Different population size change and migration histories created genetic diversity of three oaks in Tokai region, central Japan

Tamaki, Ichiro; Obora, Tomohiro; Ohsawa, Takafumi; Matsumoto, Asako; Saito, Yoko; Ide, Yuji

doi:10.1007/s10265-021-01323-2

Cited by 6 publications

(7 citation statements)

References 72 publications

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“…LGM. This result may imply that their current distribution may have been largely unaffected by the Quaternary glacial-interglacial oscillations that contributed to genetic variation and geographic adequacy (Han et al, 2020;Tamaki et al, 2018Tamaki et al, , 2021. We suggest that the strong cold tolerance of Z. tyaihyonii made it possible to avoid forcing the southern retreat of the distribution range by climate cooling during glacial periods.…”

Section: Discussionmentioning

confidence: 84%

“…The population genetic structure for a given plant species could be influenced by local differences in various extrinsic factors, such as availability of pollinators (Han et al, 2023 ), seed dispersers (Calviño‐Cancela et al, 2012 ), soil components (Nagasawa et al, 2020 ; Yamamoto et al, 2020 ), and climate conditions (Bisbing et al, 2021 ; Galliart et al, 2019 ). The degree of gene flow among populations is also considered a primary factor in shaping the population genetic structure (Tamaki et al, 2021 ). Although the relative importance of each factor may spatiotemporally change, the patterns of genetic differentiation observed in the majority of plants reflect historical, rather than current factors, particularly in East Asia (e.g., Cho et al, 2020 ; Han et al, 2020 ; Kikuchi & Osone, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

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The genetic structure and demographic history of Zabelia tyaihyonii, endemic to Korean limestone karst forests, based on genome‐wide SNP markers

Choi

Han

Wojciechowski

et al. 2023

Ecology and Evolution

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Section: Discussionmentioning

confidence: 84%

Section: Introductionmentioning

confidence: 99%

The genetic structure and demographic history of Zabelia tyaihyonii, endemic to Korean limestone karst forests, based on genome‐wide SNP markers

Choi

Han

Wojciechowski

et al. 2023

Ecology and Evolution

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Section: Methodsmentioning

confidence: 99%

“…However, the term "ABC analysis" is used ambiguously in the biomedical literature. "ABC analysis" is used for: (i) "Ap-proximate Bayesian Computation" (e.g., 3,4 ), (ii) "Antecedent-Behavior-Consequence", which is a method for analyzing behavior and comes from the field of psychology 5 , and (iii) an inventory categorization method originating in economics, where ABC occasionally stands for "Always Better Control", used in inventory control and management (e.g., [6][7][8][9] ).This report refers only to the idea underlying the latter meaning of ABC analysis, i.e., the item or inventory categorization method that aims to identify the most relevant items by dividing a set of non-negative numerical items into subsets "A", "B", and "C" 10 . However, the term "Always Better Control" for "ABC", which was never used by Juran, should not be associated with the present method.…”

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confidence: 99%

Recursive computed ABC (cABC) analysis as a precise method for reducing machine learning based feature sets to their minimum informative size

Lötsch

Ultsch

2023

Sci Rep

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Selecting the k best features is a common task in machine learning. Typically, a few features have high importance, but many have low importance (right-skewed distribution). This report proposes a numerically precise method to address this skewed feature importance distribution in order to reduce a feature set to the informative minimum of items. Computed ABC analysis (cABC) is an item categorization method that aims to identify the most important items by partitioning a set of non-negative numerical items into subsets "A", "B", and "C" such that subset "A" contains the "few important" items based on specific properties of ABC curves defined by their relationship to Lorenz curves. In its recursive form, the cABC analysis can be applied again to subset "A". A generic image dataset and three biomedical datasets (lipidomics and two genomics datasets) with a large number of variables were used to perform the experiments. The experimental results show that the recursive cABC analysis limits the dimensions of the data projection to a minimum where the relevant information is still preserved and directs the feature selection in machine learning to the most important class-relevant information, including filtering feature sets for nonsense variables. Feature sets were reduced to 10% or less of the original variables and still provided accurate classification in data not used for feature selection. cABC analysis, in its recursive variant, provides a computationally precise means of reducing information to a minimum. The minimum is the result of a computation of the number of k most relevant items, rather than a decision to select the k best items from a list. In addition, there are precise criteria for stopping the reduction process. The reduction to the most important features can improve the human understanding of the properties of the data set. The cABC method is implemented in the Python package "cABCanalysis" available at https://pypi.org/project/cABCanalysis/.

