_created":"2025-03-23T23:01:25Z","OA_type":"hybrid","publisher":"Oxford University Press","publication_status":"published","status":"public","file_date_updated":"2025-04-03T11:53:06Z","type":"journal_article","title":"Short INDELs and SNPs as markers of evolutionary processes in hybrid zones","quality_controlled":"1","month":"03","external_id":{"isi":["001415267900001"],"pmid":["39803902"]},"has_accepted_license":"1","intvolume":"        38","tmp":{"image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"ddc":["570"],"doi":"10.1093/jeb/voaf002","year":"2025","acknowledgement":"This work was supported by the Natural Environment Research Council (NE/K014021/1), European Research Council (ERC-2015-AdG-693030- BARRIERS) and Swedish Research Council VR (2018-03695) and we are also very grateful for the support of the Linnaeus Centre for Marine Evolutionary Biology at the University of Gothenburg.\r\nWe thank the Swedish Bioinformatics Advisory Program organized by SciLifeLab for feedback and assistance on the variant calling pipeline and Alan Le Moan for helpful discussions. R.K.B. and A.M.W. contributed equally to this work. We are also very grateful to Tomas Larsson and Marina Panova for their bioinformatic analyses on the genome and the annotation. The bioinformatic analyses were performed on resources at the University of Sheffield’s High Performance Computing cluster, ShARC. We thank two anonymous reviewers for helpful comments on a previous version.","abstract":[{"lang":"eng","text":"Polymorphic short insertions and deletions (INDELs \r\n 50 bp) are abundant, although less common than single nucleotide polymorphisms (SNPs). Evidence from model organisms shows INDELs to be more strongly influenced by purifying selection than SNPs. Partly for this reason, INDELs are rarely used as markers for demographic processes or to detect divergent selection. Here, we compared INDELs and SNPs in the intertidal snail Littorina saxatilis, focussing on hybrid zones between ecotypes, in order to test the utility of INDELs in the detection of divergent selection. We computed INDEL and SNP site frequency spectra using capture sequencing data. We assessed the impact of divergent selection by analyzing allele frequency clines across habitat boundaries. We also examined the influence of GC-biased gene conversion because it may be confounded with signatures of selection. We show evidence that short INDELs are affected more by purifying selection than SNPs, but part of the observed site frequency spectra difference can be attributed to GC-biased gene conversion. We did not find a difference in the impact of divergent selection between short INDELs and SNPs. Short INDELs and SNPs were similarly distributed across the genome and so are likely to respond to indirect selection in the same way. A few regions likely affected by divergent selection were revealed by INDELs and not by SNPs. Short INDELs can be useful (additional) genetic markers helping to identify genomic regions important for adaptation and population divergence."}],"scopus_import":"1","citation":{"chicago":"Perini, Samuel, Kerstin Johannesson, Roger K. Butlin, and Anja M Westram. “Short INDELs and SNPs as Markers of Evolutionary Processes in Hybrid Zones.” <i>Journal of Evolutionary Biology</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/jeb/voaf002\">https://doi.org/10.1093/jeb/voaf002</a>.","short":"S. Perini, K. Johannesson, R.K. Butlin, A.M. Westram, Journal of Evolutionary Biology 38 (2025) 367–378.","mla":"Perini, Samuel, et al. “Short INDELs and SNPs as Markers of Evolutionary Processes in Hybrid Zones.” <i>Journal of Evolutionary Biology</i>, vol. 38, no. 3, Oxford University Press, 2025, pp. 367–78, doi:<a href=\"https://doi.org/10.1093/jeb/voaf002\">10.1093/jeb/voaf002</a>.","ieee":"S. Perini, K. Johannesson, R. K. Butlin, and A. M. Westram, “Short INDELs and SNPs as markers of evolutionary processes in hybrid zones,” <i>Journal of Evolutionary Biology</i>, vol. 38, no. 3. Oxford University Press, pp. 367–378, 2025.","apa":"Perini, S., Johannesson, K., Butlin, R. K., &#38; Westram, A. M. (2025). Short INDELs and SNPs as markers of evolutionary processes in hybrid zones. <i>Journal of Evolutionary Biology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jeb/voaf002\">https://doi.org/10.1093/jeb/voaf002</a>","ama":"Perini S, Johannesson K, Butlin RK, Westram AM. Short INDELs and SNPs as markers of evolutionary processes in hybrid zones. <i>Journal of Evolutionary Biology</i>. 2025;38(3):367-378. doi:<a href=\"https://doi.org/10.1093/jeb/voaf002\">10.1093/jeb/voaf002</a>","ista":"Perini S, Johannesson K, Butlin RK, Westram AM. 2025. Short INDELs and SNPs as markers of evolutionary processes in hybrid zones. Journal of Evolutionary Biology. 38(3), 367–378."},"article_processing_charge":"Yes (in subscription journal)","issue":"3","department":[{"_id":"NiBa"}],"article_type":"original","volume":38,"publication_identifier":{"issn":["1010-061X"],"eissn":["1420-9101"]},"isi":1,"file":[{"success":1,"relation":"main_file","creator":"dernst","checksum":"01408e626a4131bfec5ffc70b0af9129","date_updated":"2025-04-03T11:53:06Z","date_created":"2025-04-03T11:53:06Z","access_level":"open_access","file_size":12826085,"content_type":"application/pdf","file_name":"2025_JourEvolBiology_Perini.pdf","file_id":"19469"}],"corr_author":"1","fulldoi":"https://doi.org/10.1093/jeb/voaf002","oa_version":"Published Version","date_updated":"2025-09-30T11:19:56Z","author":[{"first_name":"Samuel","last_name":"Perini","full_name":"Perini, Samuel"},{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"},{"full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","first_name":"Anja M"}],"language":[{"iso":"eng"}],"oa":1,"pmid":1},{"date_created":"2025-03-23T23:01:27Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2025-05-01T00:00:00Z","OA_type":"hybrid","publication_status":"published","publisher":"Wiley","page":"1042-1056","day":"01","publication":"Journal of Ecology","_id":"19442","OA_place":"publisher","has_accepted_license":"1","external_id":{"isi":["001443422900001"]},"intvolume":"       113","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","title":"Arctic tundra ecosystems under fire—Alternative ecosystem states in a changing climate?","file_date_updated":"2025-12-30T08:08:18Z","type":"journal_article","month":"05","quality_controlled":"1","article_processing_charge":"Yes (via OA deal)","issue":"5","department":[{"_id":"NiBa"}],"article_type":"review","volume":113,"doi":"10.1111/1365-2745.70022","ddc":["550","570"],"scopus_import":"1","acknowledgement":"We would like to express our sincere gratitude to all the data providers who carried out fieldwork in different regions of the Arctic and published their data, which we used for our meta-analysis. We recognise the hard work and dedication of these individuals, without whom this paper would not have been possible. We are grateful to the editor and the anonymous reviewer for their time and valuable feedback on this manuscript. We particularly appreciate the detailed and constructive comments provided by reviewer Mara Baudena, which significantly strengthened our work. We also acknowledge the Indigenous peoples and rural communities of the Arctic, whose traditional knowledge, rights, and interests are integral to the stewardship and study of these ecosystems. This work was funded in part by the U.S. National Aeronautics and Space Administration (NASA) grant 80NSSC22K1256 (GVF). Open Access funding enabled and organized by Projekt DEAL.","year":"2025","abstract":[{"text":"1. Climate change is expected to induce shifts in the composition, structure and functioning of Arctic tundra ecosystems. Increases in the frequency and severity of tundra fires have the potential to catalyse vegetation transitions with far-reaching local, regional and global consequences.\r\n2. We propose that post-fire tundra recovery, coupled with climate change, may not necessarily lead to pre-fire conditions. Our hypothesis, based on surveys and literature, suggests two climate–fire driven trajectories. One trajectory results in increased woody vegetation under low fire frequency; the other results in grass dominance under high frequency.