Research Center
for Integrative Evolutionary Science
Program of Integrative Evolutionary Science

ResearchCenterfor
Integrative
Evolutionary
ScienceResearch Center for Integrative Evolutionary Science
Program of Integrative Evolutionary Science,
Department of Advanced Studies

Marvels of
our past
and future
Contents

2

6Annual Schedule

32

From Graduate Students

10

Faculties

34

Q&A

20

Visit Classes!

36

From Alumni

22

Graduate life and course work

38

About RCIES

30

Student Aids3

Program of Integrative Evolutionary Science,
Department of Advanced Studies
Program Outline
Integrative Evolutionary Science is a new academic field that aims
not only for the development of biology but also for elucidating
the nature of human beings and solving social issues, through acomprehensive understanding of the change of living organisms,
transition of human activities, and progression of global issues
from an evolutionary perspective. The Program of Integrative
Evolutionary Science, in collaboration with the Research Center for
Integrative Evolutionary Science, aims to pursue and share truths
with society, produce future leaders in this field, and to contributebroadly to the development of science and society.
This program consists of two programs: a five-year doctoral
program for students with a bachelor's degree and a three-year
doctoral program for students with a master's degree. Students inthis program will conduct their studies and research activities at
Petaurista leucogenys

the Research Center for Integrative Evolutionary Science, locatedin Hayama, Kanagawa Prefecture.

Message from the Chair
What fuels our research? It is because we want to know more, because we are
genuinely interested, because curiosity drives us, because we are on a mission
to crack unsolved problems, and because we dream of making groundbreaking
discoveries. Although the driving forces are different for everyone, we all share thesame passion for research. Research is hard work, and often, it does not proceed
as smoothly as planned and desired, with outcomes that may not align with our
expectations. Nevertheless, we continue with our work, driven by the passion forthe subjects and themes we study, as well as the routine that characterizes thework of a researcher. Lately, I have been pondering upon this aspect.
Program of Integrative Evolutionary Science is a new course that was introduced
in 2023 at the Department of Evolutionary Studies of Biosystems, formerly known
as the Institute of the Integrative Evolutionary Science Program. Numerous
individuals have earned their PhDs from this prestigious institute. A graduatelevel degree will be offered for this new course, providing education in a pioneering
direction rooted in the founding principles of the Department of Evolutionary
Studies of Biosystems. I look forward to working with students who harbor a
profound enthusiasm for evolution, science, and their societal implications.

Chair of the Program

Nobuyuki
Kutsukake
Betta brownorum

45

Annual Schedule
Observation and sample collection on the Hayama Coast

Entrance ceremony
SOKENDAI's entrance ceremonies areheld in spring (April) and autumn (October).
New students from all programs meet
together at the Hayama Campus.

Laboratoryof Basic Biology
The Laboratory of Basic Biology
course aims to provide students
with a comprehensive view ofexperimental biology throughdirect experiences with theknowledge and techniques ofimportant and fundamental
experimental methods that havecontributed to the developmentof biology. The main practicaltraining topics include molecularbiology experiments, cell histology
experiments, neurophysiology
experiments, scanning/transmission electron microscopy,
programming and field training.
Students learn not only thetechniques of each experiment, butalso report-writing skills.

May

April

June

July

AugustSeptember

October

Students enrolled in April
Students graduating in September

Freshman Course
The Freshman Course is anintensive course mainly for new
students. The Freshman Course
has two main objectives. Firstly, itteaches the skills and objectives
that every future researcher should
acquire and think about. Secondly, itbuilds connections with people fromdifferent fields through exposure
to the intellectual breadth that only
SOKENDAI can offer. The Freshman
Course consists of three sessions:'Exploring Academia', 'Researchers
and Society' and 'Communicative
Skills for Researchers'. The Freshman
Course is held twice a year in Japaneseand English. The course content is
the same in Japanese (starting in
April) and English (starting in October)courses. Both courses are offered at
the Hayama Campus (three days andtwo nights) in person and on-demand,and students must attend all classes toreceive credit.

6

Briefing forentrance admission

Progress
ReportSummer entrance admission

Degree conferment ceremony

Open campus
At the Open Campus, entrance admissions
and research in the Center are introduced
through presentations and laboratory tours.
In addition, attendants can learn about
the research of the faculties and students
through posters, obtain information, anddiscuss research by talking to the members
in person.

Briefing forentrance admissions
The Program of Integrated Evolutionary
Science usually holds entrance admissions
in summer and winter, with briefing sessions
held in conjunction with these admissions.
The main contents are lectures by several
faculty members and an explanation of thecourse entrance admission. Attendants cantalk with the faculty members at the venue.

7Annual Schedule

Students Collaboration with the University of Tokyo
Misaki Marine Biological Station

Life Sciences
Retreat

The Research Centre forIntegrated Evolutionary Scienceand the University of Tokyo Misaki
Marine Biological Station organize
a meeting event to promotestudent exchange and collaborative
research. The main contents ofthis meeting are oral and poster
presentations, tours of theresearch facilities of the two
institutions, and socializing. It aims
for intellectual exchanges between
the two institutions that willcontinue in the future and lead to
new research activities, such as
the development of collaborative
research.

This is a student-led academic
exchange course that brings
together SOKENDAI students
and faculties engaged in life
sciences research acrossprogram boundaries. The course
aims to familiarize students
with the life sciences throughpersonal interactions. Various
events are organized, including
poster presentations, lecturesby established researchers, andsocializing events unique to thevenue.

OctoberNovember

DecemberJanuary

February

March

April

Students graduating in MarchStudents enrolled in October

Entrance Freshman course
ceremony

8

Briefing forentrance admission

Open campus

Winter entrance admission

Integrative
Evolutionary Science
Progress Report

Degreeconferment
ceremony

Integrative Evolutionary Science Progress
ReportTwice a year, the Integrated Evolutionary
Science Course holds a student research
progress conference entitled Integrative
Evolutionary Science Progress Report. The
first-year students mainly present theirresearch plans, and second-year students
are assessed for progression.
Students in the third year and above are
required to present their work in English. The
review of the sub-thesis and the preliminary
examination of the doctoral thesis also takeplace at this course. Faculty members,
students, and researchers from the ResearchCenter for Integrated Evolutionary Science
participate in this important event, which isfollowed by an enthusiastic question-andanswer session.

The SOKENDAI degree conferment
ceremony is held on the Hayama
Campus. The ceremony is held twicea year, in spring and autumn. We
wish all graduates the best of luck intheir future endeavors!
Omedetou gozaimasu!!!

9Faculty List

Associate Professor
Email
URL
Expertise✉ iida_kaori@soken.ac.jp

💻 https://researchmap.jp/iida_k🔍 history of science and technology

Keywords 👉 history of biology/genetics,

breeding studies, radiation

Selected publications

I have been interested in how genetics
interacted with society in 20th century Japan.
I have explored topics such as genetics
and breeding, genetics and radiation, andgenetics and eugenics. Currently, I am
interested in analyzing some of the dynamics
through the lens of transnational knowledge
flow and science diplomacy. While it is often
assumed that science is "international," notall knowledge flows equally and freely acrossborders. To understand the "friction" in theflow requires a transnational perspective.
For far too long, the historiography of sciencein Asia, especially during the Cold War, hasbeen heavily influenced by a US-centerednarrative. To counteract this imbalance,
we have established a research group to
reexamine science and technology in Cold
War Asia from a trans-Asian perspective andare working on a diverse set of cases.

History of Science

Kaori Iida

Iida K (2020) Peaceful atoms inJapan: Radioisotopes as sharedtechnical and sociopoliticalresources for the Atomic Bomb
Casualty Commission and theJapanese scientific community
in the 1950s. Stud Hist Philos Biol
Biomed Sci 80:101240.

Professor

Lab. for Developmental Evolution
Email
URL
Expertise✉ irie_naoki@soken.ac.jp

💻 https://rcies.soken.ac.jp/labs/irie🔍 Developmental Evolution

Keywords 👉 Animal Evolution,

Faculties
10

law in embryonic evolution,
prediction ofphenotypic evolution

Selected publications
Hu H et al. (2017) Constrainedvertebrate evolution bypleiotropic genes. Nat Ecol Evol
1:1722–1730.
Uchida Y et al. (2023) Stability
in gene expression and bodyplan development leads toevolutionary conservation.
EvoDevo 14:4.

The evolution of organismal characteristics(phenotypes) is not entirely unrestricted;
s o m e t r a i t s a re m o re p ro n e t o c h a n g ethroughout evolution than others. How dosuch differences arise? It may simply be due
to differences in the selection pressuresexerted by natural selection. On the other
hand, there might be features that inherently
generate less phenotypic variation, serving asa limited foundation for diversification. Whilethe latter idea is not new, recent studies are
increasingly providing empirical support for
it.
So, what mechanisms lead to the difficultyin generating the foundational variations
that contribute to diversification? In our
research lab, we are tackling this question
by employing various methods, including
experiments on animals and large-scale
information analyses. Ultimately, our aim is
to contribute to transforming evolutionary
studies from a discipline primarily focused on
historical aspects into a field with predictive
theories regarding which phenotypes are
more likely to evolve.

