[{"scopus_import":"1","page":"337-351","publisher":"Elsevier","intvolume":"        40","title":"Diverse pathways to speciation revealed by marine snails","date_published":"2024-04-01T00:00:00Z","article_processing_charge":"Yes (in subscription journal)","doi":"10.1016/j.tig.2024.01.002","quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledgement":"KJ, MR, and RKB were supported by grants from the Swedish Research Council (2021-0419, 2021-05243, and 2018-03695, respectively). RKB was also supported by the Leverhulme Trust (RPG-2021-141), RF by FCT- Portuguese Science Foundation (PTDC/BIA-EVL/1614/2021 and 2020.00275.CEECIND), and AMW by Norwegian Research Council RCN (Project number 315287). We thank the members of the Integration of Speciation Research network for stimulating discussions, the Littorina research community for important contributions of data and analyses, and Cynthia Riginos for useful comments on an earlier draft.","fulldoi":"https://doi.org/10.1016/j.tig.2024.01.002","type":"journal_article","file_date_updated":"2024-07-22T12:05:58Z","abstract":[{"lang":"eng","text":"Speciation is a key evolutionary process that is not yet fully understood. Combining population genomic and ecological data from multiple diverging pairs of marine snails (Littorina) supports the search for speciation mechanisms. Placing pairs on a one-dimensional speciation continuum, from undifferentiated populations to species, obscured the complexity of speciation. Adding multiple axes helped to describe either speciation routes or reproductive isolation in the snails. Divergent ecological selection repeatedly generated barriers between ecotypes, but appeared less important in completing speciation while genetic incompatibilities played a key role. Chromosomal inversions contributed to genomic barriers, but with variable impact. A multidimensional (hypercube) approach supported framing of questions and identification of knowledge gaps and can be useful to understand speciation in many other systems."}],"isi":1,"researchdata_availability":"no","month":"04","author":[{"first_name":"Kerstin","full_name":"Johannesson, Kerstin","last_name":"Johannesson"},{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"},{"last_name":"Le Moan","full_name":"Le Moan, Alan","first_name":"Alan"},{"last_name":"Rafajlović","first_name":"Marina","full_name":"Rafajlović, Marina"},{"orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","full_name":"Westram, Anja M","first_name":"Anja M"},{"first_name":"Roger K.","full_name":"Butlin, Roger K.","last_name":"Butlin"},{"last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean","first_name":"Sean"}],"file":[{"date_created":"2024-07-22T12:05:58Z","file_name":"2024_TrendsGenetics_Johannesson.pdf","date_updated":"2024-07-22T12:05:58Z","content_type":"application/pdf","file_id":"17313","access_level":"open_access","creator":"dernst","success":1,"checksum":"3077ea808c4cdc24d02dc58aced7eb35","file_size":2288340,"relation":"main_file"}],"external_id":{"pmid":["38395682"],"isi":["001224671300001"]},"issue":"4","language":[{"iso":"eng"}],"article_type":"review","ddc":["570"],"license":"https://creativecommons.org/licenses/by/4.0/","supplementarymaterial":"yes","publication_status":"published","das_tickbox":"0","has_accepted_license":"1","publication_identifier":{"eissn":["1362-4555"],"issn":["0168-9525"]},"pmid":1,"year":"2024","department":[{"_id":"NiBa"}],"citation":{"mla":"Johannesson, Kerstin, et al. “Diverse Pathways to Speciation Revealed by Marine Snails.” <i>Trends in Genetics</i>, vol. 40, no. 4, Elsevier, 2024, pp. 337–51, doi:<a href=\"https://doi.org/10.1016/j.tig.2024.01.002\">10.1016/j.tig.2024.01.002</a>.","apa":"Johannesson, K., Faria, R., Le Moan, A., Rafajlović, M., Westram, A. M., Butlin, R. K., &#38; Stankowski, S. (2024). Diverse pathways to speciation revealed by marine snails. <i>Trends in Genetics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tig.2024.01.002\">https://doi.org/10.1016/j.tig.2024.01.002</a>","chicago":"Johannesson, Kerstin, Rui Faria, Alan Le Moan, Marina Rafajlović, Anja M Westram, Roger K. Butlin, and Sean Stankowski. “Diverse Pathways to Speciation Revealed by Marine Snails.” <i>Trends in Genetics</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.tig.2024.01.002\">https://doi.org/10.1016/j.tig.2024.01.002</a>.","short":"K. Johannesson, R. Faria, A. Le Moan, M. Rafajlović, A.M. Westram, R.K. Butlin, S. Stankowski, Trends in Genetics 40 (2024) 337–351.","ama":"Johannesson K, Faria R, Le Moan A, et al. Diverse pathways to speciation revealed by marine snails. <i>Trends in Genetics</i>. 