\r\n3. Future research should address uncertainties regarding possible tundra ecosystem shifts linked to fires, using methods that encompass greater temporal and spatial scales than previously addressed. More case studies, especially in underrepresented regions and ecosystem types, are essential to broaden the empirical basis for forecasts and potential fire management strategies.\r\n4. Synthesis. Our review synthesises current knowledge on post-fire vegetation trajectories in Arctic tundra ecosystems, highlighting potential transitions and alternative ecosystem states and their implications. We discuss challenges in defining and predicting these trajectories as well as future directions.","lang":"eng"}],"citation":{"chicago":"Heim, Ramona Julia, Adrian V. Rocha, Vitalii Zemlianskii, Kirsten Barrett, Helga Bültmann, Amy Breen, Gerald Verner Frost, et al. “Arctic Tundra Ecosystems under Fire—Alternative Ecosystem States in a Changing Climate?” <i>Journal of Ecology</i>. Wiley, 2025. <a href=\"https://doi.org/10.1111/1365-2745.70022\">https://doi.org/10.1111/1365-2745.70022</a>.","mla":"Heim, Ramona Julia, et al. “Arctic Tundra Ecosystems under Fire—Alternative Ecosystem States in a Changing Climate?” <i>Journal of Ecology</i>, vol. 113, no. 5, Wiley, 2025, pp. 1042–56, doi:<a href=\"https://doi.org/10.1111/1365-2745.70022\">10.1111/1365-2745.70022</a>.","short":"R.J. Heim, A.V. Rocha, V. Zemlianskii, K. Barrett, H. Bültmann, A. Breen, G.V. Frost, T.N. Hollingsworth, R. Jandt, M. Kozlova, A. Kurka, M.T. Jorgenson, S.M. Landhäusser, M.M. Loranty, E.A. Miller, K. Narita, E. Pravdolyubova, N. Hölzel, G. Schaepman-Strub, Journal of Ecology 113 (2025) 1042–1056.","ieee":"R. J. Heim <i>et al.</i>, “Arctic tundra ecosystems under fire—Alternative ecosystem states in a changing climate?,” <i>Journal of Ecology</i>, vol. 113, no. 5. Wiley, pp. 1042–1056, 2025.","ista":"Heim RJ, Rocha AV, Zemlianskii V, Barrett K, Bültmann H, Breen A, Frost GV, Hollingsworth TN, Jandt R, Kozlova M, Kurka A, Jorgenson MT, Landhäusser SM, Loranty MM, Miller EA, Narita K, Pravdolyubova E, Hölzel N, Schaepman-Strub G. 2025. Arctic tundra ecosystems under fire—Alternative ecosystem states in a changing climate? Journal of Ecology. 113(5), 1042–1056.","ama":"Heim RJ, Rocha AV, Zemlianskii V, et al. Arctic tundra ecosystems under fire—Alternative ecosystem states in a changing climate? <i>Journal of Ecology</i>. 2025;113(5):1042-1056. doi:<a href=\"https://doi.org/10.1111/1365-2745.70022\">10.1111/1365-2745.70022</a>","apa":"Heim, R. J., Rocha, A. V., Zemlianskii, V., Barrett, K., Bültmann, H., Breen, A., … Schaepman-Strub, G. (2025). Arctic tundra ecosystems under fire—Alternative ecosystem states in a changing climate? <i>Journal of Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/1365-2745.70022\">https://doi.org/10.1111/1365-2745.70022</a>"},"date_updated":"2025-12-30T08:09:47Z","author":[{"last_name":"Heim","first_name":"Ramona Julia","full_name":"Heim, Ramona Julia"},{"full_name":"Rocha, Adrian V.","first_name":"Adrian V.","last_name":"Rocha"},{"full_name":"Zemlianskii, Vitalii","first_name":"Vitalii","last_name":"Zemlianskii"},{"first_name":"Kirsten","last_name":"Barrett","full_name":"Barrett, Kirsten"},{"full_name":"Bültmann, Helga","first_name":"Helga","last_name":"Bültmann"},{"full_name":"Breen, Amy","first_name":"Amy","last_name":"Breen"},{"first_name":"Gerald Verner","last_name":"Frost","full_name":"Frost, Gerald Verner"},{"full_name":"Hollingsworth, Teresa Nettleton","first_name":"Teresa Nettleton","last_name":"Hollingsworth"},{"full_name":"Jandt, Randi","last_name":"Jandt","first_name":"Randi"},{"full_name":"Kozlova, Maria","last_name":"Kozlova","first_name":"Maria"},{"last_name":"Kurka","first_name":"Anastasiya","full_name":"Kurka, Anastasiya"},{"first_name":"Mark Torre","last_name":"Jorgenson","full_name":"Jorgenson, Mark Torre"},{"first_name":"Simon M.","last_name":"Landhäusser","full_name":"Landhäusser, Simon M."},{"full_name":"Loranty, Michael Mark","first_name":"Michael Mark","last_name":"Loranty"},{"full_name":"Miller, Eric A.","last_name":"Miller","first_name":"Eric A."},{"first_name":"Kenji","last_name":"Narita","full_name":"Narita, Kenji"},{"full_name":"Pravdolyubova, Evgeniya","first_name":"Evgeniya","last_name":"Pravdolyubova","id":"0b30719b-13f0-11ed-ab2a-94498bc6a278"},{"full_name":"Hölzel, Norbert","first_name":"Norbert","last_name":"Hölzel"},{"last_name":"Schaepman-Strub","first_name":"Gabriela","full_name":"Schaepman-Strub, Gabriela"}],"language":[{"iso":"eng"}],"PlanS_conform":"1","oa":1,"publication_identifier":{"eissn":["1365-2745"],"issn":["0022-0477"]},"isi":1,"file":[{"content_type":"application/pdf","file_name":"2025_JournEcology_Heim.pdf","file_id":"20890","date_created":"2025-12-30T08:08:18Z","checksum":"e2785ae265e211b4dc7fc9c5b7744948","date_updated":"2025-12-30T08:08:18Z","access_level":"open_access","file_size":2662766,"creator":"dernst","relation":"main_file","success":1}],"oa_version":"Published Version","fulldoi":"https://doi.org/10.1111/1365-2745.70022"},{"date_updated":"2025-09-30T12:24:12Z","author":[{"last_name":"Zuev","first_name":"A. G.","full_name":"Zuev, A. G."},{"last_name":"Alexandrova","first_name":"A. V.","full_name":"Alexandrova, A. V."},{"full_name":"Litvinskiy, V. A.","first_name":"V. A.","last_name":"Litvinskiy"},{"id":"0b30719b-13f0-11ed-ab2a-94498bc6a278","last_name":"Pravdolyubova","first_name":"Evgeniya","full_name":"Pravdolyubova, Evgeniya"},{"first_name":"A. V.","last_name":"Tiunov","full_name":"Tiunov, A. V."}],"language":[{"iso":"eng"}],"pmid":1,"article_number":"32","publication_identifier":{"eissn":["1432-1890"],"issn":["0940-6360"]},"isi":1,"oa_version":"None","fulldoi":"https://doi.org/10.1007/s00572-025-01203-w","article_processing_charge":"No","issue":"2","department":[{"_id":"NiBa"}],"article_type":"original","volume":35,"doi":"10.1007/s00572-025-01203-w","year":"2025","abstract":[{"text":"Mycorrhizal and saprotrophic macromycetes contribute strongly to the carbon and nitrogen cycles of forest ecosystems, often studied by tracing stable isotope composition of carbon and nitrogen. The phenomenon of the saprotrophic-mycorrhizal divide highlights the difference in the stable isotope composition of fruiting bodies of mycorrhizal and saprotrophic fungi. Much less is known about the isotopic composition of the mycelium, which plays an important role in the formation of the soil organic matter and fuels the fungal trophic channel in soil food webs. In this study, we assessed whether the saprotrophic-mycorrhizal divide in the natural δ13С and δ15N values can be traced throughout entire fungal organisms. This hypothesis was tested using 16 species of ectomycorrhizal and six species of saprotrophic basidiomycetous fungi. We showed that not only fruiting bodies, but also the mycelium of ectomycorrhizal and saprotrophic fungi differs in the δ13C and δ15N values. In both ectomycorrhizal and saprotrophic fungi, the δ13C and δ15N values increased from mycelium to hymenophores and correlated positively with the total N content in the corresponding tissues. The differences between ectomycorrhizal and saprotrophic mycelium can be used to reconstruct the fungal-driven belowground carbon and nitrogen allocation, and the contribution of saprotrophic and mycorrhizal fungi to soil food webs.","lang":"eng"}],"acknowledgement":"We thank Sergey Tsurikov for the help with stable isotope analysis. Dr. Jacob D. Wickham (IEE RAS) kindly improved the English of the manuscript. This work was supported by the Russian Science Foundation (project №. 22–14–00363).","scopus_import":"1","citation":{"apa":"Zuev, A. G., Alexandrova, A. V., Litvinskiy, V. A., Pravdolyubova, E., &#38; Tiunov, A. V. (2025). Saprotrophic-mycorrhizal divide in stable isotope composition throughout the whole fungus: From mycelium to hymenophore. <i>Mycorrhiza</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00572-025-01203-w\">https://doi.org/10.1007/s00572-025-01203-w</a>","ama":"Zuev AG, Alexandrova AV, Litvinskiy VA, Pravdolyubova E, Tiunov AV. Saprotrophic-mycorrhizal divide in stable isotope composition throughout the whole fungus: From mycelium to hymenophore. <i>Mycorrhiza</i>. 