46 Works

Data from: Complex patterns of cis-regulatory polymorphisms in ebony underlie standing pigmentation variation in Drosophila melanogaster

Ryutaro Miyagi, Naoki Osada, Aya Takahashi & Noriyoshi Akiyama
Pigmentation traits in adult Drosophila melanogaster were used in this study to investigate how phenotypic variations of continuous ecological traits can be maintained in a natural population. First, pigmentation variation in the adult female was measured at seven different body positions in 20 strains from the Drosophila melanogaster Genetic Reference Panel (DGRP) originating from a natural population in North Carolina. Next, to assess the contributions of cis-regulatory polymorphisms of the genes involved in the melanin...

Data from: Ontogenetic stage-specific quantitative trait loci contribute to divergence in developmental trajectories of sexually dimorphic fins between medaka populations

Maiko Kawajiri, Kohta Yoshida, Shingo Fujimoto, Daniel Frikli Mokodongan, Mark Ravinet, Mark Kirkpatrick, Kazunori Yamahira & Jun Kitano
Sexual dimorphism can evolve when males and females differ in phenotypic optima. Genetic constraints can, however, limit the evolution of sexual dimorphism. One possible constraint is derived from alleles expressed in both sexes. Because males and females share most of their genome, shared alleles with different fitness effects between sexes are faced with intralocus sexual conflict. Another potential constraint is derived from genetic correlations between developmental stages. Sexually dimorphic traits are often favoured at adult...

Data from: Allatostatin A signalling in Drosophila regulates feeding and sleep and is modulated by PDF

Jiangtian Chen, Wencke Reiher, Christiane Hermann-Luibl, Azza Sellami, Paola Cognigni, Shu Kondo, Charlotte Helfrich-Förster, Jan A. Veenstra & Christian Wegener
Feeding and sleep are fundamental behaviours with significant interconnections and cross-modulations. The circadian system and peptidergic signals are important components of this modulation, but still little is known about the mechanisms and networks by which they interact to regulate feeding and sleep. We show that specific thermogenetic activation of peptidergic Allatostatin A (AstA)-expressing PLP neurons and enteroendocrine cells reduces feeding and promotes sleep in the fruit fly Drosophila. The effects of AstA cell activation are...

Data from: Interpreting the genomic landscape of speciation: a road map for finding barriers to gene flow

Mark Ravinet, Rui Faria, Roger K. Butlin, Juan Galindo, Nicolas Bierne, Marina Rafajlović, Mohamed A. F. Noor, Bernhard Mehlig & Anja M. Westram
Speciation, the evolution of reproductive isolation amongst populations, is continuous, complex, and involves multiple, interacting barriers. Until it is complete, the effects of this process vary along the genome and can lead to a heterogeneous genomic landscape with peaks and troughs of differentiation and divergence. When gene flow occurs during speciation, barriers restricting migration locally in the genome lead to patterns of heterogeneity. However, genomic heterogeneity can also be produced or modified by variation in...

Data from: Selective breeding and selection mapping using a novel wild-derived heterogeneous stock mice revealed two closely-linked loci for tameness

Yuki Matsumoto, Tatsuhiko Goto, Jo Nishino, Hirofumi Nakaoka, Akira Tanave, Toshiyuki Takano-Shimizu, Richard F. Mott & Tsuyoshi Koide
Tameness is a major behavioral factor for domestication, and can be divided into two potential components: motivation to approach humans (active tameness) and reluctance to avoid humans (passive tameness). We identified genetic loci for active tameness through selective breeding, selection mapping, and association analysis. In previous work using laboratory and wild mouse strains, we found that laboratory strains were predominantly selected for passive tameness but not active tameness during their domestication. To identify genetic regions...

Data from: A key metabolic gene for recurrent freshwater colonization and radiation in fishes

Asano Ishikawa, Naoki Kabeya, Koki Ikeya, Ryo Kakioka, Jennifer N. Cech, Naoki Osada, Miguel C. Leal, Jun Inoue, Manabu Kume, Atsushi Toyoda, Ayumi Tezuka, Atsushi J. Nagano, Yo Y. Yamasaki, Yuto Suzuki, Tomoyuki Kokita, Hiroshi Takahashi, Kay Lucek, David Marques, Yusuke Takehana, Kiyoshi Naruse, Seiichi Mori, Oscar Monroig, Nemiah Ladd, Carsten J. Schubert, Blake Matthews … & Jun Kitano
Colonization of new ecological niches has triggered large adaptive radiations. Although some lineages have made use of such opportunities, not all do so. The factors causing this variation among lineages are largely unknown. Here, we show that deficiency in docosahexaenoic acid (DHA), an essential ω-3 fatty acid, can constrain freshwater colonization by marine fishes. Our genomic analyses revealed multiple independent duplications of the fatty acid desaturase gene Fads2 in stickleback lineages that subsequently colonized and...

