Researcher basic information

• Ph.D. in Science, Kyoto University, Mar. 2015

• https://researchmap.jp/7000011384?lang=en

• https://orcid.org/0000-0002-1037-0350
• https://jglobal.jst.go.jp/detail?JGLOBAL_ID=201501071718458030
• https://noah.ees.hokudai.ac.jp/hayakawa/
• https://noah.ees.hokudai.ac.jp/hayakawa/english.html

• 00758493

• https://orcid.org/0000-0002-1037-0350

• U-9518-2018

• 201501071718458030

• メタボローム
• マイクロバイオーム
• トランスクリプトーム
• ゲノム
• 比較オミックス科学
• オミックス
• 腸内細菌
• Umami taste receptor
• Bitter taste receptor
• Taste receptor
• Australia
• Africa
• monotreme
• marsupial
• primates
• echidna
• platypus
• koala
• Japanese macaque
• chimpanzee
• Chemical Ecology
• Evolutionary Biology
• Mammalogy
• Marsupial Biology
• Sensory Biology
• Molecular Ecology
• Genomics
• Zoology
• Primatology

• Life Science, Ecology and environment
• Life Science, Biodiversity and systematics
• Life Science, Evolutionary biology
• Life Science, Genome biology
• Life Science, Genetics
• Life Science, Physical anthropology
• Life Science, Animal life science
• Life Science, Bioorganic chemistry
• Life Science, Applied biochemistry
• Life Science, Applied anthropology
• Life Science, System genome science
• Life Science, Laboratory animal science
• Life Science, Veterinary medical science
• Life Science, Aquatic life science
• Life Science, Food sciences
• Environmental Science/Agriculture Science, Chemical substance influence on environment
• Environmental Science/Agriculture Science, Environmental impact assessment
• Environmental Science/Agriculture Science, Social-ecological systems
• Environmental Science/Agriculture Science, Conservation of biological resources
• Life Science, Animal physiological chemistry, physiology and behavioral biology
• Life Science, Molecular biology

• Bachelor's degree program, School of Science
• Master's degree program, Graduate School of Environmental Science
• Doctoral (PhD) degree program, Graduate School of Environmental Science

Research activity information

• Aug. 2025, 日本進化学会, 研究奨励賞
  哺乳類を主な対象としたゲノム解析とフィールドワークの融合による進化生態学的研究
• Oct. 2021, 第7回 北海道大学部局横断シンポジウム「異分野融合による新領域研究」発表 金賞
  早川卓志
• 2021, 日本動物学会, 動物学教育賞
  系統樹マンダラポスターの制作を通した動物学の一般社会への普及についての貢献
  系統樹マンダラポスター制作チーム(霊長類編スタッフとして)
• Oct. 2020, 第6回 北海道大学部局横断シンポジウム「異分野融合による新領域研究」発表 研究奨励賞
  早川卓志
• 2020, 日本進化学会, 教育啓発賞
  系統樹マンダラポスターシリーズの制作を通した進化学普及への貢献
  系統樹マンダラポスター制作チーム(霊長類編スタッフとして)
• Mar. 2015, Japan Society for the Promotion of Science, Ikushi Prize
  Elucidation of molecular evolution and ecological adaptation mechanism of the bitter taste receptor gene repertoire in primates
  Takashi Hayakawa
• Jan. 2015, Japan Monkey Centre, Excellent oral presentation award
  野生チンパンジーにおける苦味受容体の遺伝的多様性と進化
  Takashi Hayakawa
• Jul. 2014, Primate Society of Japan, Excellent oral presentation award
  非侵襲糞サンプリングに基づくギニア・ボッソウの野生チンパンジーの全遺伝子配列解析
  Takashi Hayakawa
• Sep. 2013, Primate Society of Japan, Excellent oral presentation award
  野生チンパンジーにおける苦味受容体遺伝子の地域差と生態適応
  Takashi Hayakawa
• Aug. 2012, Society of Evolutionary Studies, Japan, Excellent poster presentation award
  真主齧類における苦味受容体の進化
  Takashi Hayakawa
• Jul. 2012, Primate Society of Japan, Excellent oral presentation award
  霊長類味覚受容体レパートリーの進化史
  Takashi Hayakawa

• Dynamic evolution of retroviral envelope-derived sequences in primates
  Koichi Kitao; Kirill Kryukov; Lihua Jin; Yuta Shintaku; Takashi Hayakawa; So Nakagawa
  Virus Evolution, Oxford University Press (OUP), 16 Jul. 2026, [Peer-reviewed]
  Scientific journal, Abstract
  
  It is known that several endogenous retroviruses (ERVs), remnants of ancient retroviral integrations, retain envelope (env) genes encoding fusogenic proteins in primates. While most env genes are degraded, a few have been co-opted by hosts, yet the entire evolutionary dynamics of env sequences remain poorly understood. To explore this, we screened and compared env open-reading frames (ORFs) from 247 primate genomes. In total, 8,683 nearly intact env-ORFs encoding over 400 amino acids were identified, and their copy numbers ranged from 3 to 429 across primate species. Sequence similarity clustering revealed a clear evolutionary signature that distinguishes the small set of long-term co-opted env-derived genes, which are retained at low copy numbers across lineages, from the broader pool of rapidly turning-over env-ORFs. Applying this framework, we identified a previously unrecognized, single-copy env ortholog conserved across Tarsiiformes, named env-Tar1, and experimentally demonstrated its cell fusion activity in vitro, providing the first functional evidence of an env-derived gene co-opted in a tarsier lineage. Further, we found that certain co-opted env-derived genes may have lost their functions due to nonsense or indel mutations within specific primate lineages. Considering that many env genes tend to be maintained at low copy numbers and are reported to be under purifying selection, such dynamic evolutionary turnover of env-derived genes may be driven by host-virus arms races, as viruses and endogenous retroviruses often share cell-surface receptors.
• Transcriptome analysis across reproductive stages in peripheral blood of female brown bears: a pilot study
  Asuka Nishijima; Yojiro Yanagawa; Naoya Matsumoto; Kyogo Hagino; Hideyuki Sakamoto; Takashi Hayakawa
  Scientific Reports, 17 Jun. 2026, [Peer-reviewed], [Last author, Corresponding author]
  Scientific journal
• Pressure-tolerant evolution in rhodopsin of deep-diving whales
  Hayate Takeuchi; Takashi Hayakawa
  Genome Biology and Evolution, 18, 4, evag068, Oxford University Press (OUP), 16 Mar. 2026, [Peer-reviewed], [Last author, Corresponding author]
  Scientific journal, Abstract
  
  Life in the deep sea presents extreme challenges to protein structure and function, with hydrostatic pressure serving as a significant source of molecular stress. Although cetacean rhodopsins have been thoroughly examined concerning their spectral tuning to the underwater light environment, their possible adaptations to pressure have yet to be explored. In this study, we investigated whether rhodopsin has undergone structural modifications that facilitate visual function during deep dives. Using a physicochemical property-based codon substitution model, we found that amino acid replacements associated with a radical shift in amino acid compressibility preferentially accumulated in deep-diving cetaceans belonging to the superfamily Physeteroidea and the family Ziphiidae. Molecular dynamics simulations further revealed that alanine at residue 2997.46a confers enhanced pressure tolerance of rhodopsin relative to serine, as evidenced by lower isothermal compressibility, diminished flexibility, and reduced free-energy costs under high pressure. These findings identify residue 2997.46a as a recurrent target for pressure adaptation in deep-diving cetaceans. More broadly, our study offers a novel perspective on cetacean visual adaptation, demonstrating that rhodopsins have evolved not only for spectral sensitivity but also for structural resilience under extreme hydrostatic pressure. This integrative framework, which combines evolutionary modeling with molecular dynamics simulations, advances our understanding of protein adaptation in the deep-sea environment.
• Gut microbiome changes in a captive giant panda with cardiovascular disease
  Xueying WANG; Ryoji UMEMOTO; Mizuki KATO; Takashi HAYAKAWA
  Journal of Veterinary Medical Science, Japanese Society of Veterinary Science, 2026, [Peer-reviewed], [Last author, Corresponding author]
  Scientific journal
• Whole mitochondrial genome analysis of killer whales reveals the presence of resident and transient ecotypes around Hokkaido
  Momoka Suzuki; Mami Kawai; Takashi Hayakawa; Yuki F. Kita; Yu Sato; Miho Inoue‐Murayama; Akira Shiozaki; Shin Nishida; Shimpei F. Hiruta; Hiroshi Ohizumi; Fumio Nakahara; Shigeo Saino; Yoshikazu Uni; Ayaka T. Matsuda; Takashi F. Matsuishi; Yuko Tajima; Masao Amano; Tadasu K. Yamada; Motoi Yoshioka; Yoko Mitani
  Marine Mammal Science, 42, 1, e70107, Wiley, 17 Dec. 2025, [Peer-reviewed]
  Scientific journal, ABSTRACT
  
  In the North Pacific, there are at least three genetically different ecotypes of killer whales ( Orcinus orca ), referred to as resident, offshore, and transient. A previous study suggested that killer whales around Hokkaido belong to fish‐eating (resident and/or offshore ecotypes) and mammal‐eating (transient ecotype) groups. These results were supported by haplotypes based on the combination of 1193 bp of cytochrome b and 420 bp of the control region in mitochondrial genomes. However, this analysis was not sufficient to discriminate between resident and offshore ecotypes because of the short sequence lengths. In this study, we analyzed whole mitochondrial genomes of 25 killer whales sampled around Hokkaido to clarify the ecotypes and mitochondrial genome haplotypes. Phylogenetic analysis revealed the presence of resident and transient ecotypes around Hokkaido. The whales identified as residents shared an identical haplotype, which is the most common haplotype in the western North Pacific. In contrast, the transients around Hokkaido exhibited eight haplotypes, including seven novel ones among the 19 individuals, and their haplotype richness was the highest among the North Pacific populations. This result suggests that the Hokkaido coast served as a refugium for transient killer whales during the Last Glacial Maximum.
• Post-bottleneck increase in mitochondrial DNA diversity in Yaku sika deer (Cervus nippon yakushimae) on Yakushima Island, Japan
  Yoshimi Agetsuma-Yanagihara; Takashi Hayakawa; Naoki Agetsuma
  Scientific Reports, 15, 39630, 12 Nov. 2025, [Peer-reviewed]
  Scientific journal
• Relaxation of selective constraint on the sweet-taste receptor gene TAS1R2 in lorisiform primates.
  Qinyuan Ji; Min Hou; Muhammad Shoaib Akhtar; Takashi Hayakawa; Yasuka Toda; Akihiro Itoigawa; Hiroo Imai; Takafumi Ishida; Amanda D Melin; Shoji Kawamura
  Scientific reports, 15, 1, 38091, 38091, 06 Nov. 2025, [Peer-reviewed], [International Magazine]
  English, Scientific journal, Recent research has revealed considerable evolutionary diversity in umami-taste (amino acids and nucleotides) and sweet-taste receptor TAS1R genes across vertebrate species. To contribute to a growing understanding of how diet shapes taste evolution, we studied TAS1R genes in non-anthropoid primates with highly diverse diets, including members of the Strepsirrhini, comprised of Lorisiformes (lorises) and Lemuriformes (lemurs), as well as members of the Tarsiiformes (tarsiers). We employed a targeted capture (TC) approach specifically probing all the three mammalian TAS1R genes, i.e., TAS1R1 (for sensing umami), TAS1R2 (sweet) and TAS1R3 (required for forming a heterodimer), followed by short-read massive-parallel sequencing for three lorisiform, four lemuriform, and one tarsiiform species. Analyzing together with publicly available whole-genome assemblies (WGAs) of non-anthropoids, we found that TAS1R1 and TAS1R2 of some lorisiform species were disrupted. The relative evolutionary rates in introns and synonymous sites of all the three TAS1R genes, as well as non-genic genome regions, of lorisiforms were higher than those of lemuriforms, a finding consistent with the higher genome-wide mutation rate of the lorisiforms. We found a similar pattern in the amino acid sequences and nonsynonymous sites of the sweet receptor TAS1R2 in lorisiforms. Evolutionary rates of amino acid sequences and nonsynonymous sites in TAS1R1 and TAS1R3 of lorisiforms were as slow as those of lemuriforms. This suggests that functional constraint on sweet sensing has been relaxed in lorisiform primates since their common ancestor. These results shed a new light on understanding evolutionary diversification of umami and sweet sensing in a diverse group of mammals.
• Metagenomic Insights Into the Role of Gut Microbes in the Defensive Ink “Tsunabi” of Physeteroid Whales
  Hayate Takeuchi; Takashi Fritz Matsuishi; Takashi Hayakawa
  Ecology and Evolution, Aug. 2025, [Peer-reviewed], [Last author, Corresponding author]
  Scientific journal
• Population genetics of captive spider monkeys in Japan for ex situ conservation
  Haruka Kitayama; Atsushi Shirai; Kei Nemoto; Yuko Tawa; Koshiro Watanuki; Takashi Hayakawa
  Primates, 66, 4, 375, 389, Springer Science and Business Media LLC, 06 May 2025, [Peer-reviewed], [Last author, Corresponding author]
  Scientific journal
• Genome-scale evolution in local populations of wild chimpanzees
  Takashi Hayakawa; Takushi Kishida; Yasuhiro Go; Eiji Inoue; Eri Kawaguchi; Tomoyuki Aizu; Hinako Ishizaki; Atsushi Toyoda; Asao Fujiyama; Tetsuro Matsuzawa; Chie Hashimoto; Takeshi Furuichi; Kiyokazu Agata
  Scientific Reports, 15, 1, 548, Springer Science and Business Media LLC, 02 Jan. 2025, [Peer-reviewed], [Lead author, Corresponding author]
  Scientific journal
• Fat taste receptors and fatty milk in dolphins
  Hinako Katsushima; Nobuyuki Kashiwagi; Takehisa Hamano; Kazunobu Kogi; Ryo Sato; Kensuke Nakata; Masayuki Nishino; Takashi Hayakawa
  Marine Mammal Science, 41, 2, Wiley, 24 Oct. 2024, [Peer-reviewed], [Last author, Corresponding author]
  Scientific journal, Abstract
  