2024;40(4):337-351. doi:<a href=\"https://doi.org/10.1016/j.tig.2024.01.002\">10.1016/j.tig.2024.01.002</a>","ista":"Johannesson K, Faria R, Le Moan A, Rafajlović M, Westram AM, Butlin RK, Stankowski S. 2024. Diverse pathways to speciation revealed by marine snails. Trends in Genetics. 40(4), 337–351.","ieee":"K. Johannesson <i>et al.</i>, “Diverse pathways to speciation revealed by marine snails,” <i>Trends in Genetics</i>, vol. 40, no. 4. Elsevier, pp. 337–351, 2024."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"volume":40,"publication":"Trends in Genetics","day":"01","_id":"15099","date_created":"2024-03-10T23:00:54Z","oa":1,"date_updated":"2026-10-21T08:13:54Z","oa_version":"Published Version","status":"public"},{"abstract":[{"text":"The factors that determine the tempo and mode of protein evolution continue to be a central question in molecular evolution. Traditionally, studies of protein evolution focused on the rates of amino acid substitutions. More recently, with the availability of sequence data and advanced experimental techniques, the focus of attention has shifted toward the study of evolutionary trajectories and the overall layout of protein fitness landscapes. In this review we describe the effect of epistasis on the topology of evolutionary pathways that are likely to be found in fitness landscapes and develop a simple theory to connect the number of maladapted genotypes to the topology of fitness landscapes with epistatic interactions. Finally, we review recent studies that have probed the extent of epistatic interactions and have begun to chart the fitness landscapes in protein sequence space.","lang":"eng"}],"type":"journal_article","fulldoi":"https://doi.org/10.1016/j.tig.2014.09.009","author":[{"last_name":"Kondrashov","full_name":"Kondrashov, Dmitry","first_name":"Dmitry"},{"orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","first_name":"Fyodor","full_name":"Kondrashov, Fyodor"}],"month":"01","title":"Topological features of rugged fitness landscapes in sequence space","date_published":"2015-01-01T00:00:00Z","intvolume":"        31","publisher":"Elsevier","extern":"1","page":"24 - 33","scopus_import":"1","keyword":["Mimsatch repair","Chromatin structure","Replication fork","Cancer therapy"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","acknowledgement":"This work has been supported by a grant from the HHMI International Early Career Scientist Program (#55007424), the Spanish Ministry of Economy and Competitiveness (grant #BFU2012-31329) as part of the EMBO YIP program, two grants from the Spanish Ministry of Economy and Competitiveness, Centro de Excelencia Severo Ochoa 2013–2017 (#Sev-2012-0208) and BES-2013-064004 funded by the European Regional Development Fund (ERDF), the European Union, and the European Research Council under grant agreement no 335980_EinME.","OA_type":"closed access","quality_controlled":"1","doi":"10.1016/j.tig.2014.09.009","publist_id":"6764","article_processing_charge":"No","volume":31,"citation":{"mla":"Kondrashov, Dmitry, and Fyodor Kondrashov. “Topological Features of Rugged Fitness Landscapes in Sequence Space.” <i>Trends in Genetics</i>, vol. 31, no. 1, Elsevier, 2015, pp. 24–33, doi:<a href=\"https://doi.org/10.1016/j.tig.2014.09.009\">10.1016/j.tig.2014.09.009</a>.","apa":"Kondrashov, D., &#38; Kondrashov, F. (2015). Topological features of rugged fitness landscapes in sequence space. <i>Trends in Genetics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tig.2014.09.009\">https://doi.org/10.1016/j.tig.2014.09.009</a>","short":"D. Kondrashov, F. Kondrashov, Trends in Genetics 31 (2015) 24–33.","ista":"Kondrashov D, Kondrashov F. 2015. Topological features of rugged fitness landscapes in sequence space. Trends in Genetics. 