{"entity": "researcher", "timestamp": "2026-09-23T14:54:23.423Z", "family": "Kawakami", "given": "Takeshi", "initials": "T", "orcid": "0000-0002-9204-6852", "affiliations": ["Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, 752 36, Sweden.", "Department of Animal and Plant Sciences, University of Sheffield, S10 2TN, United Kingdom."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/843ff3f21fde4acdb15729e96cb0ae4c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/843ff3f21fde4acdb15729e96cb0ae4c"}}, "publications": [{"entity": "publication", "iuid": "ffae1e4181c347cb9177c68008efad8e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ffae1e4181c347cb9177c68008efad8e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ffae1e4181c347cb9177c68008efad8e"}}, "title": "Orthopteran Neo-Sex Chromosomes Reveal Dynamics of Recombination Suppression and Evolution of Supergenes.", "authors": [{"family": "Jayaprasad", "given": "Suvratha", "initials": "S"}, {"family": "Peona", "given": "Valentina", "initials": "V", "orcid": "0000-0001-5119-1837", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/12d645d316a64a54ad02fb915cf9b2d6.json"}}, {"family": "Ellerstrand", "given": "Simon J", "initials": "SJ", "orcid": "0000-0003-2674-6997", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e36f041d79c240d2aa669a1e24e168d7.json"}}, {"family": "Rossini", "given": "Roberto", "initials": "R"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Pettersson", "given": "Olga V", "initials": "OV", "orcid": "0000-0002-5597-1870", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f513ec3fb924415a9e579d1c829c7d2d.json"}}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "RA", "orcid": "0009-0002-8357-5186", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b2a00756397a4aa58f539513e5b8b37f.json"}}, {"family": "Rubin", "given": "Carl-Johan", "initials": "CJ", "orcid": "0000-0001-8238-5052", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cc83e7c8e44145778f170d3ac49c52a6.json"}}, {"family": "Einarsdottir", "given": "Elisabet", "initials": "E", "orcid": "0000-0003-3101-2285", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ae255687b53f4926b4cb9ad06dcf6edc.json"}}, {"family": "Bonath", "given": "Franziska", "initials": "F"}, {"family": "Bradford", "given": "Tessa M", "initials": "TM", "orcid": "0000-0003-0607-1398", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/41bad8c13b55485c998822fa4c43d267.json"}}, {"family": "Cooper", "given": "Steven J B", "initials": "SJB", "orcid": "0000-0002-7843-8438", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/771a0a9bd4174d10ab02a1f2a08da9fb.json"}}, {"family": "Hansson", "given": "Bengt", "initials": "B", "orcid": "0000-0001-6694-8169", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f0451b7e0a83450698af8d37c522279e.json"}}, {"family": "Suh", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8979-9992", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e1790a31477c4376957d8c328299db1c.json"}}, {"family": "Kawakami", "given": "Takeshi", "initials": "T", "orcid": "0000-0002-9204-6852", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/843ff3f21fde4acdb15729e96cb0ae4c.json"}}, {"family": "Schielzeth", "given": "Holger", "initials": "H", "orcid": "0000-0002-9124-2261", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/185297e474cc4e09b1f2087fb7d902a1.json"}}, {"family": "Palacios-Gimenez", "given": "Octavio M", "initials": "OM", "orcid": "0000-0002-1472-9949", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4d3d53ea54b4ec293da675c9c63a0de.json"}}], "type": "journal article", "published": "2024-12-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "33", "issue": "23", "pages": "e17567", "issn-l": "0962-1083"}, "abstract": "The early evolution of sex chromosomes has remained obscure for more than a century. The Vandiemenella viatica species group of morabine grasshoppers is highly suited for studying the early stages of sex chromosome divergence and degeneration of the Y chromosome. This stems from the fact that neo-XY sex chromosomes have independently evolved multiple times by X-autosome fusions with different autosomes. Here, we generated new chromosome-level assemblies for two chromosomal races representing karyotypes with and without neo-sex chromosomes (P24XY and P24X0), and sequence data of a third chromosomal race with a different neo-XY chromosome system (P25XY). Interestingly, these two neo-XY chromosomal races are formed by different X-autosome fusions (involving chr1 and chrB, respectively), and we found that both neo-Y chromosomes