  There has been a long debate on whether cetaceans recognize external chemical compounds in water. Genetically, they lost some taste receptors due to their aquatic adaptations. In contrast, neuroanatomical and behavioral studies have suggested that young dolphins can perceive specific chemicals. In this study, we tested whether young dolphins could recognize fatty acids contained in their mother's milk. We performed mRNA sequencing of the tongue of a 1‐year‐old Indo‐Pacific bottlenose dolphin. Long‐chain fatty acid taste receptors were expressed in a V‐shaped row of the tongue, which is specific for young dolphins and has taste bud‐like structures. The lingual lipase is also expressed in the V‐shaped row, which may enhance the release of free fatty acids from triacylglycerols. Notably, the sour taste receptor was nonfunctionalized specifically in Indo‐Pacific bottlenose dolphins. We comprehensively qualified the fatty acids in the milk of captive common bottlenose dolphins. Seven saturated and 16 unsaturated long‐chain fatty acids were detected. Behavioral tests in captive common bottlenose dolphins showed that a juvenile can recognize the presence of milk in water. These results indicated that young dolphins may have functional fat taste receptors in their oral cavity that detect long‐chain fatty acids contained in their mother's milk.
• Dietary partitioning in two gleaning bats, Japanese long-eared bats (Plecotus sacrimontis) and Ussuri tube-nosed bats (Murina ussuriensis): consuming insects of same order but different developmental stages
  Hayato Takada; Akiyoshi Sato; Setsuko Katsuta; Keita Nakamura; Atsushi Ohwaki; Yuto Kane; Takashi Hayakawa; Eiji Inoue
  Animal Biology, 1, 15, Brill, 12 Jun. 2024, [Peer-reviewed]
  Scientific journal, Abstract
  
  Knowledge of diet is essential for understanding the mechanism of coexistence among multiple species. Two gleaning bats, the Japanese long-eared bat (Plecotus sacrimontis) and the Ussuri tube-nosed bat (Murina ussuriensis), have similar eco-morphological traits, but it is unclear how they coexist. We examined the seasonal fecal contents of these species in the cool temperate forest of Mount Fuji, central Japan, using microscopical analysis. Long-eared bats, which have larger pinnae, more frequently consumed tympanate insects, such as adult moths, during early spring to summer, whereas tube-nosed bats, which have smaller pinnae, more frequently consumed non-tympanate insects such as caterpillars and grasshoppers, during spring to early summer and summer to autumn, respectively. Interestingly, they consumed insects of the same order but different developmental stages (i.e., adult moths and caterpillars) during spring to early summer, which revelation was made possible by microscopic analysis, not by DNA analysis. These differences suggest that the large pinna of the long-eared bat is an adaptation for preying on tympanate insects, which resulted in food resource partitioning. Additionally, to the best of our knowledge, the Ussuri tube-nosed bat can be considered one of the bats that most frequently eats caterpillars.
• Metabarcoding analysis provides insight into the link between prey and plant intake in a large alpine cat carnivore, the snow leopard
  Hiroto Yoshimura; Takashi Hayakawa; Dale M. Kikuchi; Kubanychbek Zhumabai Uulu; Huiyuan Qi; Taro Sugimoto; Koustubh Sharma; Kodzue Kinoshita
  Royal Society Open Science, 11, 5, The Royal Society, 29 May 2024, [Peer-reviewed]
  Scientific journal, Species of the family Felidae are thought to be obligate carnivores. However, detection of plants in their faeces raises questions about the role of plants in their diet. This is particularly true for the snow leopard ( Panthera uncia ). Our study aimed to comprehensively identify the prey and plants consumed by snow leopards. We applied DNA metabarcoding methods on 90 faecal samples of snow leopards collected in Kyrgyzstan, employing one vertebrate and four plant markers. We found that argali ( Ovis ammon ) was detected only from male snow leopards. Myricaraia sp. was the most consumed among 77 plant operational taxonomic units found in snow leopard samples. It frequently appeared in samples lacking any prey animal DNA, indicating that snow leopards might have consumed this plant especially when their digestive tracts were empty. We also observed differences in the patterns of plant consumption between male and female snow leopards. Our comprehensive overview of prey and plants detected in the faeces of snow leopards and other sympatric mammals will help in formulating hypotheses and guiding future research to understand the adaptive significance of plant-eating behaviour in felids. This knowledge supports the enhancement of their captive environments and the conservation planning of their natural habitats.
• Association of maternal genetics with the gut microbiome and eucalypt diet selection in captive koalas
  Kotaro Kondo; Mirei Suzuki; Mana Amadaira; Chiharu Araki; Rie Watanabe; Koichi Murakami; Shinsaku Ochiai; Tadatoshi Ogura; Takashi Hayakawa
  PeerJ, 12, e17385, e17385, PeerJ, 27 May 2024, [Peer-reviewed], [Last author, Corresponding author]
  Scientific journal, Background
  
  Koalas, an Australian arboreal marsupial, depend on eucalypt tree leaves for their diet. They selectively consume only a few of the hundreds of available eucalypt species. Since the koala gut microbiome is essential for the digestion and detoxification of eucalypts, their individual differences in the gut microbiome may lead to variations in their eucalypt selection and eucalypt metabolic capacity. However, research focusing on the relationship between the gut microbiome and differences in food preferences is very limited. We aimed to determine whether individual and regional differences exist in the gut microbiome of koalas as well as the mechanism by which these differences influence eucalypt selection.
  
  Methods
  
  Foraging data were collected from six koalas and a total of 62 feces were collected from 15 koalas of two zoos in Japan. The mitochondrial phylogenetic analysis was conducted to estimate the mitochondrial maternal origin of each koala. In addition, the 16S-based gut microbiome of 15 koalas was analyzed to determine the composition and diversity of each koala’s gut microbiome. We used these data to investigate the relationship among mitochondrial maternal origin, gut microbiome and eucalypt diet selection.
  
  Results and Discussion
  
  This research revealed that diversity and composition of the gut microbiome and that eucalypt diet selection of koalas differs among regions. We also revealed that the gut microbiome alpha diversity was correlated with foraging diversity in koalas. These individual and regional differences would result from vertical (maternal) transmission of the gut microbiome and represent an intraspecific variation in koala foraging strategies. Further, we demonstrated that certain gut bacteria were strongly correlated with both mitochondrial maternal origin and eucalypt foraging patterns. Bacteria found to be associated with mitochondrial maternal origin included bacteria involved in fiber digestion and degradation of secondary metabolites, such as the families Rikenellaceae and Synergistaceae. These bacteria may cause differences in metabolic capacity between individual and regional koalas and influence their eucalypt selection.
  
  Conclusion
  
  We showed that the characteristics (composition and diversity) of the gut microbiome and eucalypt diet selection of koalas differ by individuals and regional origins as we expected. In addition, some gut bacteria that could influence eucalypt foraging of koalas showed the relationships with both mitochondrial maternal origin and eucalypt foraging pattern. These differences in the gut microbiome between regional origins may make a difference in eucalypt selection. Given the importance of the gut microbiome to koalas foraging on eucalypts and their strong symbiotic relationship, future studies should focus on the symbiotic relationship and coevolution between koalas and the gut microbiome to understand individual and regional differences in eucalypt diet selection by koalas.
• Reduction of bitter taste receptor gene family in folivorous colobine primates relative to omnivorous cercopithecine primates
  Min Hou; Muhammad Shoaib Akhtar; Masahiro Hayashi; Ryuichi Ashino; Akiko Matsumoto-Oda; Takashi Hayakawa; Takafumi Ishida; Amanda D. Melin; Hiroo Imai; Shoji Kawamura
  Primates, Springer Science and Business Media LLC, 11 Apr. 2024, [Peer-reviewed]
  Scientific journal, Abstract
  
  Bitter taste perception is important in preventing animals from ingesting potentially toxic compounds. Whole-genome assembly (WGA) data have revealed that bitter taste receptor genes (TAS2Rs) comprise a multigene family with dozens of intact and disrupted genes in primates. However, publicly available WGA data are often incomplete, especially for multigene families. In this study, we employed a targeted capture (TC) approach specifically probing TAS2Rs for ten species of cercopithecid primates with diverse diets, including eight omnivorous cercopithecine species and two folivorous colobine species. We designed RNA probes for all TAS2Rs that we modeled to be intact in the common ancestor of cercopithecids (“ancestral-cercopithecid TAS2R gene set”). The TC was followed by short-read and high-depth massive-parallel sequencing. TC retrieved more intact TAS2R genes than found in WGA databases. We confirmed a large number of gene “births” at the common ancestor of cercopithecids and found that the colobine common ancestor and the cercopithecine common ancestor had contrasting trajectories: four gene “deaths” and three gene births, respectively. The number of intact TAS2R genes was markedly reduced in colobines (25–28 detected via TC and 20–26 detected via WGA analysis) as compared with cercopithecines (27–36 via TC and 19–30 via WGA). Birth or death events occurred at almost every phylogenetic-tree branch, making the composition of intact genes variable among species. These results show that evolutionary change in intact TAS2R genes is a complex process, refute a simple general prediction that herbivory favors more TAS2R genes, and have implications for understanding dietary adaptations and the evolution of detoxification abilities.
• A tradeoff evolution between acoustic fat bodies and skull muscles in toothed whales
  Hayate Takeuchi; Takashi Fritz Matsuishi; Takashi Hayakawa
  Gene, 901, 148167, 148167, Elsevier BV, Apr. 2024, [Peer-reviewed], [Last author, Corresponding author]
  Scientific journal
• Color vision evolution in egg-laying mammals: insights from visual photoreceptors and daily activities of Australian echidnas
  Shiina Sakamoto; Yuka Matsushita; Akihiro Itoigawa; Takumi Ezawa; Takeshi Fujitani; Kenichiro Takakura; Yang Zhou; Guojie Zhang; Frank Grutzner; Shoji Kawamura; Takashi Hayakawa
  Zoological Letters, 10, 1, Springer Science and Business Media LLC, 02 Jan. 2024, [Peer-reviewed], [Last author, Corresponding author]
  Scientific journal, Abstract
  
  Egg-laying mammals (monotremes) are considered “primitive” due to traits such as oviparity, cloaca, and incomplete homeothermy, all of which they share with reptiles. Two groups of monotremes, the terrestrial echidna (Tachyglossidae) and semiaquatic platypus (Ornithorhynchidae), have evolved highly divergent characters since their emergence in the Cenozoic era. These evolutionary differences, notably including distinct electrosensory and chemosensory systems, result from adaptations to species-specific habitat conditions. To date, very few studies have examined the visual adaptation of echidna and platypus. In the present study, we show that echidna and platypus have different light absorption spectra in their dichromatic visual sensory systems at the molecular level. We analyzed absorption spectra of monotreme color opsins, long-wavelength sensitive opsin (LWS) and short-wavelength sensitive opsin 2 (SWS2). The wavelength of maximum absorbance (λ_max) in LWS was 570.2 in short-beaked echidna (Tachyglossus aculeatus) and 560.6 nm in platypus (Ornithorhynchus anatinus); in SWS2, λ_max was 451.7 and 442.6 nm, respectively. Thus, the spectral range in echidna color vision is ~ 10 nm longer overall than in platypus. Natural selection analysis showed that the molecular evolution of monotreme color opsins is generally functionally conserved, suggesting that these taxa rely on species-specific color vision. In order to understand the usage of color vision in monotremes, we made 24-h behavioral observations of captive echidnas at warm temperatures and analyzed the resultant ethograms. Echidnas showed cathemeral activity and various behavioral repertoires such as feeding, traveling, digging, and self-grooming without light/dark environment selectivity. Halting (careful) behavior is more frequent in dark conditions, which suggests that echidnas may be more dependent on vision during the day and olfaction at night. Color vision functions have contributed to dynamic adaptations and dramatic ecological changes during the ~ 60 million years of divergent monotreme evolution. The ethogram of various day and night behaviors in captive echidnas also contributes information relevant to habitat conservation and animal welfare in this iconic species, which is locally endangered.
• The admixed brushtail possum genome reveals invasion history in New Zealand and novel imprinted genes
  Donna M. Bond; Oscar Ortega-Recalde; Melanie K. Laird; Takashi Hayakawa; Kyle S. Richardson; Finlay.C. B. Reese; Bruce Kyle; Brooke E. McIsaac-Williams; Bruce C. Robertson; Yolanda van Heezik; Amy L. Adams; Wei-Shan Chang; Bettina Haase; Jacquelyn Mountcastle; Maximilian Driller; Joanna Collins; Kerstin Howe; Yasuhiro Go; Francoise Thibaud-Nissen; Nicholas C. Lister; Paul D. Waters; Olivier Fedrigo; Erich D. Jarvis; Neil J. Gemmell; Alana Alexander; Timothy A. Hore
  Nature Communications, 14, 1, Springer Science and Business Media LLC, 17 Oct. 2023, [Peer-reviewed]
  Scientific journal, Abstract
  