sj-xlsx-3-try-10.1177_11786469221128697 – Supplemental material for Dietary Hesperidin Suppresses Lipopolysaccharide-Induced Inflammation in Male Mice

Mizuho Sato, Alato Okuno, Keita Ishisono, Yuhei Yajima & Atsushi Toyoda
Supplemental material, sj-xlsx-3-try-10.1177_11786469221128697 for Dietary Hesperidin Suppresses Lipopolysaccharide-Induced Inflammation in Male Mice by Mizuho Sato, Alato Okuno, Keita Ishisono, Yuhei Yajima and Atsushi Toyoda in International Journal of Tryptophan Research

Data from: Segregation of a QTL cluster for home-cage activity using a new mapping method based on regression analysis of congenic mouse strains

Tsuyoshi Koide, Shogo Kato, Ayako Ishii, Akinori Nishi & Satoshi Kuriki
Recent genetic studies have shown that genetic loci with significant effects in whole-genome quantitative trait loci (QTL) analyses were lost or weakened in congenic strains. Characterisation of the genetic basis of this attenuated QTL effect is important to our understanding of the genetic mechanisms of complex traits. We previously found that a consomic strain, B6-Chr6CMSM, which carries chromosome 6 of a wild-derived strain MSM/Ms on the genetic background of C57BL/6J, exhibited lower home-cage activity than...

Data from: Sex chromosome turnover contributes to genomic divergence between incipient stickleback species

Kohta Yoshida, Takashi Makino, Katsushi Yamaguchi, Shuji Shigenobu, Mitsuyasu Hasebe, Masakado Kawata, Manabu Kume, Seiichi Mori, Catherine L. Peichel, Atsushi Toyoda, Asao Fujiyama & Jun Kitano
Sex chromosomes turn over rapidly in some taxonomic groups, where closely related species have different sex chromosomes. Although there are many examples of sex chromosome turnover, we know little about the functional roles of sex chromosome turnover in phenotypic diversification and genomic evolution. The sympatric pair of Japanese threespine stickleback (Gasterosteus aculeatus) provides an excellent system to address these questions: the Japan Sea species has a neo-sex chromosome system resulting from a fusion between an...

Data from: Caspr3-deficient mice exhibit low motor learning during the early phase of the accelerated rotarod task

Haruna Hirata, Aki Takahashi, Yasushi Shimoda & Tsuyoshi Koide
Caspr3 (Contactin-associated protein-like 3, Cntnap3) is a neural cell adhesion molecule belonging to the Caspr family. We have recently shown that Caspr3 is expressed abundantly between the first and second postnatal weeks in the mouse basal ganglia, including the striatum, external segment of the globus pallidus, subthalamic nucleus, and substantia nigra. However, its physiological role remains largely unknown. In this study, we conducted a series of behavioral analyses on Capsr3-knockout (KO) mice and equivalent wild-type...

Data from: A linkage map and QTL analysis for pyrethroid resistance in the bed bug Cimex lectularius

Toby Fountain, Mark Ravinet, Richard Naylor, Klaus Reinhardt & Roger K. Butlin
The rapid evolution of insecticide resistance remains one of the biggest challenges in the control of medically and economically important pests. Insects have evolved a diverse range of mechanisms to reduce the efficacy of the commonly used classes of insecticides and finding the genetic basis of resistance is a major aid to management. In a previously unstudied population, we performed an F2 resistance mapping cross for the common bed bug, Cimex lectularius, for which insecticide...

Data from: Convergent evolution of body color between sympatric freshwater fishes via different visual sensory evolution

Javier Montenegro, Koji Mochida, Kumi Matsui, Daniel F. Mokodongan, Bayu K. A. Sumarto, Sjamsu A. Lawelle, Andy B. Nofrianto, Renny K. Hadiaty, Kawilarang W. A. Masengi, Lengxob Yong, Nobuyuki Inomata, Takahiro Irie, Yasuyuki Hashiguchi, Yohey Terai, Jun Kitano & Kazunori Yamahira
Although there are many examples of color evolution potentially driven by sensory drive, only few studies have examined whether distinct species inhabiting the same environments evolve similar body colors via shared sensory mechanisms. In this study, we tested whether two sympatric freshwater fish taxa, halfbeaks of the genus Nomorhamphus and ricefishes of the genus Oryzias in Sulawesi Island, converge in both body color and visual sensitivity. After reconstructing the phylogeny separately for Nomorhamphus and Oryzias...