31(1), 24–33.","chicago":"Kondrashov, Dmitry, and Fyodor Kondrashov. “Topological Features of Rugged Fitness Landscapes in Sequence Space.” <i>Trends in Genetics</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.tig.2014.09.009\">https://doi.org/10.1016/j.tig.2014.09.009</a>.","ama":"Kondrashov D, Kondrashov F. Topological features of rugged fitness landscapes in sequence space. <i>Trends in Genetics</i>. 2015;31(1):24-33. doi:<a href=\"https://doi.org/10.1016/j.tig.2014.09.009\">10.1016/j.tig.2014.09.009</a>","ieee":"D. Kondrashov and F. Kondrashov, “Topological features of rugged fitness landscapes in sequence space,” <i>Trends in Genetics</i>, vol. 31, no. 1. Elsevier, pp. 24–33, 2015."},"year":"2015","status":"public","oa_version":"None","date_updated":"2026-05-19T07:23:54Z","date_created":"2018-12-11T11:49:01Z","_id":"886","publication":"Trends in Genetics","day":"01","article_type":"original","language":[{"iso":"eng"}],"issue":"1","external_id":{"pmid":["25438718"]},"pmid":1,"publication_identifier":{"eissn":["1362-4555"],"issn":["0168-9525"]},"publication_status":"published"},{"fulldoi":"https://doi.org/10.1016/j.tig.2004.05.001","type":"journal_article","abstract":[{"lang":"eng","text":"The dominance of wild-type alleles and the concomitant recessivity of deleterious mutant alleles might have evolved by natural selection or could be a by-product of the molecular and physiological mechanisms of gene action. We compared the properties of human haplosufficient genes, whose wild-type alleles are dominant over loss-of-function alleles, with haploinsufficient (recessive wild-type) genes, which produce an abnormal phenotype when heterozygous for a loss-of-function allele. The fraction of haplosufficient genes is the highest among the genes that encode enzymes, which is best compatible with the physiological theory. Haploinsufficient genes, on average, have more paralogs than haplosufficient genes, supporting the idea that gene dosage could be important for the initial fixation of duplications. Thus, haplo(in)sufficiency of a gene and its propensity for duplication might have a common evolutionary basis."}],"month":"07","author":[{"orcid":"0000-0001-8243-4694","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor","first_name":"Fyodor"},{"full_name":"Koonin, Eugene","first_name":"Eugene","last_name":"Koonin"}],"page":"287 - 291","extern":"1","publisher":"Elsevier","title":"A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications","date_published":"2004-07-01T00:00:00Z","intvolume":"        20","publist_id":"6775","doi":"10.1016/j.tig.2004.05.001","article_processing_charge":"No","OA_type":"closed access","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2004","citation":{"mla":"Kondrashov, Fyodor, and Eugene Koonin. “A Common Framework for Understanding the Origin of Genetic Dominance and Evolutionary Fates of Gene Duplications.” <i>Trends in Genetics</i>, vol. 20, no. 7, Elsevier, 2004, pp. 287–91, doi:<a href=\"https://doi.org/10.1016/j.tig.2004.05.001\">10.1016/j.tig.2004.05.001</a>.","apa":"Kondrashov, F., &#38; Koonin, E. (2004). A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications. <i>Trends in Genetics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tig.2004.05.001\">https://doi.org/10.1016/j.tig.2004.05.001</a>","short":"F. Kondrashov, E. Koonin, Trends in Genetics 20 (2004) 287–291.","ama":"Kondrashov F, Koonin E. A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications. <i>Trends in Genetics</i>. 2004;20(7):287-291. doi:<a href=\"https://doi.org/10.1016/j.tig.2004.05.001\">10.1016/j.tig.2004.05.001</a>","chicago":"Kondrashov, Fyodor, and Eugene Koonin. “A Common Framework for Understanding the Origin of Genetic Dominance and Evolutionary Fates of Gene Duplications.” <i>Trends in Genetics</i>. Elsevier, 2004. <a href=\"https://doi.org/10.1016/j.tig.2004.05.001\">https://doi.org/10.1016/j.tig.2004.05.001</a>.","ista":"Kondrashov F, Koonin E. 2004. A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications. Trends in Genetics. 20(7), 287–291.","ieee":"F. Kondrashov and E. Koonin, “A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications,” <i>Trends in Genetics</i>, vol. 20, no. 7. Elsevier, pp. 287–291, 2004."