  Combining genome assembly with population and functional genomics can provide valuable insights to development and evolution, as well as tools for species management. Here, we present a chromosome-level genome assembly of the common brushtail possum (Trichosurus vulpecula), a model marsupial threatened in parts of their native range in Australia, but also a major introduced pest in New Zealand. Functional genomics reveals post-natal activation of chemosensory and metabolic genes, reflecting unique adaptations to altricial birth and delayed weaning, a hallmark of marsupial development. Nuclear and mitochondrial analyses trace New Zealand possums to distinct Australian subspecies, which have subsequently hybridised. This admixture allowed phasing of parental alleles genome-wide, ultimately revealing at least four genes with imprinted, parent-specific expression not yet detected in other species (MLH1, EPM2AIP1, UBP1 and GPX7). We find that reprogramming of possum germline imprints, and the wider epigenome, is similar to eutherian mammals except onset occurs after birth. Together, this work is useful for genetic-based control and conservation of possums, and contributes to understanding of the evolution of novel mammalian epigenetic traits.
• Diet‐related factors strongly shaped the gut microbiota of Japanese macaques
  Wanyi Lee; Takashi Hayakawa; Mieko Kiyono; Naoto Yamabata; Hiroto Enari; Haruka S. Enari; Shiho Fujita; Tatsuro Kawazoe; Takayuki Asai; Toru Oi; Takashi Kondo; Takeharu Uno; Kentaro Seki; Masaki Shimada; Yamato Tsuji; Abdullah Langgeng; Andrew MacIntosh; Katsuya Suzuki; Kazunori Yamada; Kenji Onishi; Masataka Ueno; Kentaro Kubo; Goro Hanya
  American Journal of Primatology, 85, 12, Wiley, 28 Sep. 2023, [Peer-reviewed]
  Scientific journal, Abstract
  
  Although knowledge of the functions of the gut microbiome has increased greatly over the past few decades, our understanding of the mechanisms governing its ecology and evolution remains obscure. While host genetic distance is a strong predictor of the gut microbiome in large‐scale studies and captive settings, its influence has not always been evident at finer taxonomic scales, especially when considering among the recently diverged animals in natural settings. Comparing the gut microbiome of 19 populations of Japanese macaques Macaca fuscata across the Japanese archipelago, we assessed the relative roles of host genetic distance, geographic distance and dietary factors in influencing the macaque gut microbiome. Our results suggested that the macaques may maintain a core gut microbiome, while each population may have acquired some microbes from its specific habitat/diet. Diet‐related factors such as season, forest, and reliance on anthropogenic foods played a stronger role in shaping the macaque gut microbiome. Among closely related mammalian hosts, host genetics may have limited effects on the gut microbiome since the hosts generally have smaller physiological differences. This study contributes to our understanding of the relative roles of host phylogeography and dietary factors in shaping the gut microbiome of closely related mammalian hosts.
• Phylogenomic analyses provide insights into primate evolution
  Yong Shao; Long Zhou; Fang Li; Lan Zhao; Bao-Lin Zhang; Feng Shao; Jia-Wei Chen; Chun-Yan Chen; Xupeng Bi; Xiao-Lin Zhuang; Hong-Liang Zhu; Jiang Hu; Zongyi Sun; Xin Li; Depeng Wang; Iker Rivas-González; Sheng Wang; Yun-Mei Wang; Wu Chen; Gang Li; Hui-Meng Lu; Yang Liu; Lukas F. K. Kuderna; Kyle Kai-How Farh; Peng-Fei Fan; Li Yu; Ming Li; Zhi-Jin Liu; George P. Tiley; Anne D. Yoder; Christian Roos; Takashi Hayakawa; Tomas Marques-Bonet; Jeffrey Rogers; Peter D. Stenson; David N. Cooper; Mikkel Heide Schierup; Yong-Gang Yao; Ya-Ping Zhang; Wen Wang; Xiao-Guang Qi; Guojie Zhang; Dong-Dong Wu
  Science, 380, 6648, 913, 924, American Association for the Advancement of Science (AAAS), 02 Jun. 2023, [Peer-reviewed]
  Scientific journal, Comparative analysis of primate genomes within a phylogenetic context is essential for understanding the evolution of human genetic architecture and primate diversity. We present such a study of 50 primate species spanning 38 genera and 14 families, including 27 genomes first reported here, with many from previously less well represented groups, the New World monkeys and the Strepsirrhini. Our analyses reveal heterogeneous rates of genomic rearrangement and gene evolution across primate lineages. Thousands of genes under positive selection in different lineages play roles in the nervous, skeletal, and digestive systems and may have contributed to primate innovations and adaptations. Our study reveals that many key genomic innovations occurred in the Simiiformes ancestral node and may have had an impact on the adaptive radiation of the Simiiformes and human evolution.
• Eighty million years of rapid evolution of the primate Y chromosome
  Yang Zhou; Xiaoyu Zhan; Jiazheng Jin; Long Zhou; Juraj Bergman; Xuemei Li; Marjolaine Marie C. Rousselle; Meritxell Riera Belles; Lan Zhao; Miaoquan Fang; Jiawei Chen; Qi Fang; Lukas Kuderna; Tomas Marques-Bonet; Haruka Kitayama; Takashi Hayakawa; Yong-Gang Yao; Huanming Yang; David N. Cooper; Xiaoguang Qi; Dong-Dong Wu; Mikkel Heide Schierup; Guojie Zhang
  Nature Ecology & Evolution, 7, 7, 1114, 1130, Springer Science and Business Media LLC, 02 Jun. 2023, [Peer-reviewed]
  Scientific journal
• Cervicovaginal microbiome in patients with recurrent pregnancy loss
  Ryosuke Mori; Takashi Hayakawa; Masaaki Hirayama; Fumiko Ozawa; Hiroyuki Yoshihara; Shinobu Goto; Tamao Kitaori; Yasuhiko Ozaki; Mayumi Sugiura-Ogasawara
  Journal of Reproductive Immunology, 157, 103944, 103944, Elsevier BV, Jun. 2023, [Peer-reviewed]
  Scientific journal
• Seasonal responses and host uniqueness of gut microbiome of Japanese macaques in lowland Yakushima
  Akiko Sawada; Takashi Hayakawa; Yosuke Kurihara; Wanyi Lee; Goro Hanya
  Animal Microbiome, 4, 1, Springer Science and Business Media LLC, 27 Sep. 2022, [Peer-reviewed], [Lead author, Corresponding author]
  Scientific journal, Abstract
  
  Background
  
  Changes in the gut microbial composition is an important response to cope with the seasonal fluctuations in the environment such as food availability. We examined the bacterial gut microbiome of the wild nonhuman primate, Japanese macaque (Macaca fuscata) in Yakushima over 13 months by noninvasive continuous sampling from three identified adult females.
  
  Results
  
  Dietary composition varied considerably over the study period and displayed marked shifts with the seasons. Feeding of leaves, fruits, and invertebrates were their main foods for at least one month. Diet had a significant influence on the gut microbiome. We also confirmed significant effect of host uniqueness in the gut microbiome among the three macaques. Leaf-dominated diet shaped unique gut microbiome structures where the macaques had the highest alpha diversity and their gut microbiome was enriched with Spirochaetes and Tenericutes. Diet-related differences in the putative function were detected, such as a differentially abundant urea cycle during the leaf-feeding season.
  
  Conclusion
  
  Both diet and host individuality exerted similar amounts of effect on gut microbe community composition. Major bacterial taxa showed a similar response to monthly fluctuations of fruit and invertebrate feeding, which was largely opposite to that of leaf feeding. The main constituents of fruits and invertebrates are both digestible with the enzyme of the host animals, but that of leaves is not available as an energy source without the aid of the fermentation of the gut microbiome.
• Dietary niche breadth influences the effects of urbanization on the gut microbiota of sympatric rodents
  Jason L. Anders; Alexis M. Mychajliw; Mohamed Abdallah Mohamed Moustafa; Wessam Mohamed Ahmed Mohamed; Takashi Hayakawa; Ryo Nakao; Itsuro Koizumi
  Ecology and Evolution, 12, 9, Wiley, 09 Sep. 2022, [Peer-reviewed]
  Scientific journal, Abstract
  
  Cities are among the most extreme forms of anthropogenic ecosystem modification, and urbanization processes exert profound effects on animal populations through multiple ecological pathways. Increased access to human‐associated food items may alter species' foraging behavior and diet, in turn modifying the normal microbial community of the gastrointestinal tract (GIT), ultimately impacting their health. It is crucial we understand the role of dietary niche breadth and the resulting shift in the gut microbiota as urban animals navigate novel dietary resources. We combined stable isotope analysis of hair and microbiome analysis of four gut regions across the GIT to investigate the effects of urbanization on the diet and gut microbiota of two sympatric species of rodents with different dietary niches: the omnivorous large Japanese field mouse (Apodemus speciosus) and the relatively more herbivorous gray red‐backed vole (Myodes rufocanus). Both species exhibited an expanded dietary niche width within the urban areas potentially attributable to novel anthropogenic foods and altered resource availability. We detected a dietary shift in which urban A. speciosus consumed more terrestrial animal protein and M. rufocanus more plant leaves and stems. Such changes in resource use may be associated with an altered gut microbial community structure. There was an increased abundance of the presumably probiotic Lactobacillus in the small intestine of urban A. speciosus and potentially pathogenic Helicobacter in the colon of M. rufocanus. Together, these results suggest that even taxonomically similar species may exhibit divergent responses to urbanization with consequences for the gut microbiota and broader ecological interactions.
• Functional Diversity and Evolution of Bitter Taste Receptors in Egg-Laying Mammals
  Akihiro Itoigawa; Takashi Hayakawa; Yang Zhou; Adrian D. Manning; Guojie Zhang; Frank Grutzner; Hiroo Imai
  Molecular Biology and Evolution, 39, 6, Oxford University Press (OUP), 31 May 2022, [Peer-reviewed], [Corresponding author]
  Scientific journal, Abstract
  
  Egg-laying mammals (monotremes) are a sister clade of therians (placental mammals and marsupials) and a key clade to understand mammalian evolution. They are classified into platypus and echidna, which exhibit distinct ecological features such as habitats and diet. Chemosensory genes, which encode sensory receptors for taste and smell, are believed to adapt to the individual habitats and diet of each mammal. In this study, we focused on the molecular evolution of bitter taste receptors (TAS2Rs) in monotremes. The sense of bitter taste is important to detect potentially harmful substances. We comprehensively surveyed agonists of all TAS2Rs in platypus (Ornithorhynchus anatinus) and short-beaked echidna (Tachyglossus aculeatus) and compared their functions with orthologous TAS2Rs of marsupial and placental mammals (i.e., therians). As results, the agonist screening revealed that the deorphanized monotreme receptors were functionally diversified. Platypus TAS2Rs had broader receptive ranges of agonists than those of echidna TAS2Rs. While platypus consumes a variety of aquatic invertebrates, echidna mainly consumes subterranean social insects (ants and termites) as well as other invertebrates. This result indicates that receptive ranges of TAS2Rs could be associated with feeding habits in monotremes. Furthermore, some orthologous receptors in monotremes and therians responded to β-glucosides, which are feeding deterrents in plants and insects. These results suggest that the ability to detect β-glucosides and other substances might be shared and ancestral among mammals.
• Genome assembly of the numbat (Myrmecobius fasciatus), the only termitivorous marsupial
  Emma Peel; Luke Silver; Parice Brandies; Takashi Hayakawa; Katherine Belov; Carolyn J. Hogg
  Gigabyte, 2022, 1, 17, GigaScience Press, 17 Mar. 2022, [Peer-reviewed]
  Scientific journal, The numbat (Myrmecobius fasciatus) is an endangered Australian marsupial, and the last surviving member of the Myrmecobiidae family. The numbat regularly undergoes torpor and is unique amongst marsupials as it is the only diurnal and termitivorous species. Here we sequenced the first draft genome of the numbat using 10× Genomics Chromium linked-read technology, resulting in a 3.42 Gbp genome with a scaffold N50 of 223 kbp. A global transcriptome from liver, lung and tongue was also generated to aid genome annotation, identifying 21,465 protein-coding genes. To investigate adaptation to the numbat’s termitivorous diet and arid/semi-arid range, we interrogated the most highly expressed transcripts within the tongue and manually annotated taste, vomeronasal and aquaporin gene families. Antimicrobial proteins and proteins involved in digestion were highly expressed in the tongue, alongside umami taste receptors. However, sweet taste receptors were not expressed in this tissue, which combined with the putative contraction of the bitter taste receptor gene repertoire in the numbat genome, may indicate a potential evolutionary adaptation to their specialised termitivorous diet. Vomeronasal and aquaporin gene repertoires were similar to other marsupials. The draft numbat genome is a valuable tool for conservation and can be applied to population genetics/genomics studies and to investigate the unique biology of this interesting species.
• Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents
  Jason L. Anders; Mohamed Abdallah Mohamed Moustafa; Wessam Mohamed Ahmed Mohamed; Takashi Hayakawa; Ryo Nakao; Itsuro Koizumi
  Scientific Reports, 11, 1, Springer Science and Business Media LLC, 07 Oct. 2021, [Peer-reviewed]
  Scientific journal, Abstract
  
  Host–microbe interactions within the gastrointestinal tract (GIT) play a pivotal role in shaping host physiology, ecology, and life history. However, these interactions vary across gut regions due to changes in the physical environment or host immune system activity, thereby altering the microbial community. Each animal species may harbor their own unique microbial community due to host species-specific ecological traits such as dietary habits, micro-habitat preferences, and mating behavior as well as physiological traits. While the gut microbiota in wild animals has received much attention over the last decade, most studies comparing closely related species only utilized fecal or colon samples. In this study, we first compared the gut microbial community from the small intestine, cecum, colon, and rectum within three sympatric species of wild rodents (i.e. Apodemus speciosus, A. argenteus, and Myodes rufocanus). We then compared each gut region among host species to determine the effect of both gut region and host species on the gut microbiota. We found that the small intestine harbored a unique microbiome as compared to the lower GIT in all three host species, with the genus Lactobacillus in particular having higher abundance in the small intestine of all three host species. There were clear interspecific differences in the microbiome within all gut regions, although some similarity in alpha diversity and community structure within the small intestine was found. Finally, fecal samples may be appropriate for studying the lower GIT in these species, but not the small intestine.
• Evolution of the primate glutamate taste sensor from a nucleotide sensor
  Yasuka Toda; Takashi Hayakawa; Akihiro Itoigawa; Yosuke Kurihara; Tomoya Nakagita; Masahiro Hayashi; Ryuichi Ashino; Amanda D. Melin; Yoshiro Ishimaru; Shoji Kawamura; Hiroo Imai; Takumi Misaka
  Current Biology, 31, 20, 4641, 4649.e5, Elsevier BV, Oct. 2021, [Peer-reviewed], [Lead author]
  Scientific journal
• Early origin of sweet perception in the songbird radiation
  Yasuka Toda; Meng-Ching Ko; Qiaoyi Liang; Eliot T. Miller; Alejandro Rico-Guevara; Tomoya Nakagita; Ayano Sakakibara; Kana Uemura; Timothy Sackton; Takashi Hayakawa; Simon Yung Wa Sin; Yoshiro Ishimaru; Takumi Misaka; Pablo Oteiza; James Crall; Scott V. Edwards; William Buttemer; Shuichi Matsumura; Maude W. Baldwin
  Science, 373, 6551, 226, 231, American Association for the Advancement of Science (AAAS), 09 Jul. 2021, [Peer-reviewed]
  Scientific journal, From savory to sweet
  
  Seeing a bird eat nectar from a flower is a common sight in our world. The ability to detect sugars, however, is not ancestral in the bird lineage, where most species were carnivorous. Toda et al. looked at receptors within the largest group of birds, the passerines or songbirds, and found that the emergence of sweet detection involved a single shift in a receptor for umami (see the Perspective by Barker). This ancient change facilitated sugar detection not just in nectar feeding birds, but also across the songbird group, and in a way that was different from, though convergent with, that in hummingbirds.
  