have partly ceased to recombine with their neo-X counterpart. We show that the neo-XY chromosomes have diverged through accumulation of SNPs and structural mutations, and that many neo-Y-linked genes have degenerated since recombination ceased. However, the non-recombining regions of neo-Y chromosomes host non-degenerated genes crucial for sex determination, such as sex-lethal and transformer, alongside genes associated with spermatogenesis, fertility, and reproduction, illustrating their integrative role as a masculinizing supergene. Contrary to expectations, the neo-Y chromosomes showed (slightly) lower density of transposable elements (TEs) compared to other genomic regions. The study reveals the unique dynamics of young sex chromosomes, with evolution of recombination suppression and pronounced decay of (some) neo-sex chromosome genes, and provides a compelling case illustrating how chromosomal fusions and post-fusion mutational processes contribute to the evolution of supergenes.", "doi": "10.1111/mec.17567", "pmid": "39475093", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11589690"}], "notes": [], "created": "2026-09-23T11:34:42.294Z", "modified": "2026-09-23T11:34:42.591Z"}, {"entity": "publication", "iuid": "9cb22c53b0f3402c98ebe92994e2b7c4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9cb22c53b0f3402c98ebe92994e2b7c4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9cb22c53b0f3402c98ebe92994e2b7c4"}}, "title": "The evolutionary maintenance of ancient recombining sex chromosomes in the ostrich.", "authors": [{"family": "Yazdi", "given": "Homa Papoli", "initials": "HP", "orcid": "0000-0001-8667-6279", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5458a72b50ed40eb8ce92fa4660346d5.json"}}, {"family": "Olito", "given": "Colin", "initials": "C", "orcid": "0000-0001-6883-0367", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/228387f2fb75471fbd5fe5b98bac83e8.json"}}, {"family": "Kawakami", "given": "Takeshi", "initials": "T", "orcid": "0000-0002-9204-6852", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/843ff3f21fde4acdb15729e96cb0ae4c.json"}}, {"family": "Unneberg", "given": "Per", "initials": "P", "orcid": "0000-0001-5735-3315", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/47dae455224d4af4a35865907088f0b1.json"}}, {"family": "Schou", "given": "Mads F", "initials": "MF", "orcid": "0000-0001-5521-5269", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ada3921fcdda44e4bcc151405853080f.json"}}, {"family": "Cloete", "given": "Schalk W P", "initials": "SWP", "orcid": "0000-0002-4548-5633", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ceb42d016e2241fb8aa431dfad9f11e1.json"}}, {"family": "Hansson", "given": "Bengt", "initials": "B", "orcid": "0000-0001-6694-8169", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f0451b7e0a83450698af8d37c522279e.json"}}, {"family": "Cornwallis", "given": "Charlie K", "initials": "CK", "orcid": "0000-0003-1308-3995", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cd3a03b2536c4e2490f9610ed9845538.json"}}], "type": "journal article", "published": "2023-06-00", "journal": {"title": "PLoS Genet", "issn": "1553-7404", "volume": "19", "issue": "6", "pages": "e1010801", "issn-l": "1553-7390"}, "abstract": "Sex chromosomes have evolved repeatedly across the tree of life and often exhibit extreme size dimorphism due to genetic degeneration of the sex-limited chromosome (e.g. the W chromosome of some birds and Y chromosome of mammals). However, in some lineages, ancient sex-limited chromosomes have escaped degeneration. Here, we study the evolutionary maintenance of sex chromosomes in the ostrich (Struthio camelus), where the W remains 65% the size of the Z chromosome, despite being more than 100 million years old. Using genome-wide resequencing data, we show that the population scaled recombination rate of the pseudoautosomal region (PAR) is higher than similar sized autosomes and is correlated with pedigree-based recombination rate in the heterogametic females, but not homogametic males. Genetic variation within the sex-linked region (SLR) (\u03c0 = 0.001) was significantly lower than in the PAR, consistent with recombination cessation. Conversely, genetic variation across the PAR (\u03c0 = 0.0016) was similar to that of autosomes and dependent on local recombination rates, GC content and to a lesser extent, gene density. In particular, the region close to the SLR was as genetically diverse as autosomes, likely due to high recombination rates around the PAR boundary restricting genetic linkage with the SLR to