2025;35(2). doi:<a href=\"https://doi.org/10.1007/s00572-025-01203-w\">10.1007/s00572-025-01203-w</a>","ista":"Zuev AG, Alexandrova AV, Litvinskiy VA, Pravdolyubova E, Tiunov AV. 2025. Saprotrophic-mycorrhizal divide in stable isotope composition throughout the whole fungus: From mycelium to hymenophore. Mycorrhiza. 35(2), 32.","ieee":"A. G. Zuev, A. V. Alexandrova, V. A. Litvinskiy, E. Pravdolyubova, and A. V. Tiunov, “Saprotrophic-mycorrhizal divide in stable isotope composition throughout the whole fungus: From mycelium to hymenophore,” <i>Mycorrhiza</i>, vol. 35, no. 2. Springer Nature, 2025.","short":"A.G. Zuev, A.V. Alexandrova, V.A. Litvinskiy, E. Pravdolyubova, A.V. Tiunov, Mycorrhiza 35 (2025).","mla":"Zuev, A. G., et al. “Saprotrophic-Mycorrhizal Divide in Stable Isotope Composition throughout the Whole Fungus: From Mycelium to Hymenophore.” <i>Mycorrhiza</i>, vol. 35, no. 2, 32, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1007/s00572-025-01203-w\">10.1007/s00572-025-01203-w</a>.","chicago":"Zuev, A. G., A. V. Alexandrova, V. A. Litvinskiy, Evgeniya Pravdolyubova, and A. V. Tiunov. “Saprotrophic-Mycorrhizal Divide in Stable Isotope Composition throughout the Whole Fungus: From Mycelium to Hymenophore.” <i>Mycorrhiza</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1007/s00572-025-01203-w\">https://doi.org/10.1007/s00572-025-01203-w</a>."},"external_id":{"isi":["001467249900001"],"pmid":["40232310"]},"intvolume":"        35","status":"public","type":"journal_article","title":"Saprotrophic-mycorrhizal divide in stable isotope composition throughout the whole fungus: From mycelium to hymenophore","month":"04","quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2025-04-01T00:00:00Z","date_created":"2025-05-04T22:02:32Z","OA_type":"closed access","publisher":"Springer Nature","publication_status":"published","day":"01","_id":"19641","publication":"Mycorrhiza"},{"article_number":"e70058","isi":1,"publication_identifier":{"eissn":["1442-9993"],"issn":["1442-9985"]},"oa_version":"None","fulldoi":"https://doi.org/10.1111/aec.70058","date_updated":"2025-09-30T12:31:04Z","author":[{"last_name":"Arpigiani","first_name":"Daniela","full_name":"Arpigiani, Daniela"},{"full_name":"Aschero, Valeria","last_name":"Aschero","first_name":"Valeria"},{"full_name":"Soler Schaller, Rosina Matilde","last_name":"Soler Schaller","id":"9e668447-8c32-11ed-b0c7-8dc2d7b80803","first_name":"Rosina Matilde"},{"first_name":"Mariano M.","last_name":"Amoroso","full_name":"Amoroso, Mariano M."}],"language":[{"iso":"eng"}],"doi":"10.1111/aec.70058","scopus_import":"1","abstract":[{"text":"Silvopastoral use in native forests could impact population dynamics of key tree species, with contrasting effects at different life cycle stages. Prior studies in South American temperate forests have mainly focused on initial stages, lacking a comprehensive understanding of the entire life cycle within productive systems. We assessed the population dynamics of two key species of mixed forests in northern Patagonia (Austrocedrus chilensis and Nothofagus dombeyi) under two silvopastoral use intensities (high vs. low), using demographic techniques and population projection models. Over 3 years, we quantified vital rates (survival, fertility, growth, reversion and stasis) and used matrix models to calculate deterministic population growth rates (λ). High-intensity silvopastoral use had predominantly negative effects on the elements of the projection matrices of A. chilensis, whereas N. dombeyi exhibited mostly positive or no changes. As a result, projections indicated slight population decreases for A. chilensis (mostly λ < 1) at high silvopastoral use levels compared to low levels, while N. dombeyi showed similar projections (λ ≅ 1) between use levels. Decreased λ for A. chilensis resulted mainly from lower adult tree survival, while early life stages had limited influence on λ for these long-lived species. In summary, silvopastoral use affects population dynamics of key tree species of these mixed forests of northern Patagonia, with implications for sustainable management. Our findings highlight the importance of considering the entire life cycle and suggest targeted practices to enhance A. chilensis populations.","lang":"eng"}],"year":"2025","acknowledgement":"We would like to express our sincere gratitude to the owners of the estates, Lisandro and Oscar Lanfré, Roberto Criado and Yayo Tillería, for allowing us to conduct our research on their properties and for generously sharing their time and knowledge throughout these years. We are also deeply thankful to our field assistants, Matías Scotti, Clara Pissolito, Noel Szudruk, Mariano Varela, Ian Mott, Brisa Guenuleo, Nicolás Bistolfi, Facundo Gómez and Belén Vallerga, who tirelessly collaborated in the arduous tasks of monitoring and data collection, even in challenging weather conditions. We are grateful to CONICET for providing the doctoral scholarship to D. Arpigiani. This study received partial financial support from the Agencia MINCyT (PICT 2015-1692) and the Universidad Nacional de Río Negro (PI 40-B-478), Argentina.","citation":{"ieee":"D. Arpigiani, V. Aschero, R. M. Soler Schaller, and M. M. Amoroso, “A life-cycle approach to understand consequences of silvopastoral use on two native tree species of Northern Patagonia,” <i>Austral Ecology</i>, vol. 50, no. 4. Wiley, 2025.","apa":"Arpigiani, D., Aschero, V., Soler Schaller, R. M., &#38; Amoroso, M. M. (2025). A life-cycle approach to understand consequences of silvopastoral use on two native tree species of Northern Patagonia. <i>Austral Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/aec.70058\">https://doi.org/10.1111/aec.70058</a>","ista":"Arpigiani D, Aschero V, Soler Schaller RM, Amoroso MM. 2025. A life-cycle approach to understand consequences of silvopastoral use on two native tree species of Northern Patagonia. Austral Ecology. 50(4), e70058.","ama":"Arpigiani D, Aschero V, Soler Schaller RM, Amoroso MM. A life-cycle approach to understand consequences of silvopastoral use on two native tree species of Northern Patagonia. <i>Austral Ecology</i>. 2025;50(4). doi:<a href=\"https://doi.org/10.1111/aec.70058\">10.1111/aec.70058</a>","chicago":"Arpigiani, Daniela, Valeria Aschero, Rosina Matilde Soler Schaller, and Mariano M. Amoroso. “A Life-Cycle Approach to Understand Consequences of Silvopastoral Use on Two Native Tree Species of Northern Patagonia.” <i>Austral Ecology</i>. Wiley, 2025. <a href=\"https://doi.org/10.1111/aec.70058\">https://doi.org/10.1111/aec.70058</a>.","short":"D. Arpigiani, V. Aschero, R.M. Soler Schaller, M.M. Amoroso, Austral Ecology 50 (2025).","mla":"Arpigiani, Daniela, et al. “A Life-Cycle Approach to Understand Consequences of Silvopastoral Use on Two Native Tree Species of Northern Patagonia.” <i>Austral Ecology</i>, vol. 50, no. 4, e70058, Wiley, 2025, doi:<a href=\"https://doi.org/10.1111/aec.70058\">10.1111/aec.70058</a>."