  Science , abf6505, this issue p. 226 ; see also abj6746, p. 154
• Lactobacillus nasalidis sp. nov., isolated from the forestomach of a captive proboscis monkey (Nasalis larvatus)
  Nami Suzuki-Hashido; Sayaka Tsuchida; Takashi Hayakawa; Mitsuo Sakamoto; Akinori Azumano; Satoru Seino; Ikki Matsuda; Moriya Ohkuma; Kazunari Ushida
  International Journal of Systematic and Evolutionary Microbiology, 71, 4, Microbiology Society, 27 Apr. 2021, [Peer-reviewed]
  Scientific journal, Three strains (YZ01^T, YZ02 and YZ03) of Gram-stain-positive, facultatively anaerobic rods were isolated from the forestomach contents collected from a captive male proboscis monkey (Nasalis larvatus) at Yokohama Zoo in Japan. Phylogenetic analysis of the 16S rRNA gene sequences revealed that these strains belonged to the genus Lactobacillus . Based on the sequence similarity of the 16S rRNA gene, Lactobacillus delbrueckii subsp. indicus JCM 15610^T was the closest phylogenetic neighbour to YZ01^T. Sequence analyses of two partial concatenated housekeeping genes, the RNA polymerase alpha subunit (rpoA) and phenylalanyl-tRNA synthase alpha subunit (pheS) also indicated that the novel strains belonged to the genus Lactobacillus . The average nucleotide identity and digital DNA–DNA hybridization (dDDH) between L. delbrueckii subsp. indicus and YZ01^T were 85.9 and 31.4 %, respectively. The phylogenetic tree based on the whole genomic data of strains YZ01^T, YZ02 and YZ03 suggested that these three strains formed a single monophyletic cluster in the genus Lactobacillus , indicating that it belonged to a new species. The DNA G+C content of strain YZ01^T was 51.6 mol%. The major fatty acids were C_16 : 0 and C_18 : 1 ω9c. Therefore, based on phylogenetic, phenotypic and physiological evidence, strains YZ01^T, YZ02 and YZ03 represent a novel species of the genus Lactobacillus , for which the name Lactobacillus nasalidis sp. nov. is proposed with the type strain YZ01^T (=JCM 33769^T=DSM 110539^T).
• Phylogeographic history of Japanese macaques
  Tsuyoshi Ito; Takashi Hayakawa; Nami Suzuki–Hashido; Yuzuru Hamada; Yosuke Kurihara; Goro Hanya; Akihisa Kaneko; Takayoshi Natsume; Seitaro Aisu; Takeaki Honda; Syuji Yachimori; Tomoko Anezaki; Toshinori Omi; Shin‐ichi Hayama; Mikiko Tanaka; Hikaru Wakamori; Hiroo Imai; Yoshi Kawamoto
  Journal of Biogeography, 48, 6, 1420, 1431, Wiley, 15 Apr. 2021, [Peer-reviewed]
  Scientific journal, Abstract
  
  Aim
  
  Understanding patterns and processes of geographic genetic variation within and among closely related species is the essence of phylogeography. Japanese macaques, also called snow monkeys, have been extensively studied, particularly in the fields of sociobiology, ecology and experimental biology; however, our knowledge of their evolutionary history is relatively limited. In this study we aimed to elucidate the geographic patterns of genetic variation in Japanese macaques and the processes that underlie them.
  
  Location
  
  Japan.
  
  Taxa
  
  Japanese macaque, Macaca fuscata; rhesus macaque, M. mulatta; Taiwanese macaque, M. cyclopis.
  
  Methods
  
  Double‐digest restriction site‐associated DNA (RAD) sequencing was used to identify genome‐wide single nucleotide variants. We used fineRADstructure, ADMIXTURE and principal component analyses to estimate the genetic population structure. Phylogenetic relationships were then inferred based on neighbour‐net, neighbour‐joining, maximum likelihood and SVDquartets algorithms. We assessed gene flow using demographic inference and ABBA‐BABA tests, and estimated past distributions during the Last Glacial Maximum (LGM) using ecological niche modelling.
  
  Results
  
  Japanese macaques show a sister group relationship with a clade comprising Chinese rhesus, Indian rhesus and Taiwanese macaques. Japanese macaques comprise major north‐eastern and south‐western clades, with a boundary located near central Japan, and gene flow between the north‐eastern and south‐western lineages was detected. Refugia during the LGM were estimated to be distributed in limited areas along the south coasts of the Japanese archipelago.
  
  Main conclusions
  
  Phylogeographic variation of Japanese macaques is likely due mainly to northeast–southwest divergence, which resulted from withdrawal into refugia during the glacial period, and subsequent gene flow.
• Lowered sensitivity of bitter taste receptors to β-glucosides in bamboo lemurs: an instance of parallel and adaptive functional decline in TAS2R16?
  Akihiro Itoigawa; Fabrizio Fierro; Morgan E. Chaney; M. Elise Lauterbur; Takashi Hayakawa; Anthony J. Tosi; Masha Y. Niv; Hiroo Imai
  Proceedings of the Royal Society B: Biological Sciences, 288, 1948, The Royal Society, 14 Apr. 2021, [Peer-reviewed]
  Scientific journal, Bitter taste facilitates the detection of potentially harmful substances and is perceived via bitter taste receptors (TAS2Rs) expressed on the tongue and oral cavity in vertebrates. In primates, TAS2R16 specifically recognizes β-glucosides, which are important in cyanogenic plants' use of cyanide as a feeding deterrent. In this study, we performed cell-based functional assays for investigating the sensitivity of TAS2R16 to β-glucosides in three species of bamboo lemurs ( Prolemur simus, Hapalemur aureus and H. griseus ), which primarily consume high-cyanide bamboo. TAS2R16 receptors from bamboo lemurs had lower sensitivity to β-glucosides, including cyanogenic glucosides, than that of the closely related ring-tailed lemur ( Lemur catta ). Ancestral reconstructions of TAS2R16 for the bamboo-lemur last common ancestor (LCA) and that of the Hapalemur LCA showed an intermediate sensitivity to β-glucosides between that of the ring-tailed lemurs and bamboo lemurs. Mutagenetic analyses revealed that P. simus and H. griseus had separate species - specific substitutions that led to reduced sensitivity. These results indicate that low sensitivity to β-glucosides at the cellular level—a potentially adaptive trait for feeding on cyanogenic bamboo—evolved independently after the Prolemur – Hapalemur split in each species.
• Stomach and colonic microbiome of wild Japanese macaques
  Wanyi Lee; Takashi Hayakawa; Yosuke Kurihara; Maho Hanzawa; Akiko Sawada; Akihisa Kaneko; Yoshiki Morimitsu; Takayoshi Natsume; Seitaro Aisu; Tsuyoshi Ito; Takeaki Honda; Goro Hanya
  American Journal of Primatology, 83, 5, Wiley, 10 Feb. 2021, [Peer-reviewed]
  Scientific journal, Abstract
  
  Within the gastrointestinal tract, the physiochemical microenvironments are highly diversified among the different stages of food digestion. Accordingly, gut microbiome composition and function vary at different gut sites. In this study, we examine and compare the compositional and functional potential between the stomach and colonic microbiome of wild Japanese macaques (Macaca fuscata yakui) living in the evergreen forest of Yakushima Island. We find a significantly lower microbial diversity in the stomach than in the colon, possibly due to the stomach's acidic and aerobic environment, which is suboptimal for microbial survival. According to past studies, the microbial taxa enriched in the stomach are aero‐ and acid‐tolerant. By functional prediction through PICRUSt2, we reveal that the stomach microbiome is more enriched in pathways relating to the metabolism of simple sugars. On the contrary, the colonic microbiota is more enriched with fiber‐degrading microbes, such as those from Lachnospiracea, Ruminococcaceae, and Prevotella. Our study shows a clear difference in the microbiome between the stomach and colon of Japanese macaques in both composition and function. This study provides a preliminary look at the alpha diversity and taxonomic composition within the stomach microbiome of Japanese macaques, a hindgut‐fermenting nonhuman primate.
• Comparative analysis of sperm motility in liquid and seminal coagulum portions between Bornean orangutan (Pongo pygmaeus) and chimpanzee (Pan troglodytes)
  Kodzue Kinoshita; Yoriko Indo; Tomoyuki Tajima; Noko Kuze; Etsuko Miyakawa; Toshio Kobayashi; Tomoyuki Nakamura; Mitsuaki Ogata; Fumihiko Okumura; Takashi Hayakawa; Naruki Morimura; Yusuke Mori; Munehiro Okamoto; Yasuhiko Ozaki; Satoshi Hirata
  Primates, 62, 3, 467, 473, Springer Science and Business Media LLC, 19 Jan. 2021, [Peer-reviewed]
  Scientific journal
• Female chimpanzees giving first birth in their natal group in Mahale: attention to incest between brothers and sisters
  Takuya Matsumoto; Shunkichi Hanamura; Takanori Kooriyama; Takashi Hayakawa; Eiji Inoue
  Primates, 62, 2, 279, 287, Springer Science and Business Media LLC, 14 Jan. 2021, [Peer-reviewed]
  Scientific journal
• Platypus and echidna genomes reveal mammalian biology and evolution
  Yang Zhou; Linda Shearwin-Whyatt; Jing Li; Zhenzhen Song; Takashi Hayakawa; David Stevens; Jane C. Fenelon; Emma Peel; Yuanyuan Cheng; Filip Pajpach; Natasha Bradley; Hikoyu Suzuki; Masato Nikaido; Joana Damas; Tasman Daish; Tahlia Perry; Zexian Zhu; Yuncong Geng; Arang Rhie; Ying Sims; Jonathan Wood; Bettina Haase; Jacquelyn Mountcastle; Olivier Fedrigo; Qiye Li; Huanming Yang; Jian Wang; Stephen D. Johnston; Adam M. Phillippy; Kerstin Howe; Erich D. Jarvis; Oliver A. Ryder; Henrik Kaessmann; Peter Donnelly; Jonas Korlach; Harris A. Lewin; Jennifer Graves; Katherine Belov; Marilyn B. Renfree; Frank Grutzner; Qi Zhou; Guojie Zhang
  Nature, 592, 7856, 756, 762, Springer Science and Business Media LLC, 06 Jan. 2021, [Peer-reviewed]
  Scientific journal, Abstract
  
  Egg-laying mammals (monotremes) are the only extant mammalian outgroup to therians (marsupial and eutherian animals) and provide key insights into mammalian evolution^1,2. Here we generate and analyse reference genomes of the platypus (Ornithorhynchus anatinus) and echidna (Tachyglossus aculeatus), which represent the only two extant monotreme lineages. The nearly complete platypus genome assembly has anchored almost the entire genome onto chromosomes, markedly improving the genome continuity and gene annotation. Together with our echidna sequence, the genomes of the two species allow us to detect the ancestral and lineage-specific genomic changes that shape both monotreme and mammalian evolution. We provide evidence that the monotreme sex chromosome complex originated from an ancestral chromosome ring configuration. The formation of such a unique chromosome complex may have been facilitated by the unusually extensive interactions between the multi-X and multi-Y chromosomes that are shared by the autosomal homologues in humans. Further comparative genomic analyses unravel marked differences between monotremes and therians in haptoglobin genes, lactation genes and chemosensory receptor genes for smell and taste that underlie the ecological adaptation of monotremes.
• Key Male Glandular Odorants Attracting Female Ring-Tailed Lemurs
  Mika Shirasu; Satomi Ito; Akihiro Itoigawa; Takashi Hayakawa; Kodzue Kinoshita; Isao Munechika; Hiroo Imai; Kazushige Touhara
  Current Biology, 30, 11, 2131, 2138.e4, Elsevier BV, Jun. 2020, [Peer-reviewed]
  Scientific journal
• Fermentation Ability of Gut Microbiota of Wild Japanese Macaques in the Highland and Lowland Yakushima: In Vitro Fermentation Assay and Genetic Analyses
  Goro Hanya; Janko Tackmann; Akiko Sawada; Wanyi Lee; Sanjeeta Sharma Pokharel; Valdevino Gisele de Castro Maciel; Akito Toge; Kota Kuroki; Ryoma Otsuka; Ryoma Mabuchi; Jie Liu; Masaomi Hatakeyama; Eri Yamasaki; Christian von Mering; Rie Shimizu-Inatsugi; Takashi Hayakawa; Kentaro K. Shimizu; Kazunari Ushida
  Microbial Ecology, 80, 2, 459, 474, Springer Science and Business Media LLC, 24 Apr. 2020, [Peer-reviewed]
  Scientific journal
• Evolution of the bitter taste receptor TAS2R38 in colobines
  Laurentia Henrieta Permita Sari Purba; Kanthi Arum Widayati; Nami Suzuki-Hashido; Akihiro Itoigawa; Takashi Hayakawa; Sarah Nila; Berry Juliandi; Bambang Suryobroto; Hiroo Imai
  Primates, 61, 3, 485, 494, Springer Science and Business Media LLC, 01 Feb. 2020, [Peer-reviewed]
  Scientific journal
• Gut microbiota composition of Japanese macaques associates with extent of human encroachment
  Wanyi Lee; Takashi Hayakawa; Mieko Kiyono; Naoto Yamabata; Goro Hanya
  American Journal of Primatology, 81, 12, Wiley, Dec. 2019, [Peer-reviewed]
  Scientific journal, Abstract
  