Ethylene signaling mediates host invasion by parasitic plants

Songkui Cui, Tomoya Kubota, Tomoya Kubota, Tomoaki Nishiyama, Juliane Ishida, Shuji Shigenobu, Tomoko Shibata, Atsushi Toyoda, Mitsuyasu Hasebe, Ken Shirasu & Satoko Yoshida
Parasitic plants form a specialized organ, a haustorium, to invade host tissues and acquire water and nutrients. To understand the molecular mechanism of haustorium development, we performed a forward genetics screening to isolate mutants exhibiting haustorial defects in the model parasitic plant Phtheirospermum japonicum. We isolated two mutants that show prolonged and sometimes aberrant meristematic activity in the haustorium apex, resulting in severe defects on host invasion. Whole genome sequencing revealed that the two mutants...

Diversity of sex chromosomes in Sulawesian medaka fishes

Satoshi Ansai, Javier Montenegro, Kawilarang W. A. Masengi, Atsushi J. Nagano, Kazunori Yamahira & Jun Kitano
Recent genetic and genomic studies have revealed tremendous diversity in sex chromosomes across diverse taxa. Closely related species with different sex chromosomes provide us with excellent opportunities to investigate the driving forces and the consequences of sex chromosome turnover. In the present study, we investigated the diversity of sex chromosomes of 13 Oryzias species from Sulawesi, Indonesia, which diversified during the last 4.86 million years. Using pooled sequencing we found sex chromosomes in 9 species...

sj-xlsx-1-try-10.1177_11786469221128697 – Supplemental material for Dietary Hesperidin Suppresses Lipopolysaccharide-Induced Inflammation in Male Mice

Mizuho Sato, Alato Okuno, Keita Ishisono, Yuhei Yajima & Atsushi Toyoda
Supplemental material, sj-xlsx-1-try-10.1177_11786469221128697 for Dietary Hesperidin Suppresses Lipopolysaccharide-Induced Inflammation in Male Mice by Mizuho Sato, Alato Okuno, Keita Ishisono, Yuhei Yajima and Atsushi Toyoda in International Journal of Tryptophan Research

sj-xlsx-2-try-10.1177_11786469221128697 – Supplemental material for Dietary Hesperidin Suppresses Lipopolysaccharide-Induced Inflammation in Male Mice

Mizuho Sato, Alato Okuno, Keita Ishisono, Yuhei Yajima & Atsushi Toyoda
Supplemental material, sj-xlsx-2-try-10.1177_11786469221128697 for Dietary Hesperidin Suppresses Lipopolysaccharide-Induced Inflammation in Male Mice by Mizuho Sato, Alato Okuno, Keita Ishisono, Yuhei Yajima and Atsushi Toyoda in International Journal of Tryptophan Research

Data from: Toward the genetic origins of a potentially non-native population of threespine stickleback (Gasterosteus aculeatus) in Alberta

Andrew M. Rezansoff, Erika Crispo, Christopher Blair, Edward Cruz, Jun Kitano, Steven M. Vamosi & Sean M. Rogers
Disentangling the origin of putatively introduced/invasive species is of increasing priority in conservation biology. The presence of a previously undocumented species may be due to an undetected recent population or range expansion associated with environmental change, or due to an introduction by humans. We used molecular tools to address the origin of a population of threespine stickleback (Gasterosteus aculeatus) first identified in central Alberta, Canada in 1980 from a single lake. We characterized this inland,...

Data from: Shared and non-shared genomic divergence in parallel ecotypes of Littorina saxatilis at a local scale

Mark Ravinet, Anja Westram, Kerstin Johannesson, Roger Butlin, Carl André & Marina Panova
Parallel speciation occurs when selection drives repeated, independent adaptive divergence that reduces gene flow between ecotypes. Classical examples show parallel speciation originating from shared genomic variation, but this does not seem to be the case in the rough periwinkle (Littorina saxatilis) that has evolved considerable phenotypic diversity across Europe, including several distinct ecotypes. Small ‘wave’ ecotype snails inhabit exposed rocks and experience strong wave action, while thick-shelled, ‘crab’ ecotype snails are larger and experience crab...

Data from: Different contributions of local- and distant-regulatory changes to transcriptome divergence between stickleback ecotypes

Asano Ishikawa, Makoto Kusakabe, Kohta Yoshida, Mark Ravinet, Takashi Makino, Atsushi Toyoda, Asao Fujiyama & Jun Kitano
Differential gene expression can play an important role in phenotypic evolution and divergent adaptation. Although differential gene expression can be caused by both local- and distant-regulatory changes, we know little about their relative contribution to transcriptome evolution in natural populations. Here, we conducted expression quantitative trait loci (eQTL) analysis to investigate the genetic architecture underlying transcriptome divergence between marine and stream ecotypes of threespine sticklebacks (Gasterosteus aculeatus). We identified both local and distant eQTLs, some...