},"article_processing_charge":"No","issue":"4","department":[{"_id":"NiBa"}],"volume":50,"article_type":"original","status":"public","title":"A life-cycle approach to understand consequences of silvopastoral use on two native tree species of Northern Patagonia","type":"journal_article","month":"04","quality_controlled":"1","external_id":{"isi":["001476761500001"]},"intvolume":"        50","day":"01","publication":"Austral Ecology","_id":"19671","date_created":"2025-05-11T22:02:41Z","date_published":"2025-04-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_type":"closed access","publication_status":"published","publisher":"Wiley"},{"tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"intvolume":"        79","acknowledged_ssus":[{"_id":"ScienComp"}],"external_id":{"isi":["001490646300001"]},"has_accepted_license":"1","month":"07","quality_controlled":"1","type":"journal_article","file_date_updated":"2025-12-30T08:43:33Z","title":"Effect of assortative mating and sexual selection on polygenic barriers to gene flow","status":"public","publisher":"Oxford University Press","publication_status":"published","OA_type":"hybrid","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2025-07-01T00:00:00Z","date_created":"2025-06-23T13:51:00Z","OA_place":"publisher","_id":"19876","publication":"Evolution","related_material":{"record":[{"status":"public","id":"18712","relation":"research_data"}]},"page":"1185-1198","day":"01","oa":1,"language":[{"iso":"eng"}],"author":[{"full_name":"Surendranadh, Parvathy","orcid":"0000-0001-6395-386X","first_name":"Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87","last_name":"Surendranadh"},{"first_name":"Himani","last_name":"Sachdeva","full_name":"Sachdeva, Himani"}],"date_updated":"2025-12-30T08:44:13Z","fulldoi":"https://doi.org/10.1093/evolut/qpaf047","corr_author":"1","oa_version":"Published Version","file":[{"success":1,"relation":"main_file","checksum":"288ca936cef794d68a55356e70671846","date_updated":"2025-12-30T08:43:33Z","date_created":"2025-12-30T08:43:33Z","access_level":"open_access","creator":"dernst","file_size":2784295,"file_id":"20898","file_name":"2025_Evolution_Surendranadh.pdf","content_type":"application/pdf"}],"isi":1,"publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"volume":79,"article_type":"original","department":[{"_id":"NiBa"}],"issue":"7","article_processing_charge":"Yes (via OA deal)","citation":{"chicago":"Surendranadh, Parvathy, and Himani Sachdeva. “Effect of Assortative Mating and Sexual Selection on Polygenic Barriers to Gene Flow.” <i>Evolution</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/evolut/qpaf047\">https://doi.org/10.1093/evolut/qpaf047</a>.","short":"P. Surendranadh, H. Sachdeva, Evolution 79 (2025) 1185–1198.","mla":"Surendranadh, Parvathy, and Himani Sachdeva. “Effect of Assortative Mating and Sexual Selection on Polygenic Barriers to Gene Flow.” <i>Evolution</i>, vol. 79, no. 7, Oxford University Press, 2025, pp. 1185–98, doi:<a href=\"https://doi.org/10.1093/evolut/qpaf047\">10.1093/evolut/qpaf047</a>.","ieee":"P. Surendranadh and H. Sachdeva, “Effect of assortative mating and sexual selection on polygenic barriers to gene flow,” <i>Evolution</i>, vol. 79, no. 7. Oxford University Press, pp. 1185–1198, 2025.","apa":"Surendranadh, P., &#38; Sachdeva, H. (2025). Effect of assortative mating and sexual selection on polygenic barriers to gene flow. <i>Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/evolut/qpaf047\">https://doi.org/10.1093/evolut/qpaf047</a>","ista":"Surendranadh P, Sachdeva H. 2025. Effect of assortative mating and sexual selection on polygenic barriers to gene flow. Evolution. 79(7), 1185–1198.","ama":"Surendranadh P, Sachdeva H. Effect of assortative mating and sexual selection on polygenic barriers to gene flow. <i>Evolution</i>. 2025;79(7):1185-1198. doi:<a href=\"https://doi.org/10.1093/evolut/qpaf047\">10.1093/evolut/qpaf047</a>"},"year":"2025","acknowledgement":"We thank Nick Barton for useful comments on the manuscript. This research was supported by the Scientific Service Units (SSU) of Institute of Science and Technology Austria (ISTA) through resources provided by Scientific Computing (SciComp).","abstract":[{"lang":"eng","text":"Assortative mating and sexual selection are widespread in nature and can play an important role in speciation by facilitating the buildup and maintenance of reproductive isolation (RI). However, their contribution to genome-wide suppression of gene flow during RI is rarely quantified.\r\nHere, we consider a polygenic “magic” trait that is divergently selected across two populations connected by migration, while also serving as the basis of assortative mating, thus generating sexual selection on one or both sexes. We obtain theoretical predictions for divergence at\r\nindividual trait loci by assuming that the effect of all other loci on any locus can be encapsulated via an effective migration rate, which bears a simple relationship to measurable fitness components of migrants and various early-generation hybrids. Our analysis clarifies how “tipping\r\npoints” (characterized by an abrupt collapse of adaptive divergence) arise, and when assortative mating can shift the critical level of migration beyond which divergence collapses. We quantify the relative contributions of viability and sexual selection to genome-wide barriers to gene\r\nflow and discuss how these depend on existing divergence levels. Our results suggest that effective migration rates provide a useful way of understanding genomic divergence, even in scenarios involving multiple, interacting mechanisms of RI. "}],"scopus_import":"1","doi":"10.1093/evolut/qpaf047","ddc":["570"]},{"publisher":"Wiley","publication_status":"published","OA_type":"hybrid","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2025-11-01T00:00:00Z","date_created":"2025-08-03T22:01:31Z","OA_place":"publisher","_id":"20102","publication":"Molecular Ecology","day":"01","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":"        34","external_id":{"isi":["001538172800001"]},"has_accepted_license":"1","quality_controlled":"1","month":"11","type":"journal_article","file_date_updated":"2025-12-30T09:25:17Z","title":"Phenotypic divergence and genomic architecture between parallel ecotypes at two different points on the speciation continuum in a marine snail","status":"public","volume":34,"article_type":"original","department":[{"_id":"NiBa"}],"issue":"21","article_processing_charge":"Yes (in subscription journal)","citation":{"mla":"Raffini, Francesca, et al. “Phenotypic Divergence and Genomic Architecture between Parallel Ecotypes at Two Different Points on the Speciation Continuum in a Marine Snail.” <i>Molecular Ecology</i>, vol. 34, no. 21, e70025, Wiley, 2025, doi:<a href=\"https://doi.org/10.1111/mec.70025\">10.1111/mec.70025</a>.","short":"F. Raffini, A. De Jode, K. Johannesson, R. Faria, Z.B. Zagrodzka, A.M. Westram, J. Galindo, E. Rolán-Alvarez, R.K. Butlin, Molecular Ecology 34 (2025).","chicago":"Raffini, Francesca, Aurélien De Jode, Kerstin Johannesson, Rui Faria, Zuzanna B. Zagrodzka, Anja M Westram, Juan Galindo, Emilio Rolán-Alvarez, and Roger K. Butlin. “Phenotypic Divergence and Genomic Architecture between Parallel Ecotypes at Two Different Points on the Speciation Continuum in a Marine Snail.” <i>Molecular Ecology</i>. Wiley, 2025. <a href=\"https://doi.org/10.1111/mec.70025\">https://doi.org/10.1111/mec.70025</a>.","ama":"Raffini F, De Jode A, Johannesson K, et al. Phenotypic divergence and genomic architecture between parallel ecotypes at two different points on the speciation continuum in a marine snail. <i>Molecular Ecology</i>. 2025;34(21). doi:<a href=\"https://doi.org/10.1111/mec.70025\">10.1111/mec.70025</a>","ista":"Raffini F, De Jode A, Johannesson K, Faria R, Zagrodzka ZB, Westram AM, Galindo J, Rolán-Alvarez E, Butlin RK. 2025. Phenotypic divergence and genomic architecture between parallel ecotypes at two different points on the speciation continuum in a marine snail. Molecular Ecology. 34(21), e70025.","apa":"Raffini, F., De Jode, A., Johannesson, K., Faria, R., Zagrodzka, Z. B., Westram, A. M., … Butlin, R. K. (2025). Phenotypic divergence and genomic architecture between parallel ecotypes at two different points on the speciation continuum in a marine snail. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.70025\">https://doi.org/10.1111/mec.70025</a>","ieee":"F. Raffini <i>et al.</i>, “Phenotypic divergence and genomic architecture between parallel ecotypes at two different points on the speciation continuum in a marine snail,” <i>Molecular Ecology</i>, vol. 34, no. 21. Wiley, 2025."