  In recent decades, human–wildlife interaction and associated anthropogenic food provisioning has been increasing and becoming more severe due to fast population growth and urban development. Noting the role of the gut microbiome in host physiology like nutrition and health, it is thus essential to understand how human–wildlife interactions and availability of anthropogenic food in habitats can affect an animal's gut microbiome. This study, therefore, set out to examine the gut microbiota of Japanese macaques (Macaca fuscata) with varying accessibility to anthropogenic food and the possibility of using gut microbiota as indicator for macaques’ reliance on anthropogenic food. Using 16S ribosomal RNA gene sequencing, we described the microbial composition of Japanese macaques experiencing different types of human disturbance and anthropogenic food availability—captive, provisioned, crop‐raiding, and wild. In terms of alpha diversity, our results showed that observed richness of gut microbiota did not differ significantly between disturbance types but among collection sites, whereas Shannon diversity index differed by both disturbance types and sites. In terms of beta diversity, captive populations harbored the most distinctive gut microbial composition, and had the greatest difference compared with wild populations. Whereas for provisioned and crop‐raiding groups, the macaques exhibited intermediate microbiota between wild and captive. We identified several potential bacterial taxa at different taxonomic ranks whose abundance potentially could help in assessing macaques’ accessibility to anthropogenic food. This study revealed the flexibility of the gut microbiome of Japanese macaques and provided possible indices based on the gut microbiome profile in assessing macaques’ accessibility to/reliance on anthropogenic foods.
• Host selection of hematophagous leeches (Haemadipsa japonica): Implications for iDNA studies
  Goro Hanya; Kaori Morishima; Tomoya Koide; Yosuke Otani; Shun Hongo; Takeaki Honda; Hiroki Okamura; Yuma Higo; Masamichi Hattori; Yuki Kondo; Yosuke Kurihara; Sakura Jin; Aji Otake; Izumi Shiroisihi; Tomomi Takakuwa; Hiroki Yamamoto; Hanami Suzuki; Hisashi Kajimura; Takashi Hayakawa; Nami Suzuki‐Hashido; Takafumi Nakano
  Ecological Research, 34, 6, 842, 855, Wiley, 21 Nov. 2019, [Peer-reviewed]
  Scientific journal, Abstract
  
  The development of an efficient and cost‐effective method for monitoring animal populations or biodiversity is urgently needed, and invertebrate‐derived DNA (iDNA) may offer a promising tool for assessing the diversity and other ecological information of vertebrates. We studied the host species of a hematophagous leech (Haemadipsa japonica) in Yakushima by genetic barcoding and compared the results with those for mammal composition revealed by camera trapping. We analyzed 119 samples using two sets of primers by Sanger sequencing and one set of primer by next generation sequencing. The proportion of the samples that were successfully sequenced and identified to at least one species was 11.8–24.3%, depending on the three different methods. In all of these three methods, most of the samples were identified as sika deer (18/20, 6/15 and 16/29) or human (2/20, 7/15 and 21/29). The nonhuman mammal host species composition was significantly different from that estimated by camera trapping. Sika deer was the main host, which may be related with their high abundance, large body size and terrestriality. Ten samples included DNA derived from multiple species of vertebrates. This may be due to the contamination of human DNA, but we also found DNA from deer, Japanese macaque and a frog in the same samples, suggesting the mixture of the two meals in the gut of the leech. Using H. japonica‐derived iDNA would not be suitable to make an inventory of species, but it may be useful to collect genetic information on the targeted species, due to their high host selectivity.
• A natural point mutation in the bitter taste receptor TAS2R16 causes inverse agonism of arbutin in lemur gustation
  Akihiro Itoigawa; Takashi Hayakawa; Nami Suzuki-Hashido; Hiroo Imai
  Proceedings of the Royal Society B: Biological Sciences, 286, 1904, 20190884, 20190884, The Royal Society, 05 Jun. 2019, [Peer-reviewed]
  Scientific journal, Bitter taste enables the detection of potentially harmful substances and is mediated by bitter taste receptors, TAS2Rs, in vertebrates. Few antagonists and inverse agonists of TAS2Rs have been identified, especially natural compounds. TAS2R16s in humans, apes and Old World monkeys (Catarrhini, Anthropoidea) recognize β-glucoside analogues as specific agonists. Here, we investigated responses of TAS2R16 to β-glucosides in non-anthropoid primates, namely lemurs (Lemuriformes, Strepsirrhini). Salicin acted as an agonist on lemur TAS2R16. Arbutin acted as an agonist in the ring-tailed lemur ( Lemur catta ) but as an inverse agonist in black lemur ( Eulemur macaco ) and black-and-white ruffed lemur ( Varecia variegata ). We identified a strepsirrhine-specific amino acid substitution responsible for the inverse agonism of arbutin. In a food preference test, salicin bitterness was inhibited by arbutin in the black lemur. Structural modelling revealed this locus was important for a rearrangement of the intracellular end of transmembrane helix 7 (TM7). Accordingly, arbutin is the first known natural inverse agonist of TAS2Rs, contributing to our understanding of receptor–ligand interactions and the molecular basis of the unique feeding habit diversification in lemurs. Furthermore, the identification of a causal point mutation suggests that TAS2R can acquire functional changes according to feeding habits and environmental conditions.
• First report of foregut microbial community in proboscis monkeys: are diverse forests a reservoir for diverse microbiomes?
  Takashi Hayakawa; Senthilvel K. S. S. Nathan; Danica J. Stark; Diana A. Ramirez Saldivar; Rosa Sipangkui; Benoit Goossens; Augustine Tuuga; Marcus Clauss; Akiko Sawada; Shinji Fukuda; Hiroo Imai; Ikki Matsuda
  Environmental Microbiology Reports, 10, 6, 655, 662, Wiley, 27 Sep. 2018, [Peer-reviewed], [Lead author, Corresponding author]
  Scientific journal, Summary
  
  Foregut fermentation is well known to occur in a wide range of mammalian species and in a single bird species. Yet, the foregut microbial community of free‐ranging, foregut‐fermenting monkeys, that is, colobines, has not been investigated so far. We analysed the foregut microbiomes in four free‐ranging proboscis monkeys (Nasalis larvatus) from two different tropical habitats with varying plant diversity (mangrove and riverine forests), in an individual from a semi‐free‐ranging setting with supplemental feeding, and in an individual from captivity, using high‐throughput sequencing based on 16S ribosomal RNA genes. We found a decrease in foregut microbial diversity from a diverse natural habitat (riverine forest) to a low diverse natural habitat (mangrove forest), to human‐related environments. Of a total of 2700 bacterial operational taxonomic units (OTUs) detected in all environments, only 153 OTUs were shared across all individuals, suggesting that they were not influenced by diet or habitat. These OTUs were dominated by Firmicutes and Proteobacteria. The relative abundance of the habitat‐specific microbial communities showed a wide range of differences among living environments, although such bacterial communities appeared to be dominated by Firmicutes and Bacteroidetes, suggesting that those phyla are key to understanding the adaptive strategy in proboscis monkeys living in different habitats.
• Functional decline of sweet taste sensitivity of colobine monkeys
  Emiko Nishi; Nami Suzuki-Hashido; Takashi Hayakawa; Yamato Tsuji; Bambang Suryobroto; Hiroo Imai
  Primates, 59, 6, 523, 530, Springer Science and Business Media LLC, 06 Sep. 2018, [Peer-reviewed]
  Scientific journal
• Adaptation and conservation insights from the koala genome
  Rebecca N. Johnson; Denis O’Meally; Zhiliang Chen; Graham J. Etherington; Simon Y. W. Ho; Will J. Nash; Catherine E. Grueber; Yuanyuan Cheng; Camilla M. Whittington; Siobhan Dennison; Emma Peel; Wilfried Haerty; Rachel J. O’Neill; Don Colgan; Tonia L. Russell; David E. Alquezar-Planas; Val Attenbrow; Jason G. Bragg; Parice A. Brandies; Amanda Yoon-Yee Chong; Janine E. Deakin; Federica Di Palma; Zachary Duda; Mark D. B. Eldridge; Kyle M. Ewart; Carolyn J. Hogg; Greta J. Frankham; Arthur Georges; Amber K. Gillett; Merran Govendir; Alex D. Greenwood; Takashi Hayakawa; Kristofer M. Helgen; Matthew Hobbs; Clare E. Holleley; Thomas N. Heider; Elizabeth A. Jones; Andrew King; Danielle Madden; Jennifer A. Marshall Graves; Katrina M. Morris; Linda E. Neaves; Hardip R. Patel; Adam Polkinghorne; Marilyn B. Renfree; Charles Robin; Ryan Salinas; Kyriakos Tsangaras; Paul D. Waters; Shafagh A. Waters; Belinda Wright; Marc R. Wilkins; Peter Timms; Katherine Belov
  Nature Genetics, 50, 8, 1102, 1111, Springer Science and Business Media LLC, 02 Jul. 2018, [Peer-reviewed]
  Scientific journal
• Improving the standards for gut microbiome analysis of fecal samples: insights from the field biology of Japanese macaques on Yakushima Island
  Takashi Hayakawa; Akiko Sawada; Akifumi S. Tanabe; Shinji Fukuda; Takushi Kishida; Yosuke Kurihara; Kei Matsushima; Jie Liu; Etienne-Francois Akomo-Okoue; Waleska Gravena; Makoto Kashima; Mariko Suzuki; Kohmei Kadowaki; Takafumi Suzumura; Eiji Inoue; Hideki Sugiura; Goro Hanya; Kiyokazu Agata
  Primates, 59, 5, 423, 436, Springer Science and Business Media LLC, 25 Jun. 2018, [Peer-reviewed], [Lead author, Corresponding author]
  Scientific journal
• Evolution of vomeronasal receptor 1 (V1R) genes in the common marmoset (Callithrix jacchus)
  Keiko Moriya-Ito; Takashi Hayakawa; Hikoyu Suzuki; Kimiko Hagino-Yamagishi; Masato Nikaido
  Gene, 642, 343, 353, Elsevier BV, Feb. 2018, [Peer-reviewed]
  Scientific journal
• Morphometric and Genetic Determination of Age Class and Sex for Fecal Pellets of Sika Deer (Cervus nippon)
  Goro Hanya; Senri Naito; Erina Namioka; Yosuke Ueda; Yo Sato; Josue Alejandro Pastrana; Tianmeng He; Xiaochan Yan; Miho Saito; Raquel Filomena Pereira Costa; Morgane Allanic; Takeaki Honda; Yosuke Kurihara; Takakazu Yumoto; Takashi Hayakawa
  Mammal Study, 42, 4, 1, 8, Mammalogical Society of Japan, 18 Dec. 2017, [Peer-reviewed], [Last author]
  Scientific journal
• Direct estimation of de novo mutation rates in a chimpanzee parent-offspring trio by ultra-deep whole genome sequencing
  Shoji Tatsumoto; Yasuhiro Go; Kentaro Fukuta; Hideki Noguchi; Takashi Hayakawa; Masaki Tomonaga; Hirohisa Hirai; Tetsuro Matsuzawa; Kiyokazu Agata; Asao Fujiyama
  Scientific Reports, 7, 1, Springer Science and Business Media LLC, 01 Nov. 2017, [Peer-reviewed]
  Scientific journal, Abstract
  
