TOQUE's page:

Welcome to TOQUE's Page

Fri, 19 Jun 2026 09:02:40 +0900

TOQUE, Yukihiko Toquenaga, is an associate professor in the Institute of Life and Environmental Sciences, Univ. Tsukuba, where he teaches ecology, statistics, and computer programming as well as theoretical biology. He specializes in population biology using a wide range of materials: natural communities of egrets and herons, laboratory populations of bean weevils, natural populations of bumblebees, and digital bugs living in computers. With these materials, he asks the reason why some organisms live in groups, whereas others tend to live solitarily. He is often described as a theoretician, but he himself thinks that he is predominantly a scientific field worker. He is somehow good at capturing wild adult egrets and herons with his hands. The fate of the radio-tagged Cattle Egret in the above photo is described in here. Please read the top seven articles in Publications for further details.

A Primer for Theoretical Biology II

Mon, 01 Jul 2024 14:25:08 +0900

Lecture Note of Primer for Theoretical Biology II: Popular Mathematics for Biological Sciences.

Please click the following link: PTB2

Theoretical Population Genetics

Tue, 02 Apr 2024 08:23:18 +0900

Lecture Note of Theoretical Population Genetics: Lecture on the dark side of population genetics.

This lecture is now closed. It will be reopened at the autumn C semester in 2025.

TFEL

Tue, 02 Apr 2024 08:22:48 +0900

Theoretical Field Ecology Lab. was reopened in 2015 at Gozenyama, Ibaraki Pref. Please visit gozenmt for details.

In 2016, 2017 and 2018, it was held at Tome Forest Park. Please visit tomef for details. The aerial video was taken on 01OCT2016 with Parrot Bebop.
Click Here

From 2019 to 2021, TFEL will be held at Satomi Park. Please access 3103 for details.

During the Covid-19 disaster, TFEL was held hybrid mode of remote and field (near the Lake Kasumigaura) experiences. In 2023, TFEL was held at Satomi.

Programming I

Tue, 02 Apr 2024 08:19:36 +0900

Lecture Note for Programing I: This lecture will enable you to achieve the following equation: mater data x program = desired data. You will also learn individual based modeling with which you can realize your biological delusions.

Please click the following link: PRG1

Theoretical Ecology

Tue, 02 Apr 2024 08:19:04 +0900

Lecture Note for Theoretical Ecology: Introducing Experimental Ecology for Theoretical Understanding.

Please click the following link: TE

Animal Ecology I

Tue, 02 Apr 2024 08:18:39 +0900

Lecture Note of Animal Ecology I: Lecture on population and behavioural ecology of animals .

Please click the following link: ANIECOL

Mathematical Biology II

Thu, 28 Sep 2023 15:43:44 +0900

Lecture Note of Biological Mathematics III: Lecture on the dark side of statistics.

Please click the following link: MB2

Ringreads

Tue, 08 Jun 2021 15:02:09 +0900

The followings are R and Ruby scrips for "The Evidential Statistics of Genetic Assembly: Bootstrapping a Reference Sequence." You can download the scripts by clicking the file names. Please read the header information of each file for instruction.

Random read generator from a circular reference w/o any errors

Assemble procedure for each assembly programs

gpuga

You can install gpuga by hitting "R CMD INSTALL gauge_0.0.1.tar.gz" in your terminal window.

Tapio's Talk

Mon, 02 Mar 2020 14:03:53 +0900

This is the Tapio's Talk at Eiko Graduation Ceremony on 29FEB2020.

tapiostalkS.mp4

Collective Philopatry

Thu, 07 Mar 2019 14:38:20 +0900

More than 30 years observation revealed that herons and egrets tend to form their colonies at proximity to the previous locations.
Collective Philopatry

BioECafe Materials

Tue, 25 Dec 2018 13:20:46 +0900

These png files are materials for TOQUE's BioECafe talk. The copyright of those illustrations are reserved to TOQUE.

Bibis.png
Bibis2.png
conscr.png
iQs.png
nn.png
skagiver1.3.png
bibisfrog.png
fours.png
la.biol.png
radiotag.png
wellcontest.png
incolony.png
la.g30.png
sagimai.png

Graduation Thesis

Mon, 25 Jun 2018 16:25:46 +0900

ToqueHiko1986.pdf is the graduation thesis by Toquenaga and Hikosaka.

Tenaho

Fri, 06 Oct 2017 18:05:39 +0900

Tenaho demos

TQReport

Fri, 16 Jun 2017 12:15:26 +0900

Our mission is very simple: creating attractive and effective website for CBS.

IkimonGO

Thu, 18 May 2017 17:45:25 +0900

The manual for IkimonGO is here.

Skysurfer Real!

Mon, 15 May 2017 10:21:40 +0900

This is an invitation for helping the last Skysurfer who takes areal photos with a radio controlled vehicle.
Please click here for details.

Mandala of Statistics

Wed, 10 May 2017 13:16:07 +0900

I organised an international symposium "Bayesian, Fisherian, error, and evidential statistical approaches for population ecology" in 2014. This is a preface of the special issue of the symposium. Please visit http://link.springer.com/article/10.1007/s10144-015-0532-z.