},"year":"2025","abstract":[{"lang":"eng","text":"Speciation is rarely observable directly. A way forward is to compare pairs of ecotypes that evolved in parallel in similar contexts but have reached different degrees of reproductive isolation. Such comparisons are possible in the marine snail Littorina saxatilis by contrasting barriers to gene flow between parallel ecotypes in Spain and Sweden. In both countries, divergent ecotypes have evolved to withstand either crab predation or wave action. Here, we explore transects spanning contact zones between the Crab and the Wave ecotypes using low-coverage whole-genome sequencing, morphological and behavioural traits. Despite parallel phenotypic divergence, distinct patterns of differentiation between the ecotypes emerged: a continuous cline in Sweden indicating a weak barrier to gene flow, but two highly genetically and phenotypically divergent, and partly spatially overlapping clusters in Spain suggesting a much stronger barrier to gene flow. The absence of Spanish early-generation hybrids supported strong isolation, but a low level of gene flow is evident from molecular data. In both countries, highly differentiated loci were located in both shared and country-specific chromosomal inversions but were also present in collinear regions. Despite being considered the same species and showing similar levels of phenotypic divergence, the Spanish ecotypes are much closer to full reproductive isolation than the Swedish ones. Barriers to gene flow of very different strengths between ecotypes within the same species might be explained by dissimilarities in the spatial arrangement of habitats, the selection gradients or the ages of the systems."}],"acknowledgement":"This study was supported by European Research Council grant 693030-BARRIERS to RKB; the Swedish Research Council (grant number 2021-04191) to KJ; the Portuguese Foundation for Science and Technology (FCT: 2020.00275.CEECIND and PTDC/BIA-EVL/1614/2021) to RF; grant PID2022-137935NB-I00 by MICIU/AEI/ 10.13039/501100011033/and ERDF/EU (ED431C 2020-05) to JG, grant PID2021-124930NB-I00 funded by MICIU/AEI/ 10.13039/501100011033/and ERDF/EU to ERA, Xunta de Galicia (ED431C 2024/22), Centro singular de Investigación de Galicia accreditation 2024-2027 (ED431G 2023/07), ‘ERDF A way of making Europe’ and Norwegian Research Council RCN, project 315287 to AMW.","scopus_import":"1","doi":"10.1111/mec.70025","ddc":["570"],"oa":1,"PlanS_conform":"1","language":[{"iso":"eng"}],"date_updated":"2025-12-30T09:25:45Z","author":[{"first_name":"Francesca","last_name":"Raffini","full_name":"Raffini, Francesca"},{"full_name":"De Jode, Aurélien","last_name":"De Jode","first_name":"Aurélien"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"},{"last_name":"Zagrodzka","first_name":"Zuzanna B.","full_name":"Zagrodzka, Zuzanna B."},{"full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","first_name":"Anja M"},{"full_name":"Galindo, Juan","first_name":"Juan","last_name":"Galindo"},{"first_name":"Emilio","last_name":"Rolán-Alvarez","full_name":"Rolán-Alvarez, Emilio"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."}],"oa_version":"Published Version","fulldoi":"https://doi.org/10.1111/mec.70025","file":[{"success":1,"relation":"main_file","checksum":"ec01edda64cfbc6cbc8adf300f719644","date_created":"2025-12-30T09:25:17Z","file_size":2767745,"access_level":"open_access","date_updated":"2025-12-30T09:25:17Z","creator":"dernst","file_id":"20906","file_name":"2025_MolecEcology_Raffini.pdf","content_type":"application/pdf"}],"isi":1,"publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"article_number":"e70025"},{"date_created":"2025-09-10T05:42:23Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2025-09-02T00:00:00Z","OA_type":"hybrid","publication_status":"published","publisher":"Wiley","day":"02","publication":"Molecular Ecology","_id":"20325","OA_place":"publisher","has_accepted_license":"1","external_id":{"pmid":["40751392"],"isi":["001542913000001"]},"intvolume":"        34","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"status":"public","title":"Joint estimation of paternity, sibships and pollen dispersal in a snapdragon hybrid zone","type":"journal_article","file_date_updated":"2025-12-30T10:12:17Z","quality_controlled":"1","month":"09","article_processing_charge":"Yes (via OA deal)","issue":"15","department":[{"_id":"NiBa"}],"article_type":"original","volume":34,"ddc":["570"],"doi":"10.1111/mec.70051","scopus_import":"1","abstract":[{"text":"Inferring genealogical relationships of wild populations is useful because it gives direct estimates of mating patterns and variance in reproductive success. Inference can be improved by including information about parentage shared between siblings, or by modelling phenotypes or population data related to mating. However, we currently lack a framework to infer parent–offspring relationships, sibships and population parameters in a single analysis. To address this, we here extend a previous method, Fractional Analysis of Paternity and Sibships, to include population data for the case where one parent is known. We illustrate this with the example of pollen dispersal in a natural hybrid zone population of the snapdragon Antirrhinum majus. Pollen dispersal is leptokurtic, with half of mating events occurring within 30 m, but with a long tail of mating events up to 859 m. Using simulations, we find that both sibship and population information substantially improve pedigree reconstruction, and that we can expect to resolve median dispersal distances with high accuracy.","lang":"eng"}],"acknowledgement":"We thank a large number of field volunteers for maintaining the population sampling, and Tom White for assistance with seed collection. We thank Sylvia Rebel for plating tissue for DNA extraction, as well as Sean Stankowski and two anonymous reviewers for feedback on the manuscript. ","year":"2025","citation":{"short":"T. Ellis, D. Field, N.H. Barton, Molecular Ecology 34 (2025).","mla":"Ellis, Thomas, et al. “Joint Estimation of Paternity, Sibships and Pollen Dispersal in a Snapdragon Hybrid Zone.” <i>Molecular Ecology</i>, vol. 34, no. 15, e70051, Wiley, 2025, doi:<a href=\"https://doi.org/10.1111/mec.70051\">10.1111/mec.70051</a>.","chicago":"Ellis, Thomas, David Field, and Nicholas H Barton. “Joint Estimation of Paternity, Sibships and Pollen Dispersal in a Snapdragon Hybrid Zone.” <i>Molecular Ecology</i>. Wiley, 2025. <a href=\"https://doi.org/10.1111/mec.70051\">https://doi.org/10.1111/mec.70051</a>.","apa":"Ellis, T., Field, D., &#38; Barton, N. H. (2025). Joint estimation of paternity, sibships and pollen dispersal in a snapdragon hybrid zone. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.70051\">https://doi.org/10.1111/mec.70051</a>","ista":"Ellis T, Field D, Barton NH. 2025. Joint estimation of paternity, sibships and pollen dispersal in a snapdragon hybrid zone. Molecular Ecology. 34(15), e70051.","ama":"Ellis T, Field D, Barton NH. Joint estimation of paternity, sibships and pollen dispersal in a snapdragon hybrid zone. <i>Molecular Ecology</i>. 2025;34(15). doi:<a href=\"https://doi.org/10.1111/mec.70051\">10.1111/mec.70051</a>","ieee":"T. Ellis, D. Field, and N. H. Barton, “Joint estimation of paternity, sibships and pollen dispersal in a snapdragon hybrid zone,” <i>Molecular Ecology</i>, vol. 34, no. 15. Wiley, 2025."