Embryonic Evolution

Naoki Irie

11

Faculties

Population Genetics
and Genome Evolution
Email
URL

✉ innan_hideki@soken.ac.jp

💻 https://rcies.soken.ac.jp/labs/innan/index.html

Expertise 🔍 Population Genetics・Genome Evolution
Keywords 👉 Evolution・

Genetics・Theory

Associate Professor

Mathematical Biology Laboratory
Email
URL
Expertise✉ ohtsuki_hisashi@soken.ac.jp

💻 https://rcies.soken.ac.jp/labs/ohtsuki/index.html
🔍 Mathematical Biology

Keywords 👉 Sociobiology, Evolutionary Ecology,

Evolutionary Studies of Human Behavior

Selected publications
Innan H and Kondrashov F(2010) The evolution of gene
duplications: classifying anddistinguishing between models.
Nat Rev Genet 11: 97-108.

Selected publications
Fujimoto Y and Ohtsuki H (2023) Evolutionary stability ofcooperation in indirect reciprocity under noisy and private
assessment. Proc Natl Acad Sci USA 120:e2300544120.

Innan H and Sakamoto T (2021)
Multi-dimensional diffusion
process of allele frequencies
in population genetics. Proc
Jpn Acad Ser B 97:134-143.

Molecular Evolution

Tatsuya Ota
Associate Professor

Molecular Evolution Lab.
Email
URL

✉ ota@soken.ac.jp

💻 https://rcies.soken.ac.jp/labs/ota/

Expertise 🔍 Molecular Evolution

Keywords 👉 Molecular Evolution, Immunity, Plant domestication

Selected publications
Fawcett JA, Takeshima
R et al. (2023) Genome
sequencing reveals thegenetic architectureof heterostyly anddomestication history ofcommon buckwheat. Nat
Plants 9:1236–1251.
Thompson AW et al.
(2021) The bowfin
genome illuminates thedevelopmental evolutionof ray-finned fishes. Nat
Genet 53:1373-1384.

12

Hisashi Ohtsuki(In Japanese) Hasegawa T, Hasegawa M and Ohtsuki H (2022) Evolution
and Human Behavior, 2nd Edition, University of Tokyo Press.

The main aim of our research is tounderstand the evolution of complex
biological systems though the knowledge ofmolecular evolution and population genetics.
With analyzing ever accumulating genomic
and transcriptomic data, the evolutionary
processes of genes and/or genomes involvedin the following biological systems orprocesses have been investigated.
1. Evolution of vertebrate immune systems
Research to identify and characterizeimmunological molecules among various
vertebrate genomes, such as of lungfish,coelacanth, spotted gar, and bowfin
shed light on the significant functionalroles of immunological genes, and theirunique evolutionary patterns illustrate theimportance of various evolutionary forces tosustain living organisms.
2. Domestication process of cultivated plants
Domestication of wild plants is one ofimportant steps for human being to be able
to maintain the food (energy) sources fortheir survival. Artificial selection, whether it
is conscious or unconscious, has certainly
operated on the establishment of cultivatedplants, and many features associated withthe processes, often called as domestication
syndrome, are intriguing materials to study
evolutionary processes.

Yukinori Oonishi
Lecturer

Philosophy of Science
Email
URL
Expertise✉ oonishi_yukinori@soken.ac.jp

💻 http://www.y-onishi.sakura.ne.jp/publications.html
🔍 Philosophy of science

Keywords 👉 scientific realism debate, problem of demarcation,

confirmation theory, scientific representation,
natural kinds, machine learning

I study various questions of biologicalphenomena by using mathematics andcomputers. I am interested in both microand macroscopic phenomena. I have so far
studied following themes.
(1) Emergence and maintenance of sociality
in various organisms: Kin discrimination andcollective cooperation by microbes, Evolutionof division of labor and reproductive schedulein social insects, Evolution of altruistic
behavior and punishment in spatiallystructured populations,(2) Evolutionary ecology: Mechanisms of
mutualism between rhizobia and legumes,
Biodiversity of tropical rainforests,(3) Human behavior from evolutionary
perspectives: Evolution of indirect reciprocity,
Cumulative evolution of culture, Evolution ofmenopause, and(4) Diseases: Epidemiological dynamics ofinfectious diseases, Evolution of cancer,
Statistical analysis of human infertility.
My goal is to reveal the mechanism of
how evolution produces adaptation anddiversity, to give explanations to past andfuture biological phenomena, and to predict
future, through combining methodologies in
evolutionary studies, genetics, and ecology.
I also develop theoretical tools including
evolutionary game theory and adaptive
dynamics theory.

Mathematical Biology

Professor

Evolution of organisms is understood
through the evolution of its blueprint, thegenome. Our aim is to theoretically elucidate
the universal laws underlying this process.
Because genetic laws are fundamentally thesame across species, it becomes possible
to construct highly generalizable theories.
In some cases, this involves advanced
mathematical research incorporating natural
selection and stochastic factors. Additionally,
we conduct genome data analysis using
theoretical frameworks and verify ourtheories through empirical data analysis.

Philosophy of science studies various
aspects of science, including its method,concepts, or its social aspects. It also studies
the world view that particular scientifict h e o r i e s m a y i m p ly. A m o n g t h e s e , m yinterests are mainly in the epistemologicalissues of science. In particular, I have beenworking on projects related to the scientificrealism debate, scientific representation,and the problem of confirmation. Recently,Iʼm also interested in a new type of research
practice using emerging technologies suchas deep learning or data assimilation.

Philosophy of Science

Population Genetics

Hideki Innan

Selected publications
Bueno O and Onishi Y(2020) The likelihood ratio
measure and the logicality
requirement. Erkenntnis
87: 459-475.
Onishi Y (2017) Defending
the selective confirmation
strategy. Stud Hist Philos
Sci Part A 64: 1-10.

13

Associate Professor

Behavioral Neuroscience (Neurothology)
Email
URL

✉ kinoshita_michiyo@soken.ac.jp

💻 https://researchmap.jp/m_kinoshita/

Expertise 🔍 Neuroethology, Visual ecology, Sensory physiology,

Cognitive science, Comparative physiology
Keywords 👉 Insect, Flower foraging behavior, Target recognition

Selected publications
Kinoshita M andArikawa K (2023) ʻColorʼ
processing in the butterfly
visual system. Trends in
Neuroscience 46:338-340.
Kinoshita M et al. (2017)
Multisensory integrationin Lepidoptera: insight into
flower-visitor interactions.
Bioessays 39:1600086.

Animal Behaviour

Nobuyuki
Kutsukakeprofessor

Animal Behaviour
Email
URL

✉ kutsu@soken.ac.jp

💻 https://sites.google.com/view/nkutsukake/home
https://sites.google.com/site/sokendarwin/

Expertise 🔍 Animal Behaviour, Behavioral Ecology,

Evolutionary Biology, Primatology
Keywords 👉 animals, behaviour,

society

I am interested in how animals perceive
this world. Unfortunately, we neverexperience the world as animals perceive.
This is just because the sensory systemsof humans and animals are not the same.
However, we may predict their world bymeasuring their cognitive abilities by
behavioural assays and investigating their
nervous system. Neuroethology or behavioral
neuroscience is the field to investigate how
the brain controls behaviour and aims to"understand" their world as realistically as
possible.
My research group investigated thespectral organization of the compound eyesof swallowtail butterflies, measured theirvisual abilities by flower-visiting behaviour,and clarified the relationship between visualabilities and the system of the compoundeyes. Currently, we are investigating 1) the
encoding of spectral and polarized lightinformation in the brain, 2) the integrationof vision and olfaction in flower-visiting
behaviour, and 3) flower species visited byswallowtail butterflies in the field. In the
future, we would like to study the 'flowerinsect relationship' and the 'evolutionof vision and its cognitive abilities in
lepidopteran insects.

The observation of animals leads toquestions such as "How do they live?" "Whatare they thinking?" “What do they know andunderstand?” and so on. My goal is to analyze
the behavior and ecology of animals and toanswer those questions from a standpointof adaptive evolution. I have been studying
vertebrates, mainly mammals, but also birds
and fish. I stay in the field where wild animals
live, identify and name each individual, andrecord their behaviour every day. A good way
to understand animals is to observe the study
subject so closely that the subjects appear inyour dreams. On the other hand, an efficient
strategy to understand animals is to think
about patterns and theories common to
many animals. I hope to work with graduate
students and young researchers who havestrong interests in animals.

Jun Gojobori
Lecturer

Human Evolutionary Genetics Lab.
Email
URL
Expertise✉ gojobori_jun@soken.ac.jp

💻 https://rcies.soken.ac.jp/labs/gojobori/🔍 Physical Anthropology, Molecular Evolution,
Population Genetics

Keywords 👉 Human, Genetics, Population

Selected publications

We explore how organisms evolve at themolecular level. The major focus is on the
population process, where new mutations
arise which are subsequently subject toselection and random genetic drift. We
mainly use a theoretical approach tounderstand the evolutionary mechanisms
behind inter- and intra-specific DNA variation
under a wide range of evolutionary forces,
such as adaptive selection, balancing
selection, speciation, gene duplication. The
accumulation of these studies promises toprovide profound insights into theoverarching principles governing molecular
evolution.