Accumulation of deleterious mutations in landlocked threespine stickleback populations

Jun Kitano, Kohta Yoshida, Mark Ravinet, Takashi Makino, Atsushi Toyoda, Tomoyuki Kokita & Seiichi Mori
Colonization of new habitats often reduces population sizes and may result in the accumulation of deleterious mutations by genetic drift. Compared to the genomic basis for adaptation to new environments, genome-wide analysis of deleterious mutations in isolated populations remains limited. In the present study, we investigated the accumulation of deleterious mutations in five endangered freshwater populations of threespine stickleback (Gasterosteus aculeatus) in the central part of the mainland of Japan. Using whole genome resequencing data,...

Neuronal octopamine signaling regulates mating-induced germline stem cell increase in female Drosophila melanogaster

Ryusuke Niwa, Yuto Yoshinari, Tomotsune Ameku, Shu Kondo, Hiromu Tanimoto, Takayuki Kuraishi & Yuko Shimada-Niwa
Stem cells fuel the development and maintenance of tissues. Many studies have addressed how local signals from neighboring niche cells regulate stem cell identity and their proliferative potential. However, the regulation of stem cells by tissue-extrinsic signals in response to environmental cues remains poorly understood. Here we report that efferent octopaminergic neurons projecting to the ovary are essential for germline stem cell (GSC) increase in response to mating in female Drosophila. The neuronal activity of...

Genome-wide patterns of divergence and introgression after secondary contact between Pungitius sticklebacks

Jun Kitano
Speciation is a continuous process. Although it is known that differential adaptation can initiate divergence even in the face of gene flow, we know relatively little about the mechanisms driving complete reproductive isolation and the genomic patterns of divergence and introgression at the later stages of speciation. Sticklebacks contain many pairs of sympatric species differing in levels of reproductive isolation and divergence history. Nevertheless, most previous studies have focused on young species pairs. Here, we...

Mesozoic origin and out-of-India radiation of ricefishes (Adrianichthyidae)

Kazunori Yamahira, Satoshi Ansai, Ryo Kakioka, Hajime Yaguchi, Takeshi Kon, Hirozumi Kobayashi, Javier Montenegro, Shingo Fujimoto, Ryosuke Kimura, Yusuke Takehana, Davin Setiamarga, Yasuoki Takami, Rieko Tanaka, Ken Maeda, Hau Tran, Noriyuki Koizumi, Shinsuke Morioka, Vongvichith Bounsong, Katsutoshi Watanabe, Prachya Musikasinthorn, Sein Tun, L. K. C Yun, Kawilarang Masengi, VK Anoop, Rajeev Raghavan … & Jun Kitano
The Indian subcontinent has an origin geologically different from Eurasia, but many terrestrial animal and plant species on it have congeneric or sister species in other parts of Asia, especially in the Southeast. This faunal and floral similarity between India and Southeast Asia is explained by either of the two biogeographic scenarios, ‘into-India’ or ‘out-of-India.’ Phylogenies based on complete mitochondrial genome and five nuclear genes were undertaken for ricefishes (Adrianichthyidae) to examine which of these...

Insights into Mus musculus population structure across Eurasia revealed by whole-genome analysis

Kazumichi Fujiwara, Yosuke Kawai, Toyoyuki Takada, Toshihiko Shiroishi, Naruya Saitou, Hitoshi Suzuki & Naoki Osada
For more than 100 years, house mice (Mus musculus) have been used as a key animal model in biomedical research. House mice are genetically diverse, yet their genetic background at the global level has not been fully understood. Previous studies suggested that they originated in South Asia and diverged into three major subspecies almost simultaneously, approximately 350,000–500,000 years ago; however, they have spread across the world with the migration of modern humans in prehistoric and...

Data from: Microsatellite marker development by multiplex Ion Torrent PGM sequencing: a case study of the endangered Odorrana narina complex of frogs

Takeshi Igawa, Masafumi Nozawa, Mai Nagaoka, Shohei Komaki, Shohei Oumi, Tamotsu Fujii & Masayuki Sumida
The endangered Ryukyu tip-nosed frog Odorrana narina and its related species, Odorrana amamiensis, Odorrana supranarina, and Odorrana utsunomiyaorum, belong to the family Ranidae and are endemically distributed in Okinawa (O. narina), Amami and Tokunoshima (O. amamiensis), and Ishigaki and Iriomote (O. supranarina and O. utsunomiyaorum) Islands. Because of varying distribution patterns, this species complex is an intrinsic model for speciation and adaptation. For effective conservation and molecular ecological studies, further genetic information is needed. For...

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  • National Institute of Genetics
  • Tohoku University
  • University of the Ryukyus
  • Sam Ratulangi University
  • Ryukoku University
  • University of Oslo
  • National Institute for Basic Biology
  • Gifu Kyoritsu University
  • Fred Hutchinson Cancer Research Center
  • University of Gothenburg