},"date_updated":"2025-12-30T10:12:34Z","author":[{"first_name":"Thomas","last_name":"Ellis","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8511-0254","full_name":"Ellis, Thomas"},{"last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","orcid":"0000-0002-4014-8478","full_name":"Field, David"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"language":[{"iso":"eng"}],"oa":1,"pmid":1,"article_number":"e70051","isi":1,"publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"file":[{"success":1,"relation":"main_file","creator":"dernst","access_level":"open_access","date_updated":"2025-12-30T10:12:17Z","checksum":"5059ad4d74e6327b84b5282a39d36774","date_created":"2025-12-30T10:12:17Z","file_size":1698605,"content_type":"application/pdf","file_id":"20911","file_name":"2025_MolecularEcology_Ellis.pdf"}],"fulldoi":"https://doi.org/10.1111/mec.70051","oa_version":"Published Version","corr_author":"1"},{"publisher":"Oxford University Press","publication_status":"published","OA_type":"hybrid","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2025-11-01T00:00:00Z","date_created":"2025-09-10T05:48:04Z","OA_place":"publisher","_id":"20330","publication":"Genetics","day":"01","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":"       231","has_accepted_license":"1","external_id":{"isi":["001598595000001"]},"quality_controlled":"1","month":"11","file_date_updated":"2026-01-05T13:03:18Z","type":"journal_article","title":"The relationship between sexual dimorphism and intersex correlation: Do models support intuition?","status":"public","volume":231,"article_type":"original","project":[{"name":"Sexual conflict: resolution, constraints and biomedical implications","_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A","grant_number":"25817"},{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","grant_number":"101055327","name":"Understanding the evolution of continuous genomes"}],"department":[{"_id":"BeVi"},{"_id":"NiBa"}],"issue":"3","article_processing_charge":"Yes (via OA deal)","citation":{"ista":"Puixeu Sala G, Hayward L. 2025. The relationship between sexual dimorphism and intersex correlation: Do models support intuition? Genetics. 231(3), iyaf175.","ama":"Puixeu Sala G, Hayward L. The relationship between sexual dimorphism and intersex correlation: Do models support intuition? <i>Genetics</i>. 2025;231(3). doi:<a href=\"https://doi.org/10.1093/genetics/iyaf175\">10.1093/genetics/iyaf175</a>","apa":"Puixeu Sala, G., &#38; Hayward, L. (2025). The relationship between sexual dimorphism and intersex correlation: Do models support intuition? <i>Genetics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/genetics/iyaf175\">https://doi.org/10.1093/genetics/iyaf175</a>","ieee":"G. Puixeu Sala and L. Hayward, “The relationship between sexual dimorphism and intersex correlation: Do models support intuition?,” <i>Genetics</i>, vol. 231, no. 3. Oxford University Press, 2025.","mla":"Puixeu Sala, Gemma, and Laura Hayward. “The Relationship between Sexual Dimorphism and Intersex Correlation: Do Models Support Intuition?” <i>Genetics</i>, vol. 231, no. 3, iyaf175, Oxford University Press, 2025, doi:<a href=\"https://doi.org/10.1093/genetics/iyaf175\">10.1093/genetics/iyaf175</a>.","short":"G. Puixeu Sala, L. Hayward, Genetics 231 (2025).","chicago":"Puixeu Sala, Gemma, and Laura Hayward. “The Relationship between Sexual Dimorphism and Intersex Correlation: Do Models Support Intuition?” <i>Genetics</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/genetics/iyaf175\">https://doi.org/10.1093/genetics/iyaf175</a>."},"acknowledgement":"We thank Tim Connallon for useful discussions and correspondence, Himani Sachdeva and Nick Barton for comments on the manuscript and the Scientific Computing unit at ISTA for technical support. GP is the recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology Austria (DOC 25817) and received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant (agreement no. 665385). LH received funding from the European Research Council, under the HaplotypeStructure Grant (grant no. 101055327) to Nick Barton.","year":"2025","abstract":[{"text":"The evolution of sexual dimorphism (the difference in average trait values between females and males, SD), is often thought to be constrained by shared genetic architecture between the sexes. Indeed, it is commonly expected that SD should negatively correlate with the intersex correlation (the genetic correlation between effects of segregating variants in females and males, r fm), either because (1) traits with ancestrally low r fm are less constrained in their ability to respond to sex-specific selection and thus evolve to be more dimorphic, or because (2) sex-specific selection, driving sexual dimorphism evolution, also acts to reduce r fm. Despite the intuitive appeal and prominence of these ideas, their generality and the conditions in which they hold remain unclear. Here, we develop models incorporating sex-specific stabilizing selection, mutation and genetic drift to examine the relationship between r fm and SD. We show that the two commonly-discussed mechanisms with the potential to generate a negative correlation between SD and r fm could just as easily generate a positive association, since the standard line of reasoning hinges on a hidden assumption that sex-specific adaptation more frequently favors increased dimorphism than reduced dimorphism. Our results provide, to our knowledge, the first mechanistic framework for understanding the conditions under which a correlation between r fm and SD may arise and offer a compelling explanation for inconsistent empirical evidence. We also make the intriguing observation that—even when selection between the two sexes is identical—drift generates nonzero SD. We quantify this effect and discuss its significance.","lang":"eng"}],"scopus_import":"1","doi":"10.1093/genetics/iyaf175","ddc":["570"],"oa":1,"PlanS_conform":"1","language":[{"iso":"eng"}],"date_updated":"2026-01-05T13:04:07Z","author":[{"id":"33AB266C-F248-11E8-B48F-1D18A9856A87","last_name":"Puixeu Sala","first_name":"Gemma","full_name":"Puixeu Sala, Gemma","orcid":"0000-0001-8330-1754"},{"first_name":"Laura","last_name":"Hayward","id":"fc885ee5-24bf-11eb-ad7b-bcc5104c0c1b","full_name":"Hayward, Laura"}],"fulldoi":"https://doi.org/10.1093/genetics/iyaf175","oa_version":"Published Version","corr_author":"1","file":[{"relation":"main_file","success":1,"content_type":"application/pdf","file_id":"20946","file_name":"2025_Genetics_Puixeu.pdf","checksum":"bbb73bbf8617812d4d8db4af92be9538","creator":"dernst","access_level":"open_access","date_created":"2026-01-05T13:03:18Z","file_size":1550562,"date_updated":"2026-01-05T13:03:18Z"}],"ec_funded":1,"isi":1,"publication_identifier":{"issn":["1943-2631"]},"article_number":"iyaf175"},{"page":"1301-1313","day":"01","publication":"Plant Ecology","_id":"20429","OA_type":"closed access","date_created":"2025-10-05T22:01:36Z","date_published":"2025-12-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publisher":"Springer Nature","title":"Biotic interactions between trees and colonizing shrubs: Implications for active restoration in southern Patagonian forests","type":"journal_article","status":"public","month":"12","quality_controlled":"1","external_id":{"isi":["001581599800001"]},"intvolume":"       226","scopus_import":"1","year":"2025","abstract":[{"lang":"eng","text":"Plant–plant interactions are key to understanding ecosystem services and shaping restoration strategies, as they can produce either negative or positive effects, determining species establishment and growth. Recognizing these interactions during early-life stages provides valuable insights for restoration in human-disturbed areas. One promising approach is nucleation planting, which establishes small clusters of native species in strategically selected sites, being particularly useful in sites with large herbivores. In southern Patagonia, livestock production has historically been the main economic activity, severely impacting extensive areas of Nothofagus antarctica forest through grazing and intentional burning to increase forage. In this context, nucleation planting with Berberis microphylla, a non-palatable shrub, could foster forest recovery in degraded sites. To evaluate this, we conducted an experiment testing the response of trees to varying shrub number, while also assessing intraspecific effects in both species. We measured survival, biomass, and functional traits. Results showed that the combination of four shrubs surrounding a single tree maintained tree survival at levels comparable to trees growing alone, while seedlings exhibited conspecific negative plant number dependence. Additionally, B. microphylla increased its below- to above-ground biomass ratio under higher plant number, indicating resource reallocation and niche differentiation through spatial separation of root systems."}],"doi":"10.1007/s11258-025-01568-0","citation":{"ieee":"G. N. Bustamante <i>et al.