Gojobori J et al. (2024)
Japanese wolves are mostclosely related to dogs andshare DNA with East Eurasiandogs. Nat Commun 15:1680.
Mizuno F, Gojobori J et al.
(2021) Population dynamics
in the Japanese Archipelago
since the Pleistocene
revealed by the complete
mitochondrial genome
sequences. Scientific reports
11:12018-12018.

Akira Sasaki
Professor

Mathematical Biology Laboratory
Email
URL
Expertise✉ sasaki_akira@soken.ac.jp

💻 https://sites.google.com/site/sokendaisasaki/🔍 Mathematical Biology, Evolutionary Biology, Ecology

Keywords 👉 Mathematical models, Evolution, Ecology, Behavior

Selected publications

Selected publications

Ito HC and Sasaki A (2023)
The adaptation front equation
explains innovation-driven
taxonomic turnovers andliving fossilization. Am Nat
202:E163-E180.

Yamakawa M et al. (2024)
Helping syndrome ispartially confirmed in theeusocial naked mole-rat.
Anim Behav 210:289-301.

Sasaki A et al. (2022) Antigenic
escape selects for theevolution of higher pathogentransmission and virulence.
Nat Ecol Evol 6: 51-62.

I study, by using mathematical models,
topics such as how complex behaviors andsophisticated strategies of organisms have
evolved, in what direction interspecies
interaction evolves, and how to predict andthe spread and evolution of pathogens, pests
and invading species. Examples of recent
findings of our theoretical studies include:
the inevitable emergence of 'living fossils' inthe peripheral niches of a taxonomic groupas a consequence of Darwin-Darlington
flow of species from central to peripheral
niches; the evolution of greater virulencein pathogens such as SARS-CoV2 andinfluenza A viruses that repeated escape hostimmunity by mutation; and a greater riskof evolutionary breakdown of interspecificrelationship in mutualistic systems than inparasitic systems.

Mathematical Biology

Behavioral Neuroscience
14

MichiyoKinoshita

Evolutionary Human Genetics

Faculties

15

Faculties

Evolutionary Physiology
Email
URL

✉ satta@soken.ac.jp

💻 https://sites.google.com/site/sattalab/homeExpertise 🔍 Genomic population genetics・Human evolution
Keywords 👉 introgression・ancestral polymorphism・

computer simulation・pseudogene・natural selection

Selected publications
Lau Q et al. (2015) A limit to
the divergent allele advantage
model supported by variable
pathogen recognition across
HLA-DRB1 allele lineages.
Tissue Antigens 86:343-52.
Satta Y et al. (2019) Twodimensional site frequency
spectrum for detecting,classifying and dating
incomplete selective sweeps.
Genes Gen Syst 94:283-300.

Chromosome Biology

Hideyuki Tanabe
Associate Professor

Laboratory of Chromosome Biology
Email
URL

✉ tanabe_hideyuki@soken.ac.jp

💻 https://rcies.soken.ac.jp/scientists/scientists_hideyuki_tanabe.html

Expertise 🔍 Molecular Cytogenetics, Chromosome Biology
Keywords 👉 Chromosome territories, FISH techniques,

Karyotypic evolution
Selected publications
Kimura A et al. (2021)
Identification of chromosome
17 trisomy in a cynomolgus
monkey (Macaca fascicularis)by multicolor FISH techniques.
Cytogenet Genome Res 161:
243-248.
Tanabe H et al. (2002)
Evolutionary conservationof chromosome territory
arrangements in cell nuclei
from higher primates. Proc
Natl Acad Sci USA 99: 44244429.

Human beings, who have enjoyedunprecedented prosperity through thedevelopment of science and technology, arenow facing a variety of problems. One of theroot causes of these problems is that "man"does not fully recognize his own existence
as a living being. To recognize our existence
as an organism, it is essential to understand
how we have evolved in the naturalenvironment. In other words, phenotypicevolution, which includes morphologicaland physiological traits, has been driven by
natural selection. This process involves theadaptation of individuals to their environment
at a given time, resulting in the productionof offspring and their subsequent survival.
The existence of "man" is a consequence ofsuch adaptation to the present environment
including cultures. Our research goals areto elucidate environmental adaptations
inscribed in the genome and to determine
what "human beings as organisms" are.

Focusing on chromosomes in the cell
nucleus, I am investigating how the spatial
arrangement of chromosome territories andgenes is regulated within the cell nucleus bymolecular cytogenetic approaches, mainly
fluorescence in situ hybridization (FISH)
techniques using a great deal of cultured
cells derived from various species. In the
nuclear architecture there are hierarchicalstructures from DNA to chromosome
territories such as A/B compartments,
Topologically Associating Domains (TADs),and chromatin loop structures. The dynamics
and regulation of their spatial arrangement
as well as their relationship to karyotypicevolution remain largely unknown. Therefore,
I am aiming to elucidate the molecular basisof nuclear architecture of chromosome
territories and their hierarchical structuresby using multicolor 2D-/3D-FISH techniquesand combined other methods. Also I am
trying to construct the catalogue of wholechromosomes and karyotypes of all living
species through organizing cellular resourcesof various species.

Takumi Tsutaya
Assistant Professor

Lab of Biological Anthropology
Email
URL
Expertise✉ tsutaya_takumi@soken.ac.jp

💻 https://sites.google.com/view/anthr/

🔍 Biological anthropology, Primatology,
Bioarchaeology, Paleontology

Keywords 👉 Palaeoproteomics, Stable isotope analysis, Orangutan

Selected publications
Uchida-Fukuhara Y et al.
(2024) Palaeoproteomic
investigation of an ancienthuman skeleton withabnormal deposition ofdental calculus. Sci Rep
14:5938.

We investigate lived experiences, life
history, and evolution of Hominidae. In
particular, we use protein and isotopic
analyses to retrospectively reconstructevolution and life phenomena that cannot be
determined from DNA analysis. Our recent
focus includes the following theme, and we
employ various methodologies from the field
to the laboratory.
・Applying palaeoproteomics to archaeology
to investigate the history of disease, therelationship between humans and animals,
and gender in the past.
・Reconstructing the phylogeny, evolutionary
history, and extinction of extinct animals,
including hominins, by molecular analysis
of paleontological specimens.
・Managing a research site for wild Bornean
orangutans and conducting research related
to primate ecology, human evolution, andzoonosis.

Biological Anthropology

Professor

Tsutaya T et al. (2021)
Faecal proteomics as anovel method to study
mammalian behaviour andphysiology. Mol Ecol Resour
21:1808–1819.

Yohey Terai
Assistant Professor

Evolutionary biology
and biodiversity laboratory
Email
URL
Expertise✉ terai_yohei@soken.ac.jp

💻 https://rcies.soken.ac.jp/labs/terai/🔍 Adaptation・speciation・ancient genome

Keywords 👉 Local adaptation・vision・macaque・lichen・dog/wolf

Selected publications
Gojobori J et al. (2024) The
Japanese wolf is most closely
related to modern dogs andits ancestral genome has
been widely inherited by dogs
throughout East Eurasia. Nature
Communications 15:1680.

The earth is home to many "species"of organisms, generating biodiversity.
Biodiversity has been achieved through aprocess of "speciation," in which one species
is divided into two species, and through aprocess of "adaptation," in which organisms
survive in their habitat. We focus on thefollowing four research areas to elucidate
the mechanisms of adaptation and speciationin organisms. [Speciation]: the speciation ofseven macaque species endemic to Sulawesi
and corals based on genome analysis.
[Adaptation via symbiosis]: the mechanismof adaptation to a new environment throughsymbiosis using the lichen. [Adaptation to
the human environment]: the origin of dogs
and how dogs have adapted to their living
environment with humans based on theancient genomes of Japanese wolves andancient dogs. [Adaptation of vision to lightenvironments]: how organisms have adapted
their vision to different light environments inthe water using fish and reptiles.

Evolutionary Biology

Evolutionary Physiology
16

Yoko Satta

Yohey Terai（2018）Exploring
the Mystery of Biodiversity
DOJIN

17

Faculties

Associate Professor

Zooarchaeology
Email
URL

✉ hongouhm@soken.ac.jp

💻 https://researchmap.jp/6613530/

Expertise 🔍 Zooarchaeology

Keywords 👉 Neolithic, Neolithization, Domestication,

Faunal Remains, Southwest Asia, East Asia
Selected publications
Hongo H et al. (2021)
Beginning of pig
management in Neolithic
China: Comparison ofdomestication processes
between northern andsouthern regions. Animal
Frontiers 11:30-42.
Ervynck A et al. (2001) Born
Free? New Evidence for
the Status of Sus scrofa at
Neolithic Çayönü Tepesi(Southeastern Anatolia,
Turkey). Paléorient 27: 47-73.