  Mutations generate genetic variation and are a major driving force of evolution. Therefore, examining mutation rates and modes are essential for understanding the genetic basis of the physiology and evolution of organisms. Here, we aim to identify germlinede novomutations through the whole-genome surveyance of Mendelian inheritance error sites (MIEs), those not inherited through the Mendelian inheritance manner from either of the parents, using ultra-deep whole genome sequences (>150-fold) from a chimpanzee parent-offspring trio. We identified such 889 MIEs and classified them into four categories based on the pattern of inheritance and the sequence read depth: [i]de novosingle nucleotide variants (SNVs), [ii] copy number neutral inherited variants, [iii] hemizygous deletion inherited variants, and [iv]de novocopy number variants (CNVs). Fromde novoSNV candidates, we estimated a germlinede novoSNV mutation rate as 1.48 × 10⁻⁸per site per generation or 0.62 × 10⁻⁹per site per year. In summary, this study demonstrates the significance of ultra-deep whole genome sequencing not only for the direct estimation of mutation rates but also for discerning various mutation modes includingde novoallelic conversion andde novoCNVs by identifying MIEs through the transmission of genomes from parents to offspring.
• Functional characterization of the TAS2R38 bitter taste receptor for phenylthiocarbamide in colobine monkeys
  Laurentia Henrieta Permita Sari Purba; Kanthi Arum Widayati; Kei Tsutsui; Nami Suzuki-Hashido; Takashi Hayakawa; Sarah Nila; Bambang Suryobroto; Hiroo Imai
  Biology Letters, 13, 1, 20160834, 20160834, The Royal Society, Jan. 2017, [Peer-reviewed]
  Scientific journal, Bitterness perception in mammals is mostly directed at natural toxins that induce innate avoidance behaviours. Bitter taste is mediated by the G protein-coupled receptor TAS2R, which is located in taste cell membranes. One of the best-studied bitter taste receptors is TAS2R38, which recognizes phenylthiocarbamide (PTC). Here we investigate the sensitivities of TAS2R38 receptors to PTC in four species of leaf-eating monkeys (subfamily Colobinae). Compared with macaque monkeys (subfamily Cercopithecinae), colobines have lower sensitivities to PTC in behavioural and in vitro functional analyses. We identified four non-synonymous mutations in colobine TAS2R38 that are responsible for the decreased sensitivity of the TAS2R38 receptor to PTC observed in colobines compared with macaques. These results suggest that tolerance to bitterness in colobines evolved from an ancestor that was sensitive to bitterness as an adaptation to eating leaves.
• Variation in ligand responses of the bitter taste receptors TAS2R1 and TAS2R4 among New World monkeys
  Kei Tsutsui; Masahiro Otoh; Kodama Sakurai; Nami Suzuki-Hashido; Takashi Hayakawa; Takumi Misaka; Yoshiro Ishimaru; Filippo Aureli; Amanda D. Melin; Shoji Kawamura; Hiroo Imai
  BMC Evolutionary Biology, 16, 1, Springer Science and Business Media LLC, 12 Oct. 2016, [Peer-reviewed]
  Scientific journal
• Network modules and hubs in plant-root fungal biomes
  Hirokazu Toju; Satoshi Yamamoto; Akifumi S. Tanabe; Takashi Hayakawa; Hiroshi S. Ishii
  Journal of The Royal Society Interface, 13, 116, 20151097, 20151097, The Royal Society, Mar. 2016, [Peer-reviewed]
  Scientific journal, Terrestrial plants host phylogenetically and functionally diverse groups of below-ground microbes, whose community structure controls plant growth/survival in both natural and agricultural ecosystems. Therefore, understanding the processes by which whole root-associated microbiomes are organized is one of the major challenges in ecology and plant science. We here report that diverse root-associated fungi can form highly compartmentalized networks of coexistence within host roots and that the structure of the fungal symbiont communities can be partitioned into semi-discrete types even within a single host plant population. Illumina sequencing of root-associated fungi in a monodominant south beech forest revealed that the network representing symbiont–symbiont co-occurrence patterns was compartmentalized into clear modules, which consisted of diverse functional groups of mycorrhizal and endophytic fungi. Consequently, terminal roots of the plant were colonized by either of the two largest fungal species sets (represented by Oidiodendron or Cenococcum ). Thus, species-rich root microbiomes can have alternative community structures, as recently shown in the relationships between human gut microbiome type (i.e. ‘enterotype’) and host individual health. This study also shows an analytical framework for pinpointing network hubs in symbiont–symbiont networks, leading to the working hypothesis that a small number of microbial species organize the overall root–microbiome dynamics.
• The life history of retrocopies illuminates the evolution of new mammalian genes
  Francesco Nicola Carelli; Takashi Hayakawa; Yasuhiro Go; Hiroo Imai; Maria Warnefors; Henrik Kaessmann
  Genome Research, 26, 3, 301, 314, Cold Spring Harbor Laboratory, 04 Jan. 2016, [Peer-reviewed]
  Scientific journal, New genes contribute substantially to adaptive evolutionary innovation, but the functional evolution of new mammalian genes has been little explored at a broad scale. Previous work established mRNA-derived gene duplicates, known as retrocopies, as models for the study of new gene origination. Here we combine mammalian transcriptomic and epigenomic data to unveil the processes underlying the evolution of stripped-down retrocopies into complex new genes. We show that although some robustly expressed retrocopies are transcribed from preexisting promoters, most evolved new promoters from scratch or recruited proto-promoters in their genomic vicinity. In particular, many retrocopy promoters emerged from ancestral enhancers (or bivalent regulatory elements) or are located in CpG islands not associated with other genes. We detected 88–280 selectively preserved retrocopies per mammalian species, illustrating that these mechanisms facilitated the birth of many functional retrogenes during mammalian evolution. The regulatory evolution of originally monoexonic retrocopies was frequently accompanied by exon gain, which facilitated co-option of distant promoters and allowed expression of alternative isoforms. While young retrogenes are often initially expressed in the testis, increased regulatory and structural complexities allowed retrogenes to functionally diversify and evolve somatic organ functions, sometimes as complex as those of their parents. Thus, some retrogenes evolved the capacity to temporarily substitute for their parents during the process of male meiotic X inactivation, while others rendered parental functions superfluous, allowing for parental gene loss. Overall, our reconstruction of the “life history” of mammalian retrogenes highlights retroposition as a general model for understanding new gene birth and functional evolution.
• Rapid Expansion of Phenylthiocarbamide Non-Tasters among Japanese Macaques
  Nami Suzuki-Hashido; Takashi Hayakawa; Atsushi Matsui; Yasuhiro Go; Yoshiro Ishimaru; Takumi Misaka; Keiko Abe; Hirohisa Hirai; Yoko Satta; Hiroo Imai
  PLOS ONE, 10, 7, e0132016, e0132016, Public Library of Science (PLoS), 22 Jul. 2015, [Peer-reviewed]
  Scientific journal
• Aquatic adaptation and the evolution of smell and taste in whales
  Takushi Kishida; JGM Thewissen; Takashi Hayakawa; Hiroo Imai; Kiyokazu Agata
  Zoological Letters, 1, 1, 9, Springer Science and Business Media LLC, 13 Feb. 2015, [Peer-reviewed]
  Scientific journal
• Frequent expansions of the bitter taste receptor gene repertoire during evolution of mammals in the Euarchontoglires clade
  Takashi Hayakawa; Nami Suzuki-Hashido; Atsushi Matsui; Yasuhiro Go
  Molecular Biology and Evolution, 31, 8, 2018, 2031, Oxford University Press (OUP), 23 Apr. 2014, [Peer-reviewed], [Lead author, Corresponding author]
  Scientific journal
• Two Distinct Determinants of Ligand Specificity in T1R1/T1R3 (the Umami Taste Receptor)
  Yasuka Toda; Tomoya Nakagita; Takashi Hayakawa; Shinji Okada; Masataka Narukawa; Hiroo Imai; Yoshiro Ishimaru; Takumi Misaka
  Journal of Biological Chemistry, 288, 52, 36863, 36877, Elsevier BV, Dec. 2013, [Peer-reviewed]
  Scientific journal
• Eco-geographical diversification of bitter taste receptor genes (TAS2Rs) among subspecies of chimpanzees (Pan troglodytes)
  Takashi Hayakawa; Tohru Sugawara; Yasuhiro Go; Toshifumi Udono; Hirohisa Hirai; Hiroo Imai
  PLOS ONE, 7, 8, e43277, e43277, Public Library of Science (PLoS), 16 Aug. 2012, [Peer-reviewed], [Lead author]
  Scientific journal
• A novel composite retrotransposon derived from or generated independently of the SVA (SINE/VNTR/Alu) transposon has undergone proliferation in gibbon genomes
  Toru Hara; Yuriko Hirai; Sudarath Baicharoen; Takashi Hayakawa; Hirohisa Hirai; Akihiko Koga
  Genes & Genetic Systems, 87, 3, 181, 190, Genetics Society of Japan, 2012, [Peer-reviewed]
  Scientific journal
• Immigration of a Large Number of Adolescent Female Chimpanzees into the Mahale M Group
  Takashi Hayakawa; Mai Nakashima; Michio Nakamura
  Pan Africa News, 18, 1, 8, 10, Kyoto University Library, Jun. 2011, [Peer-reviewed], [Lead author, Corresponding author]
  Scientific journal

• 研究奨励賞受賞記 全生物ゲノム時代の哺乳類進化研究
  早川卓志, 日本進化学会ニュース, 27, 1, 16, 18, Mar. 2026
• 収斂進化
  早川卓志, 哺乳類学の百科事典, 196, 197, Nov. 2025
• ゲノム時代の到来
  早川卓志, 哺乳類学の百科事典, 184, 185, Nov. 2025
• 分子進化
  早川卓志, 哺乳類学の百科事典, 176, 177, Nov. 2025
• 遺伝子とゲノム
  早川卓志, 哺乳類学の百科事典, 164, 165, Nov. 2025
• オーストラリア・オセアニア区の哺乳類
  早川卓志, 哺乳類学の百科事典, 92, 93, Nov. 2025
• 第26回大会レポート S07: Evolutionary studies of eating
  早川, 卓志, 日本進化学会ニュース, 25, 3, 7, 9, Dec. 2024
• 霊長類の知性
  早川卓志; 岩崎はるか, Newton, 2024年, 3月号, 122, 133, 2024
• 肉食をめぐる人類学：第76回日本人類学会大会・第38回日本霊長類学会大会連合大会シンポジウム報告
  Shun HONGO; Shiaki KONDO; Rikai SAWAFUJI; Takushi HAYAKAWA; Haruka YAMAGUCHI, Primate Research, 39, 2, 97, 100, 2024
  Primate Society of Japan
• コアラ
  早川卓志, 飼育員が教えるどうぶつのディープな話 : 動物園を100倍楽しむ!, 157, 159, 10 Jul. 2023
• 森林火災のその後――生きのびたコアラ
  早川卓志, Habataki, 2023, SUMMER / AUTUMN, 5, 2023
• 苦味受容体
  早川卓志, 霊長類学の百科事典, 204, 205, 2023
• 4つの共生論：共生を「ともいき」「シンバイオーシス」「エコシステム」「インクルージョン」の4つの視点から整理する
  早川昌志; 早川卓志, 未来共創, 10, 75, 131, 2023
• 危機に瀕するオセアニアの野生動物
  早川卓志; 今井明子, Newton, 2022年, 9月号, 122, 133, 2022
• Initiation of the Primate Genome Project
  Dong-Dong Wu; Xiao-Guang Qi; Li Yu; Ming Li; Zhi-Jin Liu; Anne D. Yoder; Christian Roos; Takashi Hayakawa; Jeffrey Rogers; Tomas Marques-Bonet; Bing Su; Yong-Gang Yao; Ya-Ping Zhang; Guojie Zhang, Zoological Research, 43, 2, 147, 149, 2022
  Zoological Research
• 森林火災と再生 ～火と共に生きるコアラ～
  早川卓志, モンキー, 5, 1, 18, 19, 2021
• 世界的な森林火災を乗り越えて――オーストラリアの野生動物のいま
  早川卓志, どうぶつと動物園, 73, 3, 130, 135, 2021
• チンパンジー研究から考える人類の色覚多様性の進化的視点
  早川卓志, 日本進化学会ニュース, 22, 2, 4, 8, 2021
• 虫好きのリスザルは虫を旨く感じている ～動物園で探る霊長類の味覚・嗅覚～
  早川卓志, モンキー, 6, 3, 78, 79, 2021
• オーストラリアの有袋類と単孔類の全ゲノム解析が明らかにする哺乳類の化学感覚の進化
  早川卓志, AROMA RESEARCH, 22, 2, 105, 108, 2021
• コアラはフクログマ？ フクロザル？ ～オーストラリアの有袋類の多様性～
  早川卓志, モンキー, 3, 4, 110, 111, 2019
• Next-Generation Sequencing in Primate Molecular Ecology
  Takashi HAYAKAWA, Primate Research, 34, 1, 65, 78, 20 Jun. 2018
  Primate Society of Japan
• 樹の上で進化した味覚――北半球の霊長類，南半球のコアラ
  早川卓志, 科学, 88, 1123, 1124, 2018
• 霊長類の食べものと味覚の進化
  早川卓志, 霊長類図鑑 : サルを知ることはヒトを知ること, 98, 99, 2018
• 霊長類の系統樹マンダラの世界へようこそ――森で進化したサル、世界中に広がるヒト
  早川卓志; 高野智, 霊長類の系統樹マンダラ, 2017
• スマトラの森の響き
  早川卓志, モンキー, 2, 1, 14, 15, 2017
• 見上げてごらん、木の上のサルを
  早川卓志, 広報犬山, 1264, 22, 2017
• オオガラゴ，ショウガラゴ，デミドフコビトガラゴ，アンワンティボ，ポト，キタタラポアン
  早川卓志, 世界で一番美しいサルの図鑑, 162, 169, 2017
• 野生動物ゲノム・メタゲノム研究―できるようになったこと
  早川卓志, 日本人類学会進化人類学分科会ニューズレター, 2013/9, 17, 22, 2016
• 比較ゲノム解析が明らかにする水棲哺乳類の味覚の進化
  早川卓志, 勇魚, 64, 18, 23, 2016
• Taste of chimpanzee foods
  Takashi Hayakawa, Mahale Chimpanzees: 50 Years of Research, 246, 258, 05 Sep. 2015
  Long-term ecological research studies are rare and invaluable resources, particularly when they are as thoroughly documented as the Mahale Mountain Chimpanzee Project in Tanzania. Directed by Toshisada Nishida from 1965 until 2011, the project continues to yield new and fascinating findings about our closest neighbour species. In a fitting tribute to Nishida's contribution to science, this book brings together fifty years of research into one encyclopaedic volume. Alongside previously unpublished data, the editors include new translations of Japanese writings throughout the book to bring previously inaccessible work to non-Japanese speakers. The history and ecology of the site, chimpanzee behaviour and biology, and ecological management are all addressed through firsthand accounts by Mahale researchers. The authors highlight long-term changes in behaviour, where possible, and draw comparisons with other chimpanzee sites across Africa to provide an integrative view of chimpanzee research today., Cambridge University Press
• 次世代シークエンシングが切り拓く野生動物ゲノム・メタゲノム研究
  早川卓志, Labcab, 11, 6, 8, 2015
• ヒトとチンパンジーの“食文化”を遺伝学から探る
  早川卓志, Anthropological Letters, 2, 22, 23, 2013
• チンパンジーにおける苦味感覚の地域差と進化
  早川卓志,今井啓雄, 生物の科学 遺伝, 67, 418, 424, 2013
• オランウータンとアフリカ大型類人猿におけるゲノム多様性と進化の比較 ～味覚受容体遺伝子の研究から～
  早川卓志, 日本人類学会進化人類学分科会ニューズレター, 2016/9, 4, 6, 2013
• ゲノムから探る野生チンパンジーの世界
  早川卓志, 日本のサル学のあした―霊長類研究という「人間学」の可能性 (WAKUWAKUときめきサイエンスシリーズ 3), 22, 23, 2012
• After the Student Affairs Workshop in the XXIII Congress of International Primatological Society
  T Tajima; H Taniguchi; Y Yamanashi; Y Otani; S Ogawa; T Hayakawa; S Hongo, Primate Research, 27, 1, 57, 62, 2011
  Primate Society of Japan