</i>, “Biotic interactions between trees and colonizing shrubs: Implications for active restoration in southern Patagonian forests,” <i>Plant Ecology</i>, vol. 226. Springer Nature, pp. 1301–1313, 2025.","apa":"Bustamante, G. N., Arena, M. E., Selzer, L., Ruggirello, M., Rodríguez, P., Pedrazzani, S., … Soler Schaller, R. M. (2025). Biotic interactions between trees and colonizing shrubs: Implications for active restoration in southern Patagonian forests. <i>Plant Ecology</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11258-025-01568-0\">https://doi.org/10.1007/s11258-025-01568-0</a>","ama":"Bustamante GN, Arena ME, Selzer L, et al. Biotic interactions between trees and colonizing shrubs: Implications for active restoration in southern Patagonian forests. <i>Plant Ecology</i>. 2025;226:1301-1313. doi:<a href=\"https://doi.org/10.1007/s11258-025-01568-0\">10.1007/s11258-025-01568-0</a>","ista":"Bustamante GN, Arena ME, Selzer L, Ruggirello M, Rodríguez P, Pedrazzani S, Navarro-Cano JA, Soler Schaller RM. 2025. Biotic interactions between trees and colonizing shrubs: Implications for active restoration in southern Patagonian forests. Plant Ecology. 226, 1301–1313.","chicago":"Bustamante, Gimena Noemí, Miriam Elisabet Arena, Luciano Selzer, Matthew Ruggirello, Paula Rodríguez, Samuele Pedrazzani, Jose Antonio Navarro-Cano, and Rosina Matilde Soler Schaller. “Biotic Interactions between Trees and Colonizing Shrubs: Implications for Active Restoration in Southern Patagonian Forests.” <i>Plant Ecology</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1007/s11258-025-01568-0\">https://doi.org/10.1007/s11258-025-01568-0</a>.","short":"G.N. Bustamante, M.E. Arena, L. Selzer, M. Ruggirello, P. Rodríguez, S. Pedrazzani, J.A. Navarro-Cano, R.M. Soler Schaller, Plant Ecology 226 (2025) 1301–1313.","mla":"Bustamante, Gimena Noemí, et al. “Biotic Interactions between Trees and Colonizing Shrubs: Implications for Active Restoration in Southern Patagonian Forests.” <i>Plant Ecology</i>, vol. 226, Springer Nature, 2025, pp. 1301–13, doi:<a href=\"https://doi.org/10.1007/s11258-025-01568-0\">10.1007/s11258-025-01568-0</a>."},"article_processing_charge":"No","volume":226,"article_type":"original","department":[{"_id":"NiBa"}],"isi":1,"publication_identifier":{"eissn":["1573-5052"],"issn":["1385-0237"]},"fulldoi":"https://doi.org/10.1007/s11258-025-01568-0","oa_version":"None","language":[{"iso":"eng"}],"date_updated":"2026-01-05T13:23:57Z","author":[{"first_name":"Gimena Noemí","last_name":"Bustamante","full_name":"Bustamante, Gimena Noemí"},{"full_name":"Arena, Miriam Elisabet","last_name":"Arena","first_name":"Miriam Elisabet"},{"full_name":"Selzer, Luciano","first_name":"Luciano","last_name":"Selzer"},{"first_name":"Matthew","last_name":"Ruggirello","full_name":"Ruggirello, Matthew"},{"first_name":"Paula","last_name":"Rodríguez","full_name":"Rodríguez, Paula"},{"full_name":"Pedrazzani, Samuele","first_name":"Samuele","last_name":"Pedrazzani"},{"last_name":"Navarro-Cano","first_name":"Jose Antonio","full_name":"Navarro-Cano, Jose Antonio"},{"id":"9e668447-8c32-11ed-b0c7-8dc2d7b80803","last_name":"Soler Schaller","first_name":"Rosina Matilde","full_name":"Soler Schaller, Rosina Matilde"}]},{"OA_type":"green","date_published":"2025-10-17T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-10-26T23:01:34Z","publisher":"Oxford University Press","publication_status":"published","page":"2167-2180","day":"17","OA_place":"repository","_id":"20531","publication":"Evolution","external_id":{"pmid":["40668071"],"isi":["001547542300001"]},"intvolume":"        79","type":"journal_article","title":"Deleterious mutations and selection for sex in spatially structured, diploid populations","status":"public","month":"10","quality_controlled":"1","issue":"10","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2025.01.22.634382"}],"article_processing_charge":"No","article_type":"original","project":[{"_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A","name":"NOMIS Fellowship Program"}],"volume":79,"department":[{"_id":"NiBa"}],"acknowledgement":"L.F. is funded by the NOMIS-ISTA Fellowship Program. We thank Colin Olito and two anonymous reviewers for helpful comments, and the bioinformatics and computing services at Roscoff’s Biological Station (Abims platform) and at Institute of Science and Technology Austria for computing time.","year":"2025","abstract":[{"lang":"eng","text":"Genetic drift is potentially an important component of selection for sex, as it is a source of statistical associations between alleles at selected loci. By increasing local drift, population structure may thus amplify the evolutionary advantage of sex. However, most previous models have focused either on haploid populations or on diploid populations without spatial structure. In this article, we use two- and three-locus analytical models and multilocus simulations to explore selection for sex in a diploid population structured according to the island model, in the presence of recurrent deleterious mutations. Our results show that selection generally favors an intermediate rate of sex that decreases as the direct cost of sex increases and increases moderately as the degree of population structure increases. Selection for sex is generated by multiple effects involving genetic associations within and between loci. When selection occurs at many loci, it is generally dominated by interference effects involving deleterious alleles at different loci, captured by our three-locus model. In our multilocus simulations, we observed an irreversible spread of asexual mutants under strong costs of sex, and when deleterious mutations are partially recessive. However, population structure may prevent this spread of asexual mutants when dispersal rates are sufficiently small."}],"scopus_import":"1","doi":"10.1093/evolut/qpaf143","citation":{"ieee":"L. Fouqueau and D. Roze, “Deleterious mutations and selection for sex in spatially structured, diploid populations,” <i>Evolution</i>, vol. 79, no. 10. Oxford University Press, pp. 2167–2180, 2025.","apa":"Fouqueau, L., &#38; Roze, D. (2025). Deleterious mutations and selection for sex in spatially structured, diploid populations. <i>Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/evolut/qpaf143\">https://doi.org/10.1093/evolut/qpaf143</a>","ama":"Fouqueau L, Roze D. Deleterious mutations and selection for sex in spatially structured, diploid populations. <i>Evolution</i>. 2025;79(10):2167-2180. doi:<a href=\"https://doi.org/10.1093/evolut/qpaf143\">10.1093/evolut/qpaf143</a>","ista":"Fouqueau L, Roze D. 2025. Deleterious mutations and selection for sex in spatially structured, diploid populations. Evolution. 79(10), 2167–2180.","chicago":"Fouqueau, Louise, and Denis Roze. “Deleterious Mutations and Selection for Sex in Spatially Structured, Diploid Populations.” <i>Evolution</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/evolut/qpaf143\">https://doi.org/10.1093/evolut/qpaf143</a>.","short":"L. Fouqueau, D. Roze, Evolution 79 (2025) 2167–2180.","mla":"Fouqueau, Louise, and Denis Roze. “Deleterious Mutations and Selection for Sex in Spatially Structured, Diploid Populations.” <i>Evolution</i>, vol. 79, no. 10, Oxford University Press, 2025, pp. 2167–80, doi:<a href=\"https://doi.org/10.1093/evolut/qpaf143\">10.1093/evolut/qpaf143</a>."