Evo-devo Neurobiology
18

Takayuki
Watanabe
Assistant Professor

Laboratory of Evolutionary Developmental Neurobiology
Email
URL

✉ watanabe_takayuki@soken.ac.jp

💻 https://rcies.soken.ac.jp/labs/twatanabe/

Expertise 🔍 neuroethology, molecular evolution

Keywords 👉 neurogenetics, insect social behavior,

behavioral development, cricket
Selected publications
Watanabe T (2019) Evolution of theneural sex-determination system
in insects: does fruitless homolog
regulate neural sexual dimorphism
in basal insects? Insect Mol Biol
28:807-827.
Watanabe T et al. (2018) Immediateearly promoter-driven transgenic
reporter system for neuroethologicalresearches in a hemimetabolous
insect. eNeuro 5:e0061-18.2018.

My research concerns the relationshipbetween humans and the environment,
especially in the aspect of resource
exploitation that shaped the socio-economic
and cultural changes in human history.
Neolithization resulted in one of the mostdrastic shift in the life of humankind. I havebeen carrying out fieldworks to collectdata of animal bone remains excavatedfrom early Neolithic sites in West Asia
to investigate emergence of sedentary
settlements about 15000 years ago andthe process of domestication of plants
and animals that eventually facilitatedthe development of complex societies.
Sedentism and domestication also led toincreasing manipulation of the ecosystem
by humans, which was the beginning of the
global environmental crisis today. We needboth biological and sociocultural pointsof view to understand the coevolutionary
process of humans and animals or plants
in the course of domestication. For thisI promote integrative cooperation ofresearchers of various related fields, suchas archaeology, ancient genome analysis,
environmental sciences, behavioral ecology,
and anthropology.

Many animals, including insects,
dynamically change their body plans on their
way to adulthood through a developmental
process called metamorphosis. The
acquisition of a new body plan throughmetamorphosis requires the reorganization of
the nervous system that controls the bodyafter metamorphosis. The brain ofholometabolous insects show drastic
morphological changes during pupa, which
are required to prepare for adult-specificbehaviors. On the other hand, hemimetabolous
insects, which do not have a pupal stage,
become adults without remarkable structural
reorganization of their nervous systems but
exhibit adult-specific behaviors like courtshipthat they did not exhibit during nymphal
stages. We are using the two-spotted cricket
Gryllus bimaculatus as an experimental modelto understand the molecular mechanisms andfunctional significance of the neural circuit
reorganization that may accompany
metamorphosis. Using neurogenetic
techniques (i.e., transgenesis and genome
editing), we are investigating the molecularand neural basis and developmental
mechanisms of adult-specific and sex-specificsocial behaviors such as male aggression andcourtship behaviors.

Yuuki Watanabe

We investigate the ecology of large fishes
and marine mammals using the “bio-logging”
technique, in which measuring instruments
are attached to the animal's body. By usingstate-of-the-art equipment, we measure not
only the behavior of animals, but also theirsurrounding environment and internal states(body temperature, heart rate, etc.). We also
attach video cameras to the backs of animals
to record “animal-eye” footages and examine
what the animals are doing in the ocean.
Our primary approach is to analyze thedata collected by biologging from fieldwork
combined with data from the literature or
those obtained by other research methods, toexplore the ecological significance (ultimate
causes) that have driven the evolution of
the behavior or physiology of the species inquestion. Our research currently focuseson sharks, other large fishes, and seals. We
conduct fieldwork in Kanagawa (Sagami Bay
near SOKENDAI's Hayama campus), Kochi,
and Okinawa in Japan, and in Taiwan, Canada,
Australia, and Norway outside Japan.

Professor

Marie Ecology Lab
Email
URL

✉ watanabe_yuuki@soken.ac.jp

💻 https://rcies.soken.ac.jp/labs/ywatanabe

Expertise 🔍 Ecology, Marine Biology

Keywords 👉 Biologging, Marine Predators

Selected publications
Watanabe YY andPapastamatiou YP (2023)
Biologging and biotelemetry:
tools for understanding the
lives and environments ofmarine animals. Annu Rev
Anim Biosci 11:247-267.
Watanabe YY et al. (2020)
Ultrahigh foraging ratesof Baikal seals maketiny endemic amphipods
profitable in Lake Baikal.
Proc Natl Acad Sci USA
117:31242-31248.

AtsukoMatsushita

Marine Ecology

Bioarchaeology

Hitomi Hongo

As a research hub for Integrated
Evolutionary Science, we will promote RCIES
in various aspects.

Lecturer

Academic and Research Support group
Email
URL

✉ matsushita_atsuko@soken.ac.jp

💻 https://researchmap.jp/am9p?lang=en
Joint Use of Research Facilities
We support the use of:Confocal laser
microscopes (Nikon, Zeiss), ScanningElectron Microscope (JEOL), andTransmission Electron Microscope (Hitachi)

Mediating
Collaboration
We mediate
collaborative research
especially on evolution.

Obtaining
research funds
We support for
preparing research
grant applications.

PR
We keep appealing
activities of RCIES.

Environmental safety
We take safety measures for research
environments such as laboratories, manage
chemical substances and experimental
equipment, and report on environmental
safety management to surrounding areas.

19

Visit Classes!

Class

Laboratoryof Basic Biology
Macro Biology

TurkeyHasankeyf Höyük site

Hitomi Hongo Associate Professor
Comparing animal
characteristics basedon bone morphology

Class

Marine Animal Ecology
Yuuki Watanabe Professor

use the collection of various animal
W eskeletons,
both modern andarchaeological, as well as cast models ofhumans and rare species, housed in the
Hongo Lab. Students compare the shape ofeach skeletal element in general and some of
the unique morphological characteristics thatcan be used to differentiate species.
Macro Biology lecture covers human
evolution over 6 million years, mainly based on
the morphological changes. Casts of fossil
hominid skeletons are used to see thedifferences in Australopithecines, Homo sp.
and anatomically modern humans.
In the Laboratory of Basic Biology, we
compare postcranial skeletons and teeth ofdifferent groups of mammals, such as
primates, carnivores, herbivores, omnivores,
and rodents, noting the differences that are
related to the animals' diet and locomotion.
We also compare bird and fish skeletons withmammals. Students will be given a bag ofarchaeological animal bone remains toexperience identification of fragmented bones.

How do marine mammals livein the sea?
kind of life do sharks, penguins,
W hatseals, and other marine animals lead in

Hasankeyf Höyük site, Tigris River basin, Turkey (11,500 years ago).

Mixed herds of grazing sheep and goats in modern Turkey.

the sea, out of our sight? In the past, it wastechnically difficult to find out. However, therapid development of "bio-logging" technology
since the end of the 20th century has made it
possible to measure the ecology andphysiology of marine animals in the field. This
technique involves attaching small measuring
devices to the animal's body and measuring
parameters related to the animal's behavior,internal states (body temperature, heart rate,etc.), and surrounding environment. Thanks tothis technique, new discoveries that challenge
conventional wisdom are being made one after
another. For example, frigatebirds, which can
fly over the ocean for months, were shown tosleep while gliding in the air. Baleen whales,such as fin whales, were found to use theirabnormally large mouths to fill their mouths
with more seawater than their own body
volume and ingest fish and krill. Some sharks
and tunas were shown to maintain their bodytemperatures higher than the watertemperature, which is exceptional for fishes,
supporting their exceptional locomotion ability.
In this lecture, I will introduce new discoveries
about the ecology and physiology of marine
animals revealed by biologging and discussed
the ultimate factors that drove such evolution.

White shark (top), Weddell
seal (middle left), loggerhead
turtle (middle right), andAdélie penguin (bottom) withmeasuring devices attached.
The animals collect various
data on their own ecology,
physiology, and environmental
responses.

Watanabe and Papastamatiou (2023) Annu. Rev. Anim. Biosci.
© ArchitectureVIZ | Dreamstime.com

20

21

Graduate life and course work
Student A, field research (zooarchaeology)

Courses

Student life

Time schedule

What are your hobbies?

First year

22 credits[First semester] 10 credits

By obtaining the main
credits in my first andsecond years, I was able
to concentrate more on
my research from mythird year afterwards.

Freshman Course
Micro- and Macro-scopic Biology
Laboratory of Basic Biology
Introduction to the "Biological Science" Sub-thesis
Biostatistics
Evolutionary Behavioral Ecology[Second semester] 3 credits
Science, Technology and Society I(Present: Introduction to Philosophy of Science)

Academic English (Basic) I (Present: Integrative
Evolutionary Science Academic English (Basic) 1)

Third year

10 credits[First semester]Nothing[Second semester] 2 credits
Science, Technology and Society II(Present: Science, Technology and Society）

Environmental Archaeology

Special Seminar Series III (Present: Integrative
Evolutionary Science Special Seminar Series III)Special Seminar Series I (Present: Integrative

Evolutionary Science Special Seminar Series I)

Progress Report I (Present: Integrative Evolutionary

Science Progress Report IIIA & IIIB)

Specific Research III (Present: Dissertation Work in

Fourth year

7 credits[First semester] 1 credits

Specific Research I (Present: Dissertation Work in

Advanced Course ⅩⅨ (Present: Biological Anthropology)

Second year

Science Progress Report IVA & IVB)

[Second semester] 3 credits
Science Academic English (Advance)(Present: Integrative
Evolutionary Science Academic English (Advance) 1)

Specific Research IV (Present: Dissertation Work in
Advanced Studies IVA・IVB)

Fifth year

I sometimes work for curating culturalproperties or take part in excavations.