• コアラ沼への招待状
  早川卓志
  世界文化社, 02 Apr. 2026, 9784418264025, [Supervisor]
• 哺乳類学の百科事典
  日本哺乳類学会
  丸善出版, Nov. 2025, 9784621311967, [Joint editor]
• コアラのひみつ
  南幅, 俊輔; 早川, 卓志
  02 Apr. 2025, 9784862557568, [Supervisor]
• コアラがかわいい : 生態から癒やされる写真まで魅力のすべて
  早川, 卓志
  KADOKAWA, 03 Feb. 2025, 9784046072863, 123p, Japanese, [Supervisor]
• 飼育員が教えるどうぶつのディープな話 : 動物園を100倍楽しむ!
  大渕, 希郷
  緑書房, Jul. 2023, 9784895318907, 175p, Japanese, [Contributor]
• 霊長類学の百科事典 = The encyclopedia of primatology
  日本霊長類学会
  丸善出版, Jul. 2023, 9784621308042, xxii, 716p, 図版 [8] p, Japanese, [Contributor]
• 心の進化を語ろう : 比較認知科学からの人間探究
  松沢, 哲郎
  岩波書店, Dec. 2019, 9784000063364, ix, 265p, Japanese, [Contributor]
• 霊長類図鑑―サルを知ることはヒトを知ること
  日本モンキーセンター 編
  京都通信社, 18 Nov. 2018, 4903473619, 155, Japanese, [Joint editor]
• 世界で一番美しいサルの図鑑
  京都大学霊長類研究所
  エクスナレッジ, 26 Nov. 2017, 4767824028, 223, Japanese, [Contributor]
• Mahale chimpanzees: 50 years of research
  Nakamura, Michio; Hosaka, Kazuhiko; Itoh, Noriko; Zamma, Koichiro
  Cambridge University Press, 10 Sep. 2015, 1107052319, 797, English, [Contributor]
• 日本のサル学のあした―霊長類研究という「人間学」の可能性 (WAKUWAKUときめきサイエンスシリーズ 3)
  中川尚史; 友永雅己; 山極寿一
  京都通信社, 13 Dec. 2012, 490347352X, 240, Japanese, [Contributor]

• サイエンスダイアログ「野生動物の健康から見直すヒトの健康 ～チンパンジーとコアラの話～」
  早川卓志; 美馬のゆり
  はこだて国際科学祭2026, 30 Aug. 2026, Public discourse
  [Invited]
• 野生のコモンマーモセットが食べる樹液と腸内細菌の適応
  早川卓志
  第15回日本マーモセット研究会大会, 21 Jan. 2026, Japanese, Nominated symposium
  20 Jan. 2026 - 21 Jan. 2026, [Invited]
• ⼤型類⼈猿における新規の種・亜種判定と⾎縁の解析
  早川卓志; 北山遼
  第27回SAGA（アフリカ・アジアに生きる大型類人猿を支援する集い）シンポジウム, 29 Nov. 2025, Poster presentation
• 南半球のいきものたちの研究 アフリカ、オーストラリア、南アメリカ
  早川卓志
  いきもにあ2025, 19 Oct. 2025, Invited oral presentation
  18 Oct. 2025 - 19 Oct. 2025, [Invited]
• 北海道のトガリネズミ4種における腸内細菌の比較解析
  早川卓志; 佐藤 理子; 大舘智志; 本田直也; 小林木野実; 飯島なつみ; 河原淳
  日本哺乳類学会2025年度大会, 25 Aug. 2025, Oral presentation
• ガム食と腸内細菌を介したコモンマーモセットとシロミミオポッサムの種間相互作用
  早川卓志; Leonardo CESAR DE OLIVEIRA MELO; Valdir LUNA DA SILVA; Maria ADELIA BORSTELMANN; DE OLIVEIRA; 金綱航平; 今井啓雄
  第41回日本霊長類学会大会, Poster presentation
  11 Jul. 2025 - 13 Jul. 2025
• ユーカリの森のコアラの未来
  早川卓志
  第40回東山再生フォーラム, 30 Mar. 2025
  [Invited]
• 特別教育講演：哺乳類の進化と苦味受容体による毒物環境への適応
  早川卓志
  第167回日本獣医学会学術集会, 12 Sep. 2024, Invited oral presentation
  10 Sep. 2024 - 13 Sep. 2024, [Invited]
• チンパンジーとヒト、何が同じで何が違うのか？
  早川卓志
  札幌市円山動物園 講演会, 21 Jul. 2024
  [Invited]
• アフリカ6地域におけるチンパンジーのエクソーム比較解析
  早川卓志; 岸田拓士; 郷康広; 松尾ほだか; 井上英治; 川口恵里; 会津智幸; 石崎比奈子; 豊田敦; 藤山秋佐夫; 松沢哲郎; 橋本千絵; 古市剛史; 阿形清和
  第40回日本霊長類学会大会, 14 Jul. 2024, Oral presentation
  12 Jul. 2024 - 14 Jul. 2024
• 森林火災とコアラの行動生態：保全と保護の現場から
  早川卓志
  動物の行動と管理学会2023年度大会
  13 Sep. 2023 - 16 Sep. 2023, [Invited]
• Genomic convergence of the arboreal species in primates and marsupials
  Takashi Hayakawa
  GSA-GSJ Joint Symposium, The 95th Annual Meeting of the Genetics Society of Japan
  06 Sep. 2023 - 08 Sep. 2023, [Invited]
• 飼育スンダスローロリスF2世代における樹液選好性の低下と腸内マイクロバイオームの変動
  早川卓志; 金綱航平; 飯島なつみ
  第39回日本霊長類学会大会, 09 Jul. 2023, Oral presentation
  07 Jul. 2023 - 09 Jul. 2023
• 苦味感覚と解毒の進化：チンパンジー、コアラ、カモノハシ
  早川卓志
  第50回日本毒性学会学術年会
  19 Jun. 2023 - 21 Jun. 2023, [Invited]
• カモノハシの苦味感覚研究から見えてきた哺乳類の植物二次代謝物適応の起源
  早川卓志
  第15回化学生態学研究会
  16 Jun. 2023 - 17 Jun. 2023, [Invited]
• Gut microbiome adaptation to gum diet in mammals: slow lorises, marmoset, and opossums
  Takashi Hayakawa
  Seminar Series at Biodiversity Centre, Federal University of Pernambuco
  22 Sep. 2022, [Invited]
• 味覚と⼈類の⾁⾷
  早川卓志
  第76回日本人類学会大会・第38回日本霊長類学会大会連合大会, 18 Sep. 2022, Public symposium
  16 Sep. 2022 - 19 Sep. 2022
• ヒトの感覚の進化を分子レベルで考える
  早川卓志
  日本心理学会第86回大会
  08 Sep. 2022 - 11 Sep. 2022, [Invited]
• 中生代から続く毒物への適応：哺乳類の苦味受容体の分子進化
  早川卓志
  日本味と匂学会第56回大会
  22 Aug. 2022 - 24 Aug. 2022, [Invited]
• グルメな進化の隣人～アフリカの森がはぐくむチンパンジーの食べ物～
  早川卓志
  札幌市円山動物園 世界チンパンジーの日 特別イベント 講演会
  10 Jul. 2022, [Invited]
• 動物園由来試料を用いた霊長類のゲノム・トランスクリプトーム解析
  早川卓志
  京都大学霊長類研究所共同利用研究会・第50回ホミニゼーション研究会「人類進化と遺伝子」, 22 Mar. 2022, Public symposium
  22 Mar. 2022 - 23 Mar. 2022
• 飼育下の樹液食霊長類における樹液給餌と腸内細菌叢の関係について
  早川卓志
  第3回京都大学霊長類研究所技術部セミナー 野生から学ぶ、飼育霊長類の食事
  03 Mar. 2022, [Invited]
• おいしいユーカリの葉を求めて ～コアラはどこから来て、どこへ行くのか～
  早川卓志
  名古屋市東山動植物園 動物講演会
  07 Nov. 2021, [Invited]
• Function and evolution of bitter taste receptors as the toxin sensor
  Takashi Hayakawa
  Symposium on Animal Species Difference of Xenobiotics Metabolism and Detoxification, The 48th Annual Meeting of the Japanese Society of Toxicology
  07 Jul. 2021 - 09 Jul. 2021, [Invited]
• Gum feeding induces short-term gut microbiome change in captive slow loris
  Takashi Hayakawa
  The 14th International Conference on Environmental Enrichment
  22 Jun. 2019 - 26 Jun. 2019, [Invited]
• Life slowly, life in the dark - insight from slow loris genome
  Takashi Hayakawa
  The 11th International Symposium on Primatology and Wildlife Science
  01 Mar. 2019 - 03 Mar. 2019, [Invited]
• Did life in trees drive the adaptive evolution of taste in koala and primates?
  Takashi Hayakawa
  The 10th International Symposium on Primatology and Wildlife Science
  22 Sep. 2018 - 24 Sep. 2018, [Invited]
• 樹の上の暮らし ～北半球のサル、南半球のコアラ～
  早川卓志
  第54回東山動植物園ワークショップ
  25 Dec. 2017, [Invited]
• 大型類人猿情報ネットワークGAINを活用した生物学研究
  早川卓志
  第26回サル疾病ワークショップ
  01 Jul. 2017, [Invited]
• 野生動物ゲノム・メタゲノム研究－できるようになったこと－
  早川卓志
  日本人類学会 進化人類学分科会 第36回シンポジウム
  18 Jun. 2016, [Invited]
• 比較ゲノム解析が明らかにする海棲哺乳類の味覚の進化
  早川卓志
  2015年度勇魚会シンポジウム
  28 Nov. 2015 - 29 Nov. 2015, [Invited]
• Dietary adaptation and bitter taste receptor gene evolution in primates
  Takashi Hayakawa
  Symposium on Sensory Genetics, Ecology and Evolution of Primates. 17th Annual Meeting of Society of Evolutionary Studies, Japan
  20 Aug. 2015 - 23 Aug. 2015, [Invited]
• ゲノムの変化が駆動する感覚適応進化 ～ゲノム進化生物学入門～
  早川卓志
  第36回数理の翼夏季セミナー
  15 Aug. 2015 - 19 Aug. 2015, [Invited]
• 霊長類の味覚受容体遺伝子のゲノム進化と生態適応
  早川卓志
  日本生理人類学会 第25回若手研究者講演会
  29 May 2015, [Invited]
• DNAでサルの暮らしはどこまでわかるか？
  早川卓志
  第11回京大モンキー日曜サロン, 22 Mar. 2015, Invited oral presentation
  [Invited]
• Eco-genomics in primates
  Takashi Hayakawa
  The 2nd Annual Symposium of Leading Graduate Program in Primatology and Wildlife Science
  05 Mar. 2015 - 08 Mar. 2015, [Invited]
• チンパンジーの遺伝子・ゲノムの地域差と行動多様性の関係
  早川卓志
  日本アフリカ学会中部支部 2014年度第1回例会
  18 Oct. 2014, [Invited]
• Next-generation sequencing analysis of Indonesian colobine genome
  Takashi Hayakawa
  Kyoto University and Bogor Agricultural University International Symposium on Diversity and Conservation of Asian Primates
  18 Aug. 2014 - 21 Aug. 2014, [Invited]
• オランウータンとアフリカ大型類人猿におけるゲノム多様性と進化の比較 ～味覚受容体遺伝子の研究から～
  早川卓志
  日本人類学会 進化人類学分科会 第30回シンポジウム
  29 Jun. 2013, [Invited]

• 多様性生物学基礎論, 2024年, 修士課程, 環境科学院
• 大学院共通授業科目（一般科目）：自然科学・応用科学, 2024年, 修士課程, 大学院共通科目
• 科学・技術の世界（1単位）, 2024年, 学士課程, 全学教育
• 環境と人間, 2024年, 学士課程, 全学教育
• 多様性生物学Ⅱ, 2024年, 学士課程, 理学部
• 環境生物学Ⅱ, 2024年, 学士課程, 理学部
• 国際交流Ⅱ, 2024年, 学士課程, 国際本部
• 英語演習, 2024年, 学士課程, 全学教育

