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Kosuke Teshima Last modified date：2022.01.07

Associate Professor / Dynamic biology
Department of Biology
Faculty of Sciences


Graduate School
Department of Systems Life Sciences
Graduate School of Systems Life Sciences
Department of Biology
Graduate School of Sciences
Undergraduate School
Department of Biology
School of Sciences


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Homepage
https://kyushu-u.pure.elsevier.com/en/persons/kosuke-teshima
　Reseacher Profiling Tool　Kyushu University Pure
Academic Degree
Ph.D.
Country of degree conferring institution (Overseas)
No
Field of Specialization
Population Genetics, Population Genomics
ORCID(Open Researcher and Contributor ID)
0000-0003-4854-1060
Total Priod of education and research career in the foreign country
04years00months
Research
Research Interests
  • population genetics for continuously distributing species
    keyword : population genetics, simulation, continuous distribution
    2019.04～2021.06.
  • My research interest is to make inferences on evolutionary history of organisms based on genome sequence data.
    keyword : population genetics, molecular evolution, genomics, evolution
    2011.08～2012.06.
Academic Activities
Reports
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Papers
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1. Kotaro Dokan, Sayu Kawamura, Kosuke M Teshima, Effects of single nucleotide polymorphism ascertainment on population structure inferences., G3 (Bethesda, Md.), 10.1093/g3journal/jkab128, 2021.04, Single nucleotide polymorphism (SNP) data are widely used in research on natural populations. Although they are useful, SNP genotyping data are known to contain bias, normally referred to as ascertainment bias, because they are conditioned by already confirmed variants. This bias is introduced during the genotyping process, including the selection of populations for novel SNP discovery and the number of individuals involved in the discovery panel and selection of SNP markers. It is widely recognized that ascertainment bias can cause inaccurate inferences in population genetics and several methods to address these bias issues have been proposed. However, especially in natural populations, it is not always possible to apply an ideal ascertainment scheme because natural populations tend to have complex structures and histories. In addition, it was not fully assessed if ascertainment bias has the same effect on different types of population structure. Here we examine the effects of bias produced during the selection of population for SNP discovery and consequent SNP marker selection processes under three demographic models: the island, stepping-stone, and population split models. Results show that site frequency spectra and summary statistics contain biases that depend on the joint effect of population structure and ascertainment schemes. Additionally, population structure inferences are also affected by ascertainment bias. Based on these results, it is recommended to evaluate the validity of the ascertainment strategy prior to the actual typing process because the direction and extent of ascertainment bias vary depending on several factors..
2. Teshima KM, Innan H, The coalescent with selection on copy number variants, Genetics, 190, 3, 1077-86, 2012.05, We develop a coalescent-based simulation tool to generate patterns of single nucleotide polymorphisms (SNPs) in a wide region encompassing both the original and duplicated genes. Selection on the new duplicated copy and interlocus gene conversion between the two copies are incorporated. This simulation enables us to explore how selection on duplicated copies affects the pattern of SNPs. The fixation of an advantageous duplicated copy causes a strong reduction in polymorphism not only in the duplicated copy but also in its flanking regions, which is a typical signature of a selective sweep by positive selection. After fixation, polymorphism gradually increases by accumulating neutral mutations and eventually reaches the equilibrium value if there is no gene conversion. When gene conversion is active, the number of SNPs in the duplicated copy quickly increases by transferring SNPs from the original copy; therefore, the time when we can recognize the signature of selection is decreased. Because this effect of gene conversion is restricted only to the duplicated region, more power to detect selection is expected if a flanking region to the duplicated copy is used..
Works, Software and Database
1.
[URL].
Membership in Academic Society
  • SOCIETY OF EVOLUTIONARY STUDIES, JAPAN


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