Do you live alone? Or do you live at yourparent's home or in a shared house?

[First semester][Full year] 8 credits

NothingSpecial Seminar Series II (Present: Integrative[Second semester]

Progress Report II (Present: Integrative Evolutionary
Science Progress Report IIA & IIB)

Specific Research II (Present: Dissertation Work in
Advanced Studies IIA・IIB)

Seminar (occasional)

12:00

Lunch

13:00

Data analysis

NothingșșWhat kind of research do you do?

The ancient use of wild boar in prehistoric
periods by analyzing archaeologicalmaterials excavated from Okinawa.

Writing papers

17:00
18:00
19:00

Go back home

20:00

Arrival, then dinner

21:00

Bathing

22:00

Prepare for tomorrow[Full year] 10 credits
Progress Report IV (Present: Integrative Evolutionary

🍴

14:00

16:00

I do my research at the Okinawa
Prefecture Archaeological Center andanalyze the collected data on campus.
Basically, not much work is done at home.

H

11:00

I live alone.

Where do you do your research?

🚈(by train and bus),
about 30 minutes

15:00

10 credits

Integrative Anthropology
Advanced Course Ⅹ (Present: Genome Biology)

Evolutionary Science Special Seminar Series II)🚿🍴Science Progress Report IVA & IVB)

Specific Research IV (Present: Dissertation Work in
I have a liberal arts backgroundand was unfamiliar with biology.
However, this was taken into
account and I had no problems
earning my credits.

22

Do you have a part-time job?

Progress Report IV (Present: Integrative Evolutionary

Nothing

Commute to the campus

10:00

Nothing[Full year] 6 credits[First semester]

9:00

Meeting with friends orjust lazing around at home.

[Second semester]
11 credits

Wake up

Progress Report III (Present: Integrative Evolutionary

Science Progress Report IA & IB)
Advanced Studies IA・IB)

8:00

How do you spend your days off?

[Full year] 8 credits

Advanced Studies IIIA・IIIB)[Full year] 9 credits

Watching videos, walking

Advanced Studies IVA・IVB)

23:00

Specific Research for Sub-thesis
Total of 60 credits over 5 years

0:00

🛏

Bedtime23

Graduate life and course work
Student B, field research (marine ecology)

Courses

Student life

Time schedule (normal)

Time schedule (fieldwork)

What are your hobbies?

Third year

12 credits

Table tennis, scuba diving(occasionally), watching martial arts

[First semester] 5 credits
Laboratory of Basic Biology
Dissertation Workin Advanced Studies IIIA
Integrative Evolutionary
Science Progress Report IIIA

[Second semester] 5 credits
Integrative Evolutionary
Science Academic English(Advance) 1Life Science & Society
Dissertation Work in
Advanced Studies IIIB
Integrative Evolutionary
Science Progress Report IIIB

How do you spend your days off?

I also took courses thatwere not mandatory (e.g.,

I refresh myself by playing
games and meeting with friends.

Integrative Evolutionary
Science Academic English).

I chose these coursesthat were within my
comfort zone, because
it would be nonsense if I
could not devote enoughtime to my research.

Research Assistant only

[Full year] 2 credits
Integrative Evolutionary Science
Special Seminar Series III

Fourth year

11 credits[First semester] 3 credits

The system was very
helpful in providing
alternative arrangements
when I had to do fieldwork.

Dissertation Work in Advanced Studies IVA
Integrative Evolutionary Science Progress
Report IVA[Second semester] 8 credits
Dissertation Work in Advanced Studies IVB
Integrative Evolutionary Science Progress
Report IVB
Science, Technology and Society
Specific Research for Sub-thesis

Do you live alone? Or do you live at yourparent's home or in a shared house?

Dissertation Work in Advanced Studies VA
Integrative Evolutionary Science Progress
Report VA

Commute to the campus

10:00

Seminar (once a week)

11:00

13:00

by bicycle or bus, 1 hour

🍴

Lunch

Data analysis, writing papers, etc.

ș

14:00

Where do you do your research?
I can usually do research as long as I
have a PC, so I do my research at homeor in a cafe as well as at the campus.

17:00
18:00

🚶🕺

Table tennis
with colleagues

19:00

Total of 29 credits over 3 years

24

0:00

Boarding

0:30

Sleep until morning

8:00

Installation of recording
devices on sharks (onboard)

The ecology of wild sharks byattaching behavior recording
devices (video cameras, etc.) to them.

Go back home

21:00

Dinner, bath

22:00

Reading, etc.

🍴

📖

23:00
0:00

🛏

Bedtime

Ľ

9:00
10:00
11:00
12:00

Return to port

13:00

Lunch

14:00

Break

15:00
16:00
17:00

20:00

🚢

Wake up and prepare
for boarding

16:00[Second semester] 3 credits
Dissertation Work in Advanced Studies VB
Integrative Evolutionary Science Progress
Report VB

H

I live alone.

6 credits[First semester] 3 credits

9:00

23:00

15:00

What kind of research do you do?

Fifth year

Wake up

12:00

Do you have a part-time job?

🚌

8:00

18:00
19:00
20:00
21:00

🍴

☕

Setup of recording devices

🍴

Dinner🛏

Bedtime

22:00

25

Graduate life and course work

Student C, lab research based on experiments and data analysis
I actively participated in
the courses when it suited
my schedule. Faculties
arranged the contents ofcourses for non-experts,
so I didn't have problems.

Courses
First year

Third year

24 credits

10 credits[First semester] 11 credits[First semester] 3 credits

Freshman Course
Micro- and Macro-scopic Biology
Laboratory of Basic Biology
Introduction to the "Biological Science" Sub-thesis
Introduction to Science and Technology Studies
Evolutionary Game Theory
Advanced Course Ⅹ (Present: Population Ecology)
Advanced Course ⅩVI (Present: Biological Anthropology)

Dissertation Work in Advanced Studies IIIA
Integrative Evolutionary Science Progress
Report IIIA

[Second semester] 5 credits
It is easier toconcentrate on researchbecause there are many
intensive short-termcourses, so the numberof class days is small.

Human Genetics
Molecular Evolution
Evolutionary Behavioral Ecology
Advanced Course X(Present: Genome Biology)[Full year] 8 credits
Evolutionary Science Special Seminar Series I)

Progress Report I (Present: Integrative

Evolutionary Science Progress Report IA & IB)

Specific Research I (Present: Dissertation
Work in Advanced Studies IA・IB)[First semester]Nothing[Second semester] 4 credits

Integrative Evolutionary Science
Special Seminar Series III

I took more courses in
the first and second
years to prepare for thebusy research schedulein the upper grades.

Science, Technology and Society I

Time schedule

What are your hobbies?
Shogi, Mahjong, visiting aquariums

8:00

Wake up, breakfast,and preparations

9:00

Commute to the campus

How do you spend your days off?

I often work part-time on
Saturdays and go out to meetwith friends on Sundays.

Seminar (once a week)

12:00

Lunch

13:00

Start experiments

Do you have a part-time job?

I work as an instructor at a laboratoryclass for elementary school students.

14:00[Second semester] 9 credits
Dissertation Work in Advanced Studies IVB
Integrative Evolutionary Science Progress
Report IVB
Science, Technology and Society

Do you live alone? Or do you live at yourparent's home or in a shared house?

16:00
I am married, so I livewith my husband.

Where do you do your research?

(Past: Science, Technology and Society II)

Integrative Evolutionary Science Academic
English (Basic) 1 (Past: Academic English (Basic) I)
Specific Research for Sub-thesis

15:00

Mostly I work at the campus forexperiments. Sometimes I do data
analysis and write papers at home.

🍴

hV
ș

17:00

End experiment

18:00

Paperwork, writing papers,
etc.

19:00

Go back home

20:00

Arrival home, dinner

21:00

Checking papers while
watching cartoon videos, etc.

22:00

Hobby time(Present: Introduction to Philosophy of Science)

Science, Technology and Society II(Present: Science, Technology and Society)

Academic English (Basic) I (Present: Integrative
Evolutionary Science Academic English (Basic) 1)
Advanced Course XX(Present: Evolutionary Developmental Neurobiology)[Full year] 8 credits
Special Seminar Series II(Present: Integrative Evolutionary Science Special Seminar Series II)

Progress Report II(Present: Integrative Evolutionary Science Progress Report IIA & IIB)

Specific Research II(Present: Dissertation Work in Advanced Studies IIA・IIB)

26

Fifth year

(plan) 6 credits

What kind of research do you do?

[First semester] 3 credits
Dissertation Work in Advanced Studies VA
Integrative Evolutionary Science Progress
Report VA[Second semester] 3 credits
Dissertation Work in Advanced Studies VB
Integrative Evolutionary Science Progress
Report VB
Total of 64 credits over 5 years

The evolution of visionin fish from a molecularbiological perspective.