Site fidelity vs. habitat preference

Wed, 10 May 2017 13:08:37 +0900

We found the change in relative importance between site fidelity and habitat preference in the course of colony formation over decades. Please visit http://onlinelibrary.wiley.com/doi/10.1111/jav.01255/full.

Scale Adaptation

Wed, 10 May 2017 12:50:48 +0900

We found that herons and egrets can adjust scales for searching colony sites at habitats of different landscape complexities. Please visit http://www.sciencedirect.com/science/article/pii/S1476945X15000951

Plot by Grey Heorns

Wed, 10 May 2017 12:45:41 +0900

We found that Grey Herons have played important roles for heronry persistence as well as formation. Please visit http://www.bioone.org/doi/full/10.1675/063.037.0403.

Egrets on Random Forest

Wed, 10 May 2017 12:40:56 +0900

We applied Random Forest, a classification technique to extract important factors for heronry formation.
Please visit http://link.springer.com/article/10.1007/s11284-014-1147-0.

Lab. Assignment

Mon, 16 Jan 2017 16:28:52 +0900

This is a link to the Lab. assignment system for Colleges of Biological Sciences. Please hit here .

A Little Egret mated with a Chinese Pond Heron

Sun, 21 Feb 2016 17:43:20 +0900

Supplementary Videos for the following paper: Natural Hybridization between a Little Egret (Egretta garzetta)
and a Chinese Pond Heron (Ardeola bacchus) in Japan

Mashiko M., M. Fujioka, K. Moriya, T. Hagimoto, M. Yamagchi and Y. Toquenaga
Waterbirds 35(1): 160-163 (2012).

Nest Building, 20sec., 732K (click here to play):
A Little Egret with a stick in its bill flew to a bamboo thicket, where a Chinese Pond Heron was sitting. The Chinese Pond Heron received the stick from the Little Egret and placed it in its sitting position, a typical nest-building behavior, or `tremble-shaving.' Video recorded on 9 Jun. 2010.

mSLCA

Sun, 21 Feb 2016 17:16:44 +0900

R scripts for mSLCA

Yukihiko TOQUENAGA
Doctoral Program in Biological Sciences, University of Tsukuba, JAPAN
last modified on 16 Mar. 2013

mSLCA.r is a R script that analyses full-sib structures of genetic polymorphic data based on the mSLCA algorithm (Kokuvo et al. 2007 Env. Entomol. 36(6): 1523-1528).

Assume that you have a data file named "YourData." The data file should consist of lines each of which contains an individual ID followed by genotypes for examined loci. Lines starts with '#' are taken as comment lines. Please see the example data files (TORAall-6loc.txt and mpK5loc.txt).

ICCS

Sun, 21 Feb 2016 17:14:08 +0900

Critical States of Fitness Landscapes

Yukihiko TOQUENAGA
Doctoral Program in Biological Sciences, University of Tsukuba, JAPAN

The following files are submitted and revised as an article for InterJournal (ICCS 2000 at Nashua, NH).

LaTeX file (csfl.tex)
BibTeX source file (csfl.bib)
postscript file (csfl.ps)
archived figures(figs.tgz)

If you want every thing at once, please try the following file.

Archived all files (revised.tgz)

If you have any trouble to obtain the above files, please make contact with toque@biol.tsukuba.ac.jp.

W3T2T2

Sun, 21 Feb 2016 17:12:55 +0900

You can transform your TOEFUL or TOIEC scores to the corresponding English score for the entrance examination of the Graduate School of Environmental Sciences, University of Tsukuba. This page depends on transform.rb, a subroutine for the T2T ver.1.9., which requires toeflp2ci.dat for score conversion.

Click W3T2T2 for using W3T2T2.

10 Years Dynamics of Heronries

Sun, 21 Feb 2016 17:08:06 +0900

MIYUKI MASHIKO & YUKIHIKO TOQUENAGA
FORKTAIL 29 (2013): 71–77

Download pdf of this article

Long-term population dynamics of colonial herons and egrets are well documented in Europe and the USA, but not in East and South-East Asia. Here the population dynamics of mixed-species colonies from 2002 to 2011 in Ibaraki prefecture, east Kanto, Japan, are reported. From censuses based on a combination of aerial and ground surveys, the number of breeding colonies was found to vary from 15 to 20. The population dynamics of Great Egret Casmerodius albus and Black-crowned Night Heron Nycticorax nycticorax remained relatively constant, while Grey Heron Ardea cinerea and Intermediate Egret Mesophoyx intermedia increased, but Little Egret Egretta garzetta and Cattle Egret Bubulcus ibis decreased. When data for the six species were combined, the sum of their populations was almost constant, but variation increased in colony size, species composition ratio and the number of years that individual colonies existed. The population of colonies typically ranged from 200 to 2,000 individuals up to 2004, but smaller (under 200 individuals) and larger (over 2,000 individuals) colonies appeared after 2006. Increased variation in the number of consecutive years colonies existed was closely related to increased variation in colony size. Increased variation in species composition ratios in colonies was not a by-product of the increased variation in colony size, and the occurrence of colonies dominated by Grey Heron, Intermediate Egret or Black-crowned Night Heron after 2006 played an important role in the structural changes of mixed-species colonies.

WWWBLAST

Sun, 21 Feb 2016 17:06:37 +0900

Click WWWBLAST for using BLAST server.

ToquEnglish

Sun, 21 Feb 2016 17:01:40 +0900