• 動物の行動と管理学会
• 日本進化学会
• 日本哺乳類学会
• 日本霊長類学会

• 霊長類の系統樹マンダラ
  日本モンキーセンター, 2017

• 高山生態系における人と野生動物の軋轢問題ー家畜襲撃の外的および内的要因の解明ー
  科学研究費助成事業
  Apr. 2024 - Mar. 2028
  木下 こづえ; 早川 卓志; 菊地 デイル万次郎; 村山 美穂
  日本学術振興会, 基盤研究(B), 京都大学, Coinvestigator, 24K03130
• 遺伝的エビデンスに基づくアジアの希少動物の生息域外保全の実践
  公益財団法人 JAC環境動物保護財団 2026年度助成金
  Jul. 2026 - Jun. 2027
  早川卓志
  公益財団法人 JAC環境動物保護財団, 動物園・水族館
• コモンマーモセットのガム食が生み出す種間相互作用の解明
  日本学術振興会 学術国際交流事業 二国間交流事業共同研究
  Apr. 2025 - Mar. 2027
  早川卓志
  Principal investigator, JPJSBP120259905
• Establishment and practice of a forest symbiosis model using the conservation genomics methods: the relationship between koalas and eucalypts
  Grants-in-Aid for Scientific Research
  Apr. 2023 - Mar. 2027
  早川 卓志; 戸田 安香; 土田 さやか
  Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Hokkaido University, Principal investigator, 23H03579
• Cross-site conservation study of wild and captive mammals endemic in Australia and Japan
  Grants-in-Aid for Scientific Research
  Oct. 2021 - Mar. 2027
  木下 こづえ; 早川 卓志; 小倉 匡俊
  各国固有種である、コアラ、ニホンザル、ヤマネコを対象に研究を実施した。国内に関しては、コアラでは淡路ファームパークイングランドの丘で行動観察を実施するとともに、糞便サンプルを集めて、腸内細菌叢の解析および尿中コルチゾール（ストレスホルモン）分析を実施した。行動に関しては、採食やストレスに関連する行動や採食パターンの記録と分析を行った。本動物園は、国内で唯一、北方系と南方系の2つの系統を飼育しており、これらの間で餌の好みに差があることが明らかとなった。また動物園における飼育管理の中に存在するストレス要因について調べ、騒音から受けるストレスについて明らかにした。腸内細菌叢に関しては、2021年度に平川動物公園で実施した研究データと合わせて比較分析したところ、ユーカリ選択と腸内細菌叢の間に関連が見られた。
  また、日本のコアラ飼育園7園のコアラ飼育従事者にアンケートを依頼し、コアラの性格評定を行った。因子分析の結果、コアラには性格と呼ぶべき、個体差が存在することが示された。またゲノムワイド関連分析をおこない、性格と関連があると思われるゲノム変異を検出した。さらに、ニホンザルおよびヤマネコのゲノム多様性やストレスおよび繁殖生理に関わる知見を収集した。
  国外に関しては、2022年8月と2023年3月に南オーストラリアのカンガルー島へ渡航し、保護区における野生コアラの観察研究を開始した。カンガルー島は2019-2020年に大規模森林火災で大部分のユーカリ林が焼失したが、今回、ユーカリ林の再生を確認し、コアラの再生したユーカリへの適応が観察できた。また、シドニー大学、アデレード大学、タロンガ動物園でセミナーを実施し、本プロジェクトのオーストラリア対応者と共同研究の進捗を確認しあった。
  Japan Society for the Promotion of Science, Fund for the Promotion of Joint International Research (Fostering Joint International Research (B)), Kyoto University, Coinvestigator, 21KK0106
• 飼育下繁殖と野生復帰の改善に向けたバクの腸内細菌叢、MHC、におい物質の解析
  科学研究費助成事業
  Apr. 2024 - Mar. 2026
  早川 卓志
  日本学術振興会, 特別研究員奨励費, 北海道大学, Principal investigator, 24KF0002
• Adaptive evolution/change in mammals to exogenous chemicals (xenobiotics)
  Grants-in-Aid for Scientific Research
  Apr. 2021 - Mar. 2026
  石塚 真由美; 早川 卓志; 武田 一貴; 川合 佑典; 山崎 淳平; 池中 良徳; 中山 翔太
  我々はこれまでの研究により、高次の動物が外来性の化学物質（Xenobiotics）への「適応」ために、化学物質の代謝や排泄など、解毒のカスケードに沿って薬物 代謝酵素などの一連の多様性を発展させてきたとの仮説を立てた。化学物質感受性には多様性があり、解毒代謝酵素の解析から、この多様性獲得の主要因は食餌 由来の化学物質である可能性を報告した。本研究では食性の観点および重度環境汚染域に棲息する動物を中心に、哺乳類が日常的に曝露される化学物質にどのように適応してきたのか、多様な種を用いてその進化を機能面から明らかにする。これまでの研究で構築してきた多様な動物試料を用いた研究体制を生かし、食性 のユニークな動物種を対象としたウェットな実験や、データベースを用いた網羅的解析により、外来性の化学物質に対する動物の「適応」と「共存」メカニズム を明らかにする。
  2022年度は、食肉目クマ科を中心に、ゲノムデータベースを用いた遺伝子解析を行った。外来化学物質の代謝を担う第I相反応酵 素シトクロムP450、第II相反応のグルクロン酸転移酵素や硫酸転移酵素について、種間比較を行い、食性との関連性について解析した。第I相反応において重要なCytochrome P450（CYP）のうち、CYP1-CYP3ファミリーについて、遺伝子情報を網羅的に比較、解析することで進化的な背景を明らかにした。雑食性の動物であるクマ（ヒグマ、アメリカクロクマ）、アナグマ、イヌにおいて異物代謝に重要なサブファミリーであるCYP2Cと3Aにおいて特徴的な遺伝子重複が確認した。哺乳類で第II相反応を担うグルクロン酸転移酵素（UGT）について、データベースを用いたUGT遺伝子の網羅的解析を行ったところ、イヌ科、ヒグマ、アメリカクロクマにおいてUGT1Aの遺伝的拡大（遺伝子数の増加）が確認された。
  Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (A), Hokkaido University, Coinvestigator, 21H04919
• 日本とオーストラリアの絶滅危惧哺乳類の地球縦断型比較ゲノム研究の確立
  学術国際交流事業 二国間交流事業共同研究
  Apr. 2021 - Mar. 2023
  早川卓志
  日本学術振興会, 北海道大学, Principal investigator, JPJSBP120219902
• 比較オミックス解析による霊長類の発声行動と音声コミュニケーションの遺伝基盤の解明
  科学研究費助成事業
  Apr. 2020 - Mar. 2022
  早川 卓志
  多様なオミックス解析（ゲノム、エクソーム、トランスクリプトームなど）の手法を駆使して、霊長類の発声行動と音声コミュニケ―ションについて、生態・行動のレベルから、分子神経のレベルまでつなぎたいとう展望を持って、本研究計画に取り組んだ。ほとんどの霊長類が構造化された音節・音声の組合せによる音声コミュニケーションをするが、ヒトでいうところの「歌」と呼べるレベルまで昇華された霊長類は少なく、その代表が熱帯アジアの森林に生息するテナガザル類である。それぞれの種に特異的な歌（ソロやデュエット）が知られており、その遺伝的基盤を探るべく、国内動物園で亡くなったシロテテナガザル複数個体の剖検時に採取された脳から、発声や音声コミュニケーションに関連すると思われる脳領域を分取し、RNAseqの手法で網羅的な遺伝子発現解析をおこなった。採材にはナショナルバイオリソースプロジェクト（NBRP）の大型類人猿情報ネットワーク（GAIN）の支援を受けた。複数領域の比較RNA解析から、発声行動と音声コミュニケ―ションに関連すると思われる脳領域において特異的に発現量が増減している遺伝子候補群を検出することができた。また、本邦の固有霊長類であるニホンザルでは、歌と呼べるような複雑な音声はないものの、クーコールと呼ばれる長距離音声で、群れ内の個体間コミュニケーションをしている。餌付け群である地獄谷野猿公苑や、飼育群である函館市熱帯植物園のニホンザルでの行動観察をおこない、こうしたクーコールに関連する行動特徴についての調査に着手した。COVID-19による行動制限の影響を受けて、霊長類の動物園や生息地に出向いての調査が限られたが、機会的な剖検個体における脳からのオミックス解析や、分子神経のデータを行動・生態の分析と組み合わせる研究基盤が整った。
  日本学術振興会, 新学術領域研究(研究領域提案型), 北海道大学, Principal investigator, 20H04987
• Elucidation of convergent evolution of genome and metagenome of primates and non-primate mammals in terms of feeding adaptation
  Grants-in-Aid for Scientific Research
  Apr. 2019 - Mar. 2022
  Hayakawa Takashi
  Animals have extreme diverse diet characteristics. In addition to carnivores, omnivores, and herbivores as classical understanding, there are species-specific adaptations to a variety of feeding resources, such as folivores, frugivores, Exudivores, and nectarivores. Among the various animal taxa, primates, with around 500 species, have species with all of these diet types and are an important model of adaptive radiation in terms of feeding traits. Genomic and metagenomic adaptations were analyzed in primates and non-primate mammals with similar feeding traits under the convergent evolution, such as the exudivorous gut bacterial microbiome of slow loris (primates) vs opossum (marsupials) and taste receptor genes in the folivorous colobines (primats) vs. koala (marsupial). We found that there are evolutionary mechanisms shared between primates and non-primate mammals.
  Japan Society for the Promotion of Science, Grant-in-Aid for Early-Career Scientists, Hokkaido University, Principal investigator, 19K16241
• Determination of dependence of Japanese macaques on farmland using gut micro bacteria and establishment of a method to judge the level of damage
  Grants-in-Aid for Scientific Research
  Apr. 2017 - Mar. 2021
  Kiyono Mieko
  The Japanese macaque is endemic to Japan and has been recognized as harmful animals. In this study, we investigated the effects of the anthropogenic environment on the gut microbiota. The results showed that the intestinal microflora of the crop-raiding and captive troops differed from that of the natural group. Further studies revealed that the differences in the intestinal microflora were not only related to the anthropogenic environment but also to regional differences. In this study, we examined the possibility of using the gut microbiota as an index for determining the level of aggression for conservation management of Japanese macaques. Although the gut microbiota is effective in determining the level of damage, it also suggests that even crop-raiding troops have characteristics similar to those of natural groups. The gut microbiota is useful as a method to reconsider the Japanese macaque population as a gradation that does not depend on whether it is a crop-raiding troop or not.
  Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Kobe University, Coinvestigator, 17H01911
• Evolution of genome and metagenome association in primates
  Grants-in-Aid for Scientific Research
  Apr. 2016 - Mar. 2019
  Hayakawa Takashi
  This study aimed to elucidate the genome and metagenome association in captive and wild primates. Fecal samples of about 50 captive chimpanzees in Kyoto University were collected and subject to 16S rRNA sequencing analysis for symbiont gut bacteria. Relationship between individual background (especially genomic polymorphisms) and 16S diversity was analyzed. Fecal and oral bacterial samples of many primate species in Japan Monkey Centre and some field areas were collected for analysis of metagenomic profile in terms of species specificity and phylogenetic constraint.
  Japan Society for the Promotion of Science, Grant-in-Aid for Young Scientists (B), Kyoto University, Principal investigator, 16K18630
• 哺乳類の味覚の進化的起源の解明を目的としたオーストラリア産有袋類・単孔類の味覚受容体の分子生態学研究
  平成29年度 笹川科学研究助成
  Apr. 2017 - Feb. 2018
  早川卓志
  日本科学協会, 京都大学霊長類研究所, Principal investigator, 29-534
• Investigation of feeding strategies of African cercopithecids by using genetic and/or morphological methods
  Grants-in-Aid for Scientific Research
  Oct. 2013 - Mar. 2017
  IHOBE HIROSHI; SHIMIZU Daisuke; KOYABU Daisuke
  Feeding strategies of African cercopithecids were investigated by using ecological, genetic and morphological methods. Food overlaps among guenons were different between combinations of guenon species. Colobus monkeys used the same food “species” which guenons used, but the differences of “parts eaten” were found between colobus monkeys and guenons. Monkeys, which frequently fed on hard leaves or hard fruits, had strong jaws and teeth adapting to wear down. The difference of bitter taste receptor gene repertoires among investigated species was found and this difference was suggested to be related with the difference of feeding strategy of each species.
  Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (A), Sugiyama Jogakuen University, Coinvestigator, 25257409
• 苦味受容体の遺伝的多様性がチンパンジーの地域特異な採食行動にもたらす影響の解明
  科学研究費助成事業
  Apr. 2012 - Mar. 2015
  早川 卓志
  本研究は「苦味受容体の遺伝的多様性がチンパンジーの地域特異な採食行動にもたらす影響」を解明することが目的である。初年度及び第二年度において行った研究を前進させた。これまでに、西アフリカ・ギニア共和国・ボッソウ地域において、全頭個体識別がなされた野生のチンパンジー12個体と、隣接するニンバ山から観察路に残された排泄物試料を収集し、DNAを抽出している。また、東アフリカ・タンザニア連合共和国・マハレ地域においても、同様に個体識別された野生チンパンジー60個体から排泄物試料を収集し、DNAを抽出している。本年度は、更に東アフリカの異なるチンパンジーの生息地であるウガンダ共和国・カリンズ地域において、個体識別された野生チンパンジーの排泄物試料を収集し、前年度までに樹立した排泄物由来のDNAに関して個体由来の塩基配列決定に必要な分析評価系の手法を用いて、カリンズ地域においても苦味受容体遺伝子の配列決定を行った。その結果、西アフリカのボッソウとギニア、東アフリカのマハレとカリンズについて東西亜種差があり、更にそれぞれの亜種内でも地域差があることを見出した。また、カリンズにおいてチンパンジーと同所的に生息し、重複した食物レパートリーを持つオナガザル数種についても、調査を行い、糞DNAを分析した。東アフリカにおいて採食される植物に含まれる苦味物質を受容すると考えられる苦味受容体遺伝子について、機能解析を実施した。
  日本学術振興会, 特別研究員奨励費, 京都大学, Principal investigator, 12J04270

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