only ~50Kb. The potential for alleles with antagonistic fitness effects in males and females to drive chromosome degeneration is therefore limited. While some regions of the PAR had divergent male-female allele frequencies, suggestive of sexually antagonistic alleles, coalescent simulations showed this was broadly consistent with neutral genetic processes. Our results indicate that the degeneration of the large and ancient sex chromosomes of the ostrich may have been slowed by high recombination in the female PAR, reducing the scope for the accumulation of sexually antagonistic variation to generate selection for recombination cessation.", "doi": "10.1371/journal.pgen.1010801", "pmid": "37390104", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10343094"}, {"db": "pii", "key": "PGENETICS-D-22-01416"}], "notes": [], "created": "2026-09-23T11:23:49.861Z", "modified": "2026-09-23T11:23:50.061Z"}, {"entity": "publication", "iuid": "3ffbbae506964a319867f2ec2cd7656a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3ffbbae506964a319867f2ec2cd7656a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3ffbbae506964a319867f2ec2cd7656a"}}, "title": "Substantial Heritable Variation in Recombination Rate on Multiple Scales in Honeybees and Bumblebees.", "authors": [{"family": "Kawakami", "given": "Takeshi", "initials": "T", "orcid": "0000-0002-9204-6852", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/843ff3f21fde4acdb15729e96cb0ae4c.json"}}, {"family": "Wallberg", "given": "Andreas", "initials": "A", "orcid": "0000-0002-9081-9663", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/612978d6845d4e70949078f2bbf1cc62.json"}}, {"family": "Olsson", "given": "Anna", "initials": "A"}, {"family": "Wintermantel", "given": "Dimitry", "initials": "D"}, {"family": "de Miranda", "given": "Joachim R", "initials": "JR", "orcid": "0000-0002-0335-0386", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/57fc43785bcb40af8d8e6379b39664b0.json"}}, {"family": "Allsopp", "given": "Mike", "initials": "M"}, {"family": "Rundl\u00f6f", "given": "Maj", "initials": "M"}, {"family": "Webster", "given": "Matthew T", "initials": "MT", "orcid": "0000-0003-1141-2863", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/89b55655555f44b7b870a3bb45d1152d.json"}}], "type": "journal article", "published": "2019-08-00", "journal": {"title": "Genetics", "issn": "1943-2631", "volume": "212", "issue": "4", "pages": "1101-1119", "issn-l": "0016-6731"}, "abstract": "Meiotic recombination shuffles genetic variation and promotes correct segregation of chromosomes. Rates of recombination vary on several scales, both within genomes and between individuals, and this variation is affected by both genetic and environmental factors. Social insects have extremely high rates of recombination, although the evolutionary causes of this are not known. Here, we estimate rates of crossovers and gene conversions in 22 colonies of the honeybee, Apis mellifera, and 9 colonies of the bumblebee, Bombus terrestris, using direct sequencing of 299 haploid drone offspring. We confirm that both species have extremely elevated crossover rates, with higher rates measured in the highly eusocial honeybee than the primitively social bumblebee. There are also significant differences in recombination rate between subspecies of honeybee. There is substantial variation in genome-wide recombination rate between individuals of both A. mellifera and B. terrestris and the distribution of these rates overlap between species. A large proportion of interindividual variation in recombination rate is heritable, which indicates the presence of variation in trans-acting factors that influence recombination genome-wide. We infer that levels of crossover interference are significantly lower in honeybees compared to bumblebees, which may be one mechanism that contributes to higher recombination rates in honeybees. We also find a significant increase in recombination rate with distance from the centromere, mirrored by methylation differences. We detect a strong transmission bias due to GC-biased gene conversion associated with noncrossover gene conversions. Our results shed light on the mechanistic causes of extreme rates of recombination in social insects and the genetic architecture of recombination rate variation.", "doi": "10.1534/genetics.119.302008", "pmid": "31152071", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC6707477"}, {"db": "pii", "key": "genetics.119.302008"}], "notes": [], "created": "2026-09-23T09:51:54.200Z", "modified": "2026-09-23T10:25:55.212Z"}]}