🚈

H

11:00

(plan) 12 credits

Dissertation Work in Advanced Studies IVA
Integrative Evolutionary Science Progress
Report IVA(train, bus), 1 hour

10:00

[Full year] 2 credits[First semester] 3 credits

Special Seminar Series I (Present: Integrative

12 credits

Environmental Archaeology
Biodiversity
Dissertation Work in Advanced Studies IIIB
Integrative Evolutionary Science Progress
Report IIIB

Fourth year

Advanced Course XVISecond year

[Second semester] 5 credits

Student life

🍴

23:00
0:00

Bathing, prepare
for tomorrow

0:30

Bedtime🛏
27

Graduate life and course work

Student D, research in science, technology and society

What are your hobbies?

Courses

Student life

Time schedule

What are your hobbies?

First year

Third year

16 credits

Running

11 credits[First semester] 4 credits[First semester] 9 credits
Freshman Course
Laboratory of Basic Biology
Introduction to the "Biological
Science" Sub-thesis
Dissertation Work in
Advanced Studies IA
Integrative Evolutionary
Science Progress Report IA

I took basic courses
as early as possible sothat I could broaden
my perspective before
starting my Ph.D.
research.

[Second semester] 5 credits
STS and History of Science 1
Introduction to Philosophy of Science
Dissertation Work in Advanced Studies IB
Integrative Evolutionary Science Progress Report IB

Molecular Evolution
Dissertation Work in Advanced Studies IIIA
Integrative Evolutionary Science
Progress Report IIIA

[Second semester] 5 credits
Integrative Evolutionary Science
Academic English (Advance) 1
STS and History of Science 3
Dissertation Work in Advanced Studies IIIB
Integrative Evolutionary Science
Progress Report IIIB

Second year

14 credits[First semester] 5 credits

I also took biology

courses to obtain
Biostatistics
basic knowledge.
Dissertation Workin Advanced Studies IIA
Integrative Evolutionary Science Progress Report IIA[Second semester] 7 credits
STS and History of Science 2Life Science & Society
Science, Technology and Society
Integrative Evolutionary Science Academic English (Basic) 1
Dissertation Work in Advanced Studies IIB
Integrative Evolutionary Science Progress Report IIB[Full year] 2 credits
Integrative Evolutionary Science
Special Seminar Series II

Integrative Evolutionary Science
Special Seminar Series III

Fourth year

8:00

Commute to the campus

9:00

Reading literature

How do you spend your days off?

Visiting bookstores and cafes

10:00
Do you have a part-time job?

11:00

I worked as a cram school teacher
until I received a JSPS fellowship.

[First semester] 4 credits

I took an international
internship to obtain
international experience.

International Internship
Dissertation Workin Advanced Studies IVA
Integrative Evolutionary Science
Progress Report IVA[Second semester] 5 credits
Dissertation Work in Advanced Studies IVB
Integrative Evolutionary Science
Progress Report IVB
Specific Research for Sub-thesis

Fifth year

Do you live alone? Or do you live at yourparent's home or in a shared house?

11 credits

6 credits[First semester] 3 credits
Dissertation Work in Advanced Studies VA
Integrative Evolutionary Science
Progress Report VA[Second semester] 3 credits
Dissertation Work in Advanced Studies VB
Integrative Evolutionary Science
Progress Report VB
Total of 58 credits over 5 years

28

Wake up, breakfast,
preparation

Living alone

Where do you do your research?

I do my research in different places
such as cafes, libraries, and student
rooms, because I keep doing the same
work such as reading and writing.

What kind of research do you do?

The possibilities of scientificexplanations in researchusing machine learning.

ș

🚈

🍴

12:00

Lunch

13:00

Writing reports[Full year] 2 credits[Full year] 2 credits
Integrative Evolutionary Science
Special Seminar Series I

7:00

ș
H

14:00
15:00

Seminar (once a week)

16:00

Break

17:00

Reading group

18:00

Go back home and dinner

19:00

Break

20:00

Paper reading
for seminar

📖

📖

21:00
22:00

Free time

23:00
0:00

🍴

Bedtime🛏29

Student Aids
Both SOKENDAI and Integrative Evolutionary Science Program offer
extensive support systems for students' daily lives and research activities.

1.

Integrative Evolutionary
Science Program Research
Assistant (RA)This support is designed to encourage
outstanding students to participate ineducational and research projects conductedat the Hayama Campus as research assistants
to promote effective educational and research
activities and to cultivate the ability to conduct
research as emerging scholars.
Upon appointment, the RA will work as apart-time employee of SOKENDAI for a
maximum of 7 hours per day, not exceeding 20
hours per week.
In the Integrative Evolutionary Science
Program, the upper limit is 335 hours per year
at 1,600 yen per hour in FY2023, with theintention to provide students with financial
support equivalent to the annual tuition fee toensure that it does not hinder their academic
pursuits. Basically, all new SOKENDAI
students are eligible.

2.

SOKENDAI
Student Dispatch ProgramThis program encourages SOKENDAI
students to seek a short-term research
opportunity abroad and/or a long-term
collaborative research project in and outside
Japan that may lead to their career in the
future. The program follows the educational
goals of SOKENDAI, "advanced specialties andexpertise," "broad perspective," and"international competitiveness," and intends
to financially support such research
opportunities for SOKENDAI students.
Reference URL:

https://www.soken.ac.jp/education/dispatch/sokendai_studentdispatchprogram/

3.

5.

The purpose of the student mobility support
in the Integrative Evolutionary Science
Program is to provide students with advanced
specialized knowledge and abilities that will
enable them to play a leading roleinternationally and to foster researchers withbroad perspectives and advanced researchcapabilities that can be harnessed both
domestically and internationally. This covers
travel costs for presenting the results of a
studentʼs own research at domestic orinternational conferences, conducting research
activities or collecting materials necessary forstudies including doctoral dissertation
research at a research institution, etc.

This support provides full or partial support
for the costs for submission and publication of
papers in journals. The objective is to promoteand encourage students' research activities
and disseminate the accomplishments both
domestically and internationally.

Reference URL:

A laptop computer is lent to students to
support their research activities. Students canuse the accommodation facilities at the
Hayama campus with their supervisor's
permission (with washing machine and shower
facilities) to support their research activities
over the long hours of the day. The number ofstudents is small compared to the number offaculties, so each student is well supported.
In addition, a system is in place for students
to consult specialists in the event of various
problems arising. Detailed support is available
from academic advisors regarding student lifeand research activities, and an external mental
health counselor is available once a month.

Student Mobility Support in
the Integrative Evolutionary
Science Program

https://ies.soken.ac.jp/en_life.html

Reference URL:

https://ies.soken.ac.jp/en_life.html

4.

Student Travel
Expense Subsidies
Travel expense subsidies cover activities forregular courses that promote educational andresearch activities beyond the framework of
SOKENDAIʼs programs and contribute to
SOKENDAIʼs philosophy of fosteringresearchers with internationally-recognized
and advanced research qualities and broad
perspectives in fundamental academic fields.
SOKENDAI will provide subsidies for all or partof expenses in accordance with SOKENDAI
regulations based on applications from thestudents registered in the course. Based on
applications from the students, subsidies will
be paid to the SOKENDAI regular students.

Integrated Evolutionary
Science Program Publication
Support

6.

OthersReference URL:

https://ies.soken.ac.jp/en_life.html

Reference URL:

https://www.soken.ac.jp/en/education/
dispatch/trv_supp/30

31

From Graduate Students

Q5 Do you have any advice for undergraduate students?

Second-year student (D2) majoring in Marine Ecology
Q1 What motivated you to enroll at SOKENDAI?

The highly productive research environment is theprimary motivation. Firstly, I have the opportunity toreceive direct supervision from renowned researchers in
the field of animal behavior and conduct research withina rich research environment. Moreover, all the essential
equipment and facilities required for my research are readily
accessible. Furthermore, the five-year program enables me
to consistently concentrate on one research theme, which I
believe is especially beneficial for graduate students.

Q2 What are the benefits ofenrolling at SOKENDAI?

At SOKENDAI, one of the benefits is the opportunity toreceive lectures from experts in various fields such as
genetics, neuroscience, and behavioral studies on thetheme of "evolution." Unlike many universities wherestudents typically interact with professors in closely
related fields, here at SOKENDAI, we have the opportunity
to receive guidance and insights from top scholars acrossdiverse disciplines, which is truly exciting.

Fourth-year doctoral student (D4) majoring in Mathematical Biology
Q1 What motivated you to enroll at SOKENDAI?

My specialization is mathematical modeling in ecology
and evolutionary biology. Although I gained fundamental
knowledge in biology during my master's degree, I felt my
proficiency in mathematics and physics was insufficient.
Therefore, I aimed to pursue this specialization to actively
engage in daily discussions with my current supervisor,
who is among the top experts in mathematical biology.

Q2 What are the benefits ofenrolling at SOKENDAI?

Our campus, situated atop a small hill, provides anenvironment conducive to focused research. Additionally,
being located near Zushi and Yokosuka allows easy
access to Tokyo and Kanagawa, as well as convenienttransportation links to shinkansen and airports, facilitating
nationwide travel. Furthermore, the low barriers between
research labs foster a sense of community, with numerous
events such as welcome parties for new students andmochitsuki (rice pounding) gatherings involving bothstudents and faculty members.