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“…The following supporting information can be downloaded at: . References [ 169 , 170 , 171 , 172 , 173 , 174 , 175 , 176 , 177 , 178 , 179 , 180 , 181 , 182 , 183 , 184 , 185 , 186 , 187 , 188 , 189 , 190 , 191 , 192 , 193 , 194 , 195 , 196 , 197 , 198 , 199 , 200 , 201 , 202 , 203 , 204 , 205 , 206 , 207 , 208 , 209 , 210 , 211 , 212 , 213 , 214 , 215 , 216 , 217 , 218 , 219 , 220 , 221 , 222 , 223 , …”

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Multiomics Molecular Research into the Recalcitrant and Orphan Quercus ilex Tree Species: Why, What for, and How

Maldonado‐Alconada

Castillejo

Rey

et al. 2022

IJMS

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The holm oak (Quercus ilex L.) is the dominant tree species of the Mediterranean forest and the Spanish agrosilvopastoral ecosystem, “dehesa.” It has been, since the prehistoric period, an important part of the Iberian population from a social, cultural, and religious point of view, providing an ample variety of goods and services, and forming the basis of the economy in rural areas. Currently, there is renewed interest in its use for dietary diversification and sustainable food production. It is part of cultural richness, both economically (tangible) and environmentally (intangible), and must be preserved for future generations. However, a worrisome degradation of the species and associated ecosystems is occurring, observed in an increase in tree decline and mortality, which requires urgent action. Breeding programs based on the selection of elite genotypes by molecular markers is the only plausible biotechnological approach. To this end, the authors’ group started, in 2004, a research line aimed at characterizing the molecular biology of Q. ilex. It has been a challenging task due to its biological characteristics (long life cycle, allogamous, high phenotypic variability) and recalcitrant nature. The biology of this species has been characterized following the central dogma of molecular biology using the omics cascade. Molecular responses to biotic and abiotic stresses, as well as seed maturation and germination, are the two main objectives of our research. The contributions of the group to the knowledge of the species at the level of DNA-based markers, genomics, epigenomics, transcriptomics, proteomics, and metabolomics are discussed here. Moreover, data are compared with those reported for Quercus spp. All omics data generated, and the genome of Q. ilex available, will be integrated with morphological and physiological data in the systems biology direction. Thus, we will propose possible molecular markers related to resilient and productive genotypes to be used in reforestation programs. In addition, possible markers related to the nutritional value of acorn and derivate products, as well as bioactive compounds (peptides and phenolics) and allergens, will be suggested. Subsequently, the selected molecular markers will be validated by both genome-wide association and functional genomic analyses.

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Different population size change and migration histories created genetic diversity of three oaks in Tokai region, central Japan

Cited by 6 publications

References 72 publications

The genetic structure and demographic history of Zabelia tyaihyonii, endemic to Korean limestone karst forests, based on genome‐wide SNP markers

The genetic structure and demographic history of Zabelia tyaihyonii, endemic to Korean limestone karst forests, based on genome‐wide SNP markers

Recursive computed ABC (cABC) analysis as a precise method for reducing machine learning based feature sets to their minimum informative size

Multiomics Molecular Research into the Recalcitrant and Orphan Quercus ilex Tree Species: Why, What for, and How

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