},"volume":20,"publication":"Trends in Genetics","day":"01","date_updated":"2026-09-30T13:38:03Z","date_created":"2018-12-11T11:48:58Z","_id":"875","status":"public","oa_version":"None","external_id":{"pmid":["15219392"]},"article_type":"original","language":[{"iso":"eng"}],"issue":"7","publication_status":"published","pmid":1,"publication_identifier":{"issn":["0168-9525"],"eissn":["1362-4555"]}},{"scopus_import":"1","page":"115 - 119","intvolume":"        19","date_published":"2003-03-01T00:00:00Z","title":"Evolution of alternative splicing: Deletions, insertions and origin of functional parts of proteins from intron sequences","extern":"1","publisher":"Elsevier","quality_controlled":"1","article_processing_charge":"No","doi":"10.1016/S0168-9525(02)00029-X","publist_id":"6776","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","acknowledgement":"We thank Peer Bork, Mikhail Gelfand, Alexey Kondrashov, David Lipman and Shamil Sunyaev for critical reading of the manuscript and useful suggestions and the Koonin group members for helpful discussions.","OA_type":"closed access","type":"journal_article","fulldoi":"https://doi.org/10.1016/S0168-9525(02)00029-X","abstract":[{"text":"Alternative splicing is thought to be a major source of functional diversity in animal proteins. We analyzed the evolutionary conservation of proteins encoded by alternatively spliced genes and predicted the ancestral state for 73 cases of alternative splicing (25 insertions and 48 deletions). The amino acid sequences of most of the inserts in proteins produced by alternative splicing are as conserved as the surrounding sequences. Thus, alternative splicing often creates novel isoforms by the insertion of new, functional protein sequences that probably originated from noncoding sequences of introns.","lang":"eng"}],"author":[{"full_name":"Kondrashov, Fyodor","first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694"},{"last_name":"Koonin","first_name":"Eugene","full_name":"Koonin, Eugene"}],"month":"03","external_id":{"pmid":["12615001"]},"issue":"3","article_type":"original","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1362-4555"],"issn":["0168-9525"]},"pmid":1,"year":"2003","volume":19,"citation":{"ieee":"F. Kondrashov and E. Koonin, “Evolution of alternative splicing: Deletions, insertions and origin of functional parts of proteins from intron sequences,” <i>Trends in Genetics</i>, vol. 19, no. 3. Elsevier, pp. 115–119, 2003.","ista":"Kondrashov F, Koonin E. 2003. Evolution of alternative splicing: Deletions, insertions and origin of functional parts of proteins from intron sequences. Trends in Genetics. 19(3), 115–119.","ama":"Kondrashov F, Koonin E. Evolution of alternative splicing: Deletions, insertions and origin of functional parts of proteins from intron sequences. <i>Trends in Genetics</i>. 2003;19(3):115-119. doi:<a href=\"https://doi.org/10.1016/S0168-9525(02)00029-X\">10.1016/S0168-9525(02)00029-X</a>","chicago":"Kondrashov, Fyodor, and Eugene Koonin. “Evolution of Alternative Splicing: Deletions, Insertions and Origin of Functional Parts of Proteins from Intron Sequences.” <i>Trends in Genetics</i>. Elsevier, 2003. <a href=\"https://doi.org/10.1016/S0168-9525(02)00029-X\">https://doi.org/10.1016/S0168-9525(02)00029-X</a>.","short":"F. Kondrashov, E. Koonin, Trends in Genetics 19 (2003) 115–119.","mla":"Kondrashov, Fyodor, and Eugene Koonin. “Evolution of Alternative Splicing: Deletions, Insertions and Origin of Functional Parts of Proteins from Intron Sequences.” <i>Trends in Genetics</i>, vol. 19, no. 3, Elsevier, 2003, pp. 115–19, doi:<a href=\"https://doi.org/10.1016/S0168-9525(02)00029-X\">10.1016/S0168-9525(02)00029-X</a>.","apa":"Kondrashov, F., &#38; Koonin, E. (2003). Evolution of alternative splicing: Deletions, insertions and origin of functional parts of proteins from intron sequences. <i>Trends in Genetics</i>. Elsevier. <a href=\"https://doi.org/10.1016/S0168-9525(02)00029-X\">https://doi.org/10.1016/S0168-9525(02)00029-X</a>"},"day":"01","publication":"Trends in Genetics","oa_version":"None","status":"public","_id":"876","date_created":"2018-12-11T11:48:58Z","date_updated":"2026-05-28T13:49:56Z"}]