Q3 How do you typically spend your days off?

wake up early in the morning and head to the publicbath or go for a run along the seaside. It's like spending a
day off just like my grandma does. Haha.

If you learn statistics concurrently with data collection
and analysis, you may realize that there are more
appropriate analysis methods than the ones you learned
initially. This realization may lead you to redo everythingfrom scratch. I recommend starting early, even after theentrance exams.

Q4 How do you conduct your research?

Do you have a message of encouragement
for those hoping to enroll?

Since my research primarily involves data analysis, I
mainly work from home.

The entrance exams are just around the corner. Goodluck!

Q3 How do you typically spend your days off?
I am a member of a community orchestra and regularly
participate in instrumental performances. When a concert
is approaching, I dedicate myself to practicing for it, butotherwise, I make a point to rest as much as possible andrefrain from engaging too much in research.

Q5 Do you have any advice for undergraduate students?
One thing I aim to improve is developing a habit ofreading. Without a consistent reading habit, I sometimes
find it daunting to go through research papers.

Do you have a message of encouragement
for those hoping to enroll?

Q4 How do you conduct your research?

I ensure to come to campus three days a week toprevent myself from slacking off with remote work. On
the remaining days, I either work remotely or conduct
research at other research institutions.

We only live once, so it's worth considering immersing
yourself in research on a topic you're passionate about. If
you feel a strong connection with your potential supervisor,or find the research environment appealing, we would bedelighted to welcome you into our program. Both students
and faculty are eager to have you join us!

Q3 How do you typically spend your days off?

Q5 Do you have any advice for undergraduate students?

When I'm at home, I prioritize maximizing sleep and thenengage in activities such as watching videos, anime, or myfavorite content, as well as playing games. I aim to spend
as much time as possible in bed. When I go out, I enjoy avariety of activities including walking, shopping, visiting
aquariums, shrines and temples, and attending live events.
My level of activity varies greatly from day to day.

・Studying English: While accumulating knowledge ofFourth-year doctoral student (D4) majoring in Marine molecular biology
Q1 What motivated you to enroll at SOKENDAI?

- I've found that the research program provides a highlevel of autonomy. With professors from diverse fields
available, there's a broad range of feasible research
topics and experiments to explore.
- I'm particularly drawn to evolutionary behavioral
ecology, where I can observe animal behavior to uncoverits significance and develop general theories applicable
to multiple organisms.
- I was confident that I could pursue my passion forstudying sea slugs and elucidating organism behavior
from various perspectives.

32

Q2 What are the benefits ofenrolling at SOKENDAI?

- The program offers a wide range of feasible research
opportunities, providing significant freedom to choose
topics without being confined to strict boundaries.
- There is ample research funding available, and thefacilities are well-equipped.
- The close relationship between students and professors
allows for active discussions and consultations regarding
research topics, and everyone is approachable andfriendly.
- The program fosters a vibrant community among
students, leading to enjoyable interactions andexchanges.

Q4 How do you conduct your research?

My activities vary according to the life cycle of theresearch subject. From spring to summer, I engage
in fieldwork such as collecting marine organisms andconducting dissections on campus. From autumn to winter,
I focus on molecular biology experiments and data analysis
on campus. Occasionally, I may also work from home.

vocabulary, grammar, and other aspects is important, I
wish I had focused more on speaking English and become
more accustomed to it.
・(Even though I don't remember anything anymore): Since
I chose physics in high school, I think it would have been
better to learn the basics of biology, including high schoollevel, early on.
・I would have trained myself to be able to collect researchorganisms.

Do you have a message of encouragement
for those hoping to enroll?

I believe SOKENDAI provides an unparalleled andfantastic environment for conducting research! Let's
enjoy our lives as researchers together! I look forward tomeeting everyone!

33

Q & A session with first-year students!

Q & A session with prospective students!

We asked ﬁrst-year students about SOKENDAI!
Here is a summary of what ﬁrst-year students want to say!

Here is a summary of frequently asked questions from prospective students!

Q 1

Q 4

Q 1

What did you do to prepare
for entrance exams?

What impressions did you
have about the sub-thesis
before and after enrollment?

Is it necessary to choose a supervisor
at the time of entrance exams?

A 4

A 1

A 1
English: I practiced TOEFL-ITP practice tests,
studied materials for TOEIC, and read books
recommended by teachers.
Specialized subjects: I read books written byteachers I hoped to be instructed by, as well as books
recommended by them. I read "Molecular Biology of
the Cell" by Albert et al., "Campbell Biology" byCampbell et al., and "An Introduction to Behavioral
Ecology" by Davies et al. Additionally, I practiced
repeatedly presenting my research topic.

Q 2
When did you decide on
your research topic?

A 2
Some people already had a research topic theywanted to pursue, while others decided on a roughresearch topic around the winter of their third yearof undergraduate studies. Some decided on theirresearch topic around May after enrollment. The
timing of deciding on a research topic varies fromperson to person.

Some students felt that they needed to conduct
research more thoroughly and to think deeply about
their topics more than they had anticipated before
enrollment. They also mentioned that it provided
an opportunity to consider societal implications as
a researcher and to reevaluate the interdisciplinary
aspects of their main thesis. In the Integrated
Evolutionary Science Course, there were also
opinions that conducting interviews was technicallychallenging.

Q 5
What are the good pointsof our course (major)?

A 5
One of the best aspects is the close relationshipbetween professors and students, making it easy toconsult even with professors from other fields! Bothprofessors and students have ample time, making
it easy to approach them for discussions. Since
most classes are intense lectures, it's easy to focus
on research! Regular seminars featuring external
speakers are held, providing opportunities to hear
about various research topics!

Q 2
No, it's not necessary!
You can enter without selecting a supervisor. Afterenrollment, you can explore different supervisors
through rotations and make a decision around
November, before the Progress. You have theopportunity to visit multiple labs before making yourchoice.

Q 3

What is the relationship likeamong the faculties andstudents within the course?

A 2
The relationship among students,
instructors, and postdoctoral fellows
is excellent.
While students often organize parties andgatherings, there are also events where professors
and postdocs frequently participate. Participation is
optional, so it's okay if you don't feel like joining.

Are there any fun events?

A 3
Absolutely!
Participation is voluntary, so feel free
to join in if you'd like. Let's have a greattime together! Also, if you have any ideas
for new events, we'd love to hear them!

Q 3
Did you visit labs before you apply?

A 3
All of the first-year students I asked had visited
candidate labs at the Hayama Campus. While it's
possible to contact professors directly to arrange
lab visits, you can also visit labs during information
sessions or open campus events held at the Hayama
Campus! Some students also participated in
information sessions for other departments (courses)
at SOKENDAI online!

34

Q 6
Do students hang out
together outside of classes?

A 6
Among peers, we sometimes go to movies, horseraces, aquariums, and restaurants together. We also
participate in student-led events held on campus,
where we interact not only with our peers but alsowith seniors.

35

From Alumni
1

XIAYIREXIAOKAITI
Degree obtainedin 2023 September
Current occupation

Assistant researcher,
Institute of Archaeology,
Chinese Academy of Social Sciences
Career trajectory from post-graduation to present
Current position since 2023

Research topic conducted at SOKENDAIMy PhD research focused on the analysis of dog
remains from archaeological sites as dog was the
only animal domesticated by hunter-gatherers before
Neolithic period, and established close relationships
with humans. My work aims to reveal the origin andearly stages of dog evolution by genomic analysis ofancient DNA (aDNA) preserved in dog remains fromdifferent periods in East Asia which would ultimately
help us to reconstruct evolutionary process of dogs andhuman-animal relationships.
Memories at SOKENDAI

I had such a very wonderful time during my stay withthe excellent guidance, great support, and friendly helpthat I received from all the members of the Department
of Evolutionary Studies of Biosystem, SOKENDAI. My
accomplishment would not have been possible without them.
Reasons for pursuing your current profession

I was sponsored by the scholarship (MEXT) for doctorate
study and was very fortunate to have the opportunity
to apply for this position at the most prestigious
institute for Archaeological research in China after thegraduation. With more attention given to the applicationof scientific methods in archaeological research, theinstitute established the Center of Archaeological
Sciences where I can apply the newest aDNA extraction
method and the genome analysis method that I havelearned during my PhD at SOKENDAI.
A few words to prospective students

SOKENDAI is no doubt a great place where you canlearn how to do research and become a researcher.
It offers a cutting-edge and very relaxing research
environment, and has a great finical supporting system
for student. It is a place where my research life started,and I really appreciate for all the support that I havereceived from SOKENDAI. And I am looking forward tocarrying out collaborative research with SOKENDAI.