},"language":[{"iso":"eng"}],"author":[{"last_name":"Fouqueau","id":"1676e173-8143-11ed-8927-fe165216a93f","first_name":"Louise","full_name":"Fouqueau, Louise","orcid":"0000-0003-0371-9339"},{"full_name":"Roze, Denis","first_name":"Denis","last_name":"Roze"}],"date_updated":"2025-12-01T15:03:54Z","pmid":1,"oa":1,"publication_identifier":{"eissn":["1558-5646"]},"isi":1,"fulldoi":"https://doi.org/10.1093/evolut/qpaf143","oa_version":"Preprint"},{"has_accepted_license":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"status":"public","file_date_updated":"2026-03-01T23:30:03Z","type":"dissertation","title":"Using genealogies to study the genomic basis of species divergence","month":"11","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2025-11-25T00:00:00Z","date_created":"2025-11-25T13:19:11Z","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"publication_status":"published","related_material":{"record":[{"status":"public","id":"12159","relation":"part_of_dissertation"},{"id":"14796","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"20190","relation":"part_of_dissertation"}]},"page":"268","day":"25","_id":"20694","OA_place":"publisher","date_updated":"2026-04-28T13:20:36Z","author":[{"id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","last_name":"Pal","first_name":"Arka","full_name":"Pal, Arka","orcid":"0000-0002-4530-8469"}],"language":[{"iso":"eng"}],"oa":1,"publication_identifier":{"issn":["2663-337X"]},"file":[{"date_created":"2025-12-01T13:53:36Z","file_size":42723135,"access_level":"open_access","date_updated":"2026-03-01T23:30:03Z","checksum":"7a10a738d58524aebb5dcbd9b34c21c5","creator":"apal","file_name":"2025_Pal_Arka_Thesis.pdf","file_id":"20721","content_type":"application/pdf","embargo":"2026-03-01","relation":"main_file"},{"relation":"source_file","embargo_to":"open_access","checksum":"166d832b08d0434ce407f8f3cb930fe5","date_created":"2025-12-01T13:53:39Z","date_updated":"2026-03-01T23:30:03Z","creator":"apal","file_size":60632116,"access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"20722","file_name":"2025_Pal_Arka_Thesis.docx"}],"fulldoi":"https://doi.org/10.15479/AT-ISTA-20694","oa_version":"Published Version","corr_author":"1","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"project":[{"grant_number":"101055327","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","name":"Understanding the evolution of continuous genomes"},{"_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","grant_number":"P32166","name":"Snapdragon Speciation"}],"doi":"10.15479/AT-ISTA-20694","ddc":["576","578"],"abstract":[{"text":"Understanding the mechanisms underlying speciation is a central aim of evolutionary biology.\r\nA persistent challenge in the field is to identify loci that contribute to reproductive isolation,\r\nwhile disentangling signals of selection from demography, linkage and intrinsic genomic\r\nfeatures. Traditional population genomic approaches that rely on site-based statistics in\r\narbitrary fixed windows face inherent limitations, as they conflate historical and\r\ncontemporary processes of divergence and overlook haplotype structure. Recent advances in\r\nwhole-genome sequencing and methods to infer ancestral recombination graphs (ARGs) now\r\noffer the opportunity to study genealogical relationships explicitly, revealing how lineages\r\ncoalesce and recombine through time. By directly analysing haplotype clustering by species\r\nor phenotype and their patterns of coalescence, ARG-based methods show promise for\r\ndiagnosing sweeps, identifying barrier loci maintained under divergent selection amid gene\r\nflow, and tracing their evolutionary history.\r\nIn this thesis, I explore the utility of genealogical approaches for studying species\r\ndivergence. In chapter 2, I propose a conceptual framework for defining haplotype blocks\r\nthrough the structure of the ARG, using simulations and empirical data to highlight how\r\ngenealogical processes generate rich and often overlooked haplotypic patterns.\r\nIn chapter 3, I examine the genomic basis of a key evolutionary innovation in marine\r\nsnails Littorina. These snails offer a unique opportunity to study an innovation because they\r\ninclude a very recent transition from egg-laying to live bearing, yet snails with the different\r\nreproductive modes are not reciprocally monophyletic. I exploited this by using topology\r\nclustering in ARG-derived local genealogical trees to pinpoint narrow genomic regions or\r\nhaplotype blocks that carry swept alleles, thus revealing that the transition from egg-laying\r\nto live-bearing involves multiple, live-bearer-specific sweeps.\r\nChapter 4 establishes a population-scale, phased genomic resource for Antirrhinum\r\nmajus, using cost-effective haplotagging, then optimizes imputation from low-coverage data\r\nagainst high-accuracy KASP sequencing to maximize sequence completeness with modest\r\naccuracy trade-offs against a traditional short-read sequence pipeline. A hybrid phasing\r\nstrategy combines molecular phasing with statistical phasing to generate phased whole\r\ngenome sequences of 1084 Antirrhinum individuals at a fraction of long-read sequencing\r\ncosts.\r\nIn chapter 5, I analyse hybridising populations from two replicate hybrid zones to find\r\na parallel genetic basis of flower colour, amidst the noise in genomic differentiation landscape\r\ndriven by variation in demographic history. While outlier genome scans of FST failed to dissect\r\nthe causes of differentiation, ARG-based topology clustering revealed a reuse of colour\r\nassociated haplotypes across hybrid zones. In addition to the biological insight, this chapter\r\nalso presents a comparison of the latest ARG inference tools, showing that signals of\r\nAbstract\r\nviii\r\ntopological clustering qualitatively agree between methods, despite differences in the tree\r\nsequences.\r\nNext, in chapter 6, by leveraging ~1000 individuals in one of the hybrid zones, I\r\nintegrated genome-wide association studies of floral pigmentation with genealogical\r\ninference, to test for additional colour loci, and confirm the effect of previously described loci.\r\nThis work demonstrates that flower colour variation is driven by a small number of large effect\r\nloci, while also hinting at the presence of a new candidate regulatory factor.\r\nFinally in chapter 7, in a preliminary analysis, I begin to dissect the genomic island of\r\nspeciation around Rosea/Eluta to understand its evolutionary origins. My results show that it\r\nconsists of 5 highly divergent loci, each of which is associated with flower colour. Using\r\npatterns of coalescence in genealogical trees, I find evidence of staggered selective sweeps\r\nand a persistent localized barrier to gene flow within an otherwise permeable genome.\r\nTogether, these chapters add to the increasing pool of studies using genealogical\r\napproaches to complement and extend site-based statistics to use haplotype structures in\r\nspeciation research. By tracking haplotypes directly and connecting genealogical clustering to\r\npopulation processes, ARG-based inference promises to provide new insights into how local\r\nselective pressures, demographic history, and long-term barriers interact to shape the\r\ngenomic architecture of divergence. By underscoring the value of ARGs in revealing the finescale origins and maintenance of biodiversity, this thesis presents cautious optimism about\r\nthe benefits of using genealogical inference to learn more than what site-based statistics\r\ncould tell us.","lang":"eng"}],"year":"2025","citation":{"short":"A. Pal, Using Genealogies to Study the Genomic Basis of Species Divergence, Institute of Science and Technology Austria, 2025.","mla":"Pal, Arka. <i>Using Genealogies to Study the Genomic Basis of Species Divergence</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20694\">10.15479/AT-ISTA-20694</a>.","chicago":"Pal, Arka. “Using Genealogies to Study the Genomic Basis of Species Divergence.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20694\">https://doi.org/10.15479/AT-ISTA-20694</a>.","apa":"Pal, A. (2025). <i>Using genealogies to study the genomic basis of species divergence</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20694\">https://doi.org/10.15479/AT-ISTA-20694</a>","ista":"Pal A. 2025. Using genealogies to study the genomic basis of species divergence. Institute of Science and Technology Austria.","ama":"Pal A. Using genealogies to study the genomic basis of species divergence. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20694\">10.15479/AT-ISTA-20694</a>","ieee":"A. Pal, “Using genealogies to study the genomic basis of species divergence,” Institute of Science and Technology Austria, 2025."},"alternative_title":["ISTA Thesis"]}]