36

2

3

Career paths for degree holders

Naoko Kato-Nitta
Degree obtainedin 2012 March
Current occupation

Associate Professor,
J. F. Oberlin University
Career trajectory from post-graduation to present
2016-2016 Researcher, Institute of Health and Sports Sciences,
University of Tsukuba
2016-2017 Researcher, College of Agriculture, Ibaraki University
2017-2019 Project Researcher, Joint Support-Center for Data
Science Research/The Institute of Statistical Mathematics,
Research Organization of Information and Systems
2019-2021 Project Assistant Professor, Joint Support-Center for Data
Science Research/The Institute of Statistical Mathematics,
Research Organization of Information and Systems
2021-2023 Project Associate Professor, Joint Support-Center for Data
Science Research/The Institute of Statistical Mathematics,
Research Organization of Information and Systems
Current position since 2023

Research topic conducted at SOKENDAI

Science, Technology and Society
Memories at SOKENDAIIn the fourth year of my five-year doctoral course, I had
to give a presentation to obtain competitive funding fromthe university. My doctoral research was in a difficult
situation at first, as if I was walking in a dark tunnel, butjust before the presentation there was an opportunitythat opened my eyes and I was able to get out of thetunnel. As a result, I was able to present with confidence
on the day and succeeded in obtaining the funding for
my doctoral research. President Takahata, who attended
the presentation, said: "When I heard your presentation,
I thought, 'Oh, Kato-san, you've taken off from the land'".
He talked to me as such just before I completed mydoctoral course, which has encouraged me since then.
Reasons for pursuing your current profession

I was enrolled in SOKENDAI after working outsideacademia and decided to pursue a career as a researcher
because I truly enjoyed research at SOKENDAI. Seminars
and other programs in SOKENDAI trained me to approach
my own research themes from a broad perspective
and with original ideas, without being bound by existing
frameworks. I believe this experience is my foundation
to continue producing research attainments as anindependent researcher after obtaining the Ph.D. degree.
A few words to prospective students

The faculties work together to support students infostering the ability to continue challenging themselveswith original research. SOKENDAI is a unique graduate
school where students can get a distinctive education.

Other

Masato Yamamichi

PrivatesectorDegree obtainedin 2012 March
Current occupation

Associate Professor, National Institute of Genetics /SOKENDAI

Research topic conducted at SOKENDAI・Theory of population dynamics driven by prey rapid

evolution and phenotypic plasticity
・Theory of single-gene speciation promoted by
predators
・Inference of the process of human-chimpanzee
speciation
・Research object biases of conservation ecology inJapan
Memories at SOKENDAI

During my time at SOKENDAI, I was able to receive
support from various faculties and engaged in a broad
spectrum of theoretical and empirical research. I
also actively participated in academic conferences
and summer schools. Furthermore, I had a wealth ofdiverse international experiences, such as spending
several months at Cornell University and attending
academic exchange seminars with foreign universities.
Reasons for pursuing your current profession

Through my various experiences at SOKENDAI, I
realized the importance of conducting research abroadand combining mathematical ecology, population
genetics, and theoretical and empirical approaches.
As a result, after conducting research in the USA andAustralia, I moved to my current position to further
develop my research.
A few words to prospective students

I hope you enjoy your research utilizing the abundantresources of SOKENDAI!

(domestic)

Researcher of university/
research institution(overseas)

Faculty of university/
research institution(overseas)

Researcher of university/
research institution

Career trajectory from post-graduation to present
2012-2014 JSPS Postdoctoral Fellow for Research
Abroad, Cornell University (USA)
2014-2017 Program-Specific Assistant Professor, Hakubi
Center for Advanced Research/Center for
Ecological Research, Kyoto University
2017-2020 Lecturer, Department of General Systems
Studies, The University of Tokyo
2020-2023 Senior Lecturer, School of Biological Sciences,
The University of Queensland (Australia)
Current position since 2023

Faculty of university/
research institution(domestic)Awards received by graduates
JSPS Ikushi Prize
February 2022
February 2018

Takahiro Sakamoto, 13th JSPS Ikushi Prize
Shiho Kariyazono, 8th JSPS Ikushi Prize

SOKENDAI Award, Nagakura Research
Incentive Award, SOKENDAI Future Scientist
Award, SOKENDAI Research Award
March 2023
March 2021
December 2018
April 2017
October 2016
October 2016

Takahiro Sakamoto, 10th SOKENDAI Award
Masato Sato, 6th SOKENDAI Award
Shiho Kariyazono, 23rd Nagakura Research
Incentive Award
Takahiro Kato, Sokendai Future Scientist
Award
Kohei Takeda, 21st Nagakura Research
Incentive Award
May Masahito Morita, SOKENDAI Research
Award

Conference Poster Award
and Oral Presentation Award
September 2022 Yusuke Kuwano

Best Poster Award 32nd Annual Meeting of
the Japanese Society for Mathematical Biology
November 2021 Takahiro Sakamoto
BP Award 93rd Annual Meeting of the
Genetics Society of Japan
August 2018
Takashi Seiko
Best Oral Presentation Award 20th Annual
Meeting of the Evolutionary Society of Japan
October 2016
Takahiro Kato
Poster Award 2016 Meeting of the JapaneseOrnithological Society
September 2016 Yuu Utsumi
Poster Award 26th Annual Meeting of theJapanese Society for Mathematical Biology
September 2016 Takahiro Kato
Poster Award 2016 Annual Meeting of theJapanese Society for Ornithology
October 2015
Gaku Oya
Poster Award 2015 Annual Meeting of theJapanese Society for Mathematical Biology
December 2014 Tokiho Akiyama
Best Presentation Award 70th Annual
Meeting of the Japanese Society for
Physiological Anthropology

37

About RCIES
About

Collaboration
As the only research center in Japan with"evolution" at its core, the center aims tocreate a new academic field of "Integrated
Evolutionary Science" in collaboration withdomestic and overseas research institutions.
The word "evolution" evokes the evolution ofliving organisms, but technology, culture, andsociety also evolve.
We consider evolution in such a broad sense
and try to address how the system oforganisms was created and changed in the 3.8
billion years-long history of life, how humanactivities (society, psychology, language,

Organizational
Structure

culture, etc.) have changed, how global
problems in the Anthropocene progress, andwhat possible solutions can becomprehensively examined from theperspective of evolution. The Research Center
for Integrative Evolutionary Science thus aims
to reconsider the concept of "evolution" andcreate a new research field "Integrated
Evolutionary Science", which not only
advances the knowledge system of biology but
also incorporates the findings of evolutionary
science into human understanding andsolutions to social issues.

Divisions

RCIES promotes evolutionary studies by
providing various levels of collaboration toresearchers, from giving simple one-time
advice or frequent consultation to prolonged
collaboration (with members in the center)
and, if appropriate, we may also introduce
some experts (both domestic andinternational) who may assist your research
project.

Joint-usage Facilities

Director
RCIES actively promotes the joint use of
research equipment to enhance collaborative
research The equipment includes a ScanningElectron Microscope, Transmission Electron
Microscope, and Confocal Laser Scanning
Microscope.

Executive Board

Faculty Committee

Division of Integrative
Human Science

Division of
Evolutionary Diversity

Division of
Evolutionary Studies
of Complex Systems

Board Member
Director: Prof. Hideki Innan
Deputy Director: Prof. Naoki Irie
Steering Committee: Prof. Hideki Innan (Chair)Prof. Yoko Satta Prof. Naoki Irie
Prof. Nobuyuki Kutsukake Prof. Akira Sasaki
Prof. Yuuki Watanabe Prof. Takehiko Kobayashi (External)
Distinguished Prof. Tetsu Sato (External) Prof. Toru Miura (External)
Emeritus Prof. Yoh Iwasa (External)
Distinguished Prof. Kentaro Arikawa (Observer)
Assoc. Prof. Kaori Iida (Observer)
38

Scanning Electron Microscope

Transmission Electron
Microscope

Communications with Other Institutes
RCIES promotes communications with otherinstitutions. For example, student exchange
meetings with Misaki Marine Biological Station(MMBS), the University of Tokyo have been
held every year.
In FY2022, a poster presentation was held atthe Hayama Campus to deepen exchanges. In
FY2023, oral presentations were held the
MMBS.

39

View of Sagami Bay from the Research Center for Integrative Evolutionary Science.

Access & Contact

Detailed
Access Routes

The Graduate University for Advanced
Studies, SOKENDAI

Research Center for Integrative
Evolutionary Science
OdawaraShonanVillageResearch Center for Integrative
Evolutionary Science

Shin-Yokohama

https://www.soken.ac.jp/access/Kamakura
Ofuna

Zushi/
HayamaShinagawa

Zushi
Yokohama
Kanazawa
Hakkei
ShioiriJR
KeikyuBus
Walk
Highway bus

Yokosuka Chuo

The Graduate University for Advanced Studies,
SOKENDAI

KeikyuKamataTokyo

NaritaAirportAddress: Shonan Village, Hayama,
Kanagawa, 240-0193, Japan
Research Center for Integrative
Evolutionary Science
The Graduate University for
Advanced Studies
Tel:+81-468581577 or +81-468581595
E-mail: hayamajimu@ml.soken.ac.jp

Haneda Airport

Contributed by: Misa Osada, Sayaka Chiku, Yuka Yamada
Editing: Public Relations Committee, Research Center for
Integrative Evolutionary Science
Illustration by Yo Hosoyamada
Design by Hosoyamada Design officePublished in July 2024／Translated in June 2024