Kyoko Aoki's research while affiliated with Kyoto University and other places

... However, based on historical climate data and tolerance of cool temperature of the component species of these forests, some ecologists have proposed that these forests might also have survived in multiple refugia along the Pacific coasts of the main islands as well as on the southern end of Kyushu during the glacial periods (Maeda 1980;Kamei and Research Group for the Biogeography from Würm Glacial 1981;Nakanishi 1996;Hattori 2002). However, it has been difficult to resolve the detailed demographic history of the plant species currently inhabiting the broadleaved evergreen forests, especially Castanopsis-type forest, because of the limited fossilized pollen records and of the relatively slow molecular evolution of chloroplast DNA in plants (Wolfe et al. 1987;Chase et al. 1993;Aoki et al. 2005) and the extremely low levels of intraspecific variation in the chloroplast DNA of Japanese broadleaved evergreen species (Aoki et al. 2003(Aoki et al. , 2004a(Aoki et al. , 2016. Application of the ABC method to reconstruct the demography of the dominant species in the type of the forest can help to understand detailed history from the information of the locations of refugia, the diverged time and the population size changes. ...

... Primary succession of coastal forests typically occurs very slowly when site conditions are unfavorable to most plants, with only few unique plant species being able to thrive; therefore, selecting and sowing plant species adapted to such environments could encourage primary succession (Ito & Yoshizaki, 2013;Yoshizaki, 2011). Nevertheless, as many species exhibit genetic variations in Japan (Fujii et al., 2002;Fukuda et al., 2011aFukuda et al., , 2011bHayakawa et al., 2012Hayakawa et al., , 2014Iwasaki et al., 2010Iwasaki et al., , 2012Matsumura et al., 2009;Saitou et al., 2007;Sakaguchi et al., 2017;Yamaji et al., 2007;Figure 1. Lysimachia mauritiana Lam (A) gross picture, (B) dehiscent fruits (bar = 30mm), (C) seed (bar = 0.5mm). ...

... Notably, however, on the basis of our Stairway Plot2 analysis, we failed to detect any evident decline in the population size of the Yakushima alpine taxa, at least during the LG period (Figure 4b), and their current population genetic diversity was found to be comparable to that of the counterpart taxa (Table S5). The relatively high or moderate genetic diversity among Yakushima populations has similarly been reported in previous phylogeographic studies (Aoki et al., 2014;Kimura et al., 2014) and palaeontological evidence indicates that temperate forests may have become established on the island during the LG period (Tsukada, 1984). This evidence accordingly implies that Yakushima ...

... These studies also showed that the rugged volcanic terrain and diverse altitudes within the Japanese Islands contribute further to isolation [23,24]. Consequently, most insect species exhibit population genetic structures reflecting the geohistory of the Japanese Islands [25][26][27][28][29][30], while a few species with strong dispersal abilities show weaker genetic differentiation [31][32][33]. ...

... Population genetic differentiation in phytophagous insects is influenced by multiple factors, such as specialization to host plants, dispersal abilities, phenological differences, and geographical location (Loxdale and Lushai 1999, Aoki et al. 2011, Antwi et al. 2015, Vindstad et al. 2019. Although differences in host plants can influence genetic structure in specialist species (Antwi et al. 2015), geographical distance has a substantial effect on population genetic structure in generalist species (Vindstad et al. 2019). ...

... In addition to these single species studies, Iwasaki et al. (2012) revealed genetic structure shared among four species and proposed two major routes of northward migrations in deciduous forests. Comparative study was also performed in six species of broad-leaved evergreen forests (Aoki et al. 2004), which suggested refugia in southern Kyushu as well as the Pacific coast of western Japan based on a number of rare haplotypes. ...

... Recently, the complete chloroplast genome sequences of Photinia × fraseri, Photinia davidsoniae, and Photinia glabra have been sequenced and published 1,27,28 . However, at present, no mitogenome of any species in Photinia has been reported. ...

... Genomic DNA was extracted from the silica gel-dried leaves using the Tiangen Plant Genomic DNA Extraction Kit (DP320) according to the instructions of the manufacturer. A total of 15 primer pairs of nuclear SSRs (Table 5) were screened from those originally reported in Castanopsis and Castanea species [46][47][48]. Quadruple fluorescent polymerase chain reaction (PCR) was amplified using the Type-it microsatellite PCR kit (QIAGEN, Hilden, Germany). PCR was performed in a mixture including 20 ng of genomic DNA, 1× PCR Master Mix, 1× Q -Solution, and 10 µM of each primer. ...

... In the present study, C. glandium was enriched in NW ( Fig. 8 and Supplementary Table S11). In winter in Nagano, sika deer might prefer to eat acorns because weevil larvae often grow in acorns over the winter 38 . Acorns themselves are rich in starch and lipids 39 . ...

... The sequences were concatenated in a single matrix (24 taxa, 919 characters) using Mesquite v3.2 software (Maddison & Maddison 2017). (Liede 2001;Potgieter & Albert 2001;Aoki et al. 2003;Rapini et al. 2003Rapini et al. , 2007Verhoeven et al. 2003;Meve & Liede 2004;Livshultz et al. 2007;Simões et al. 2007;Wanntorp et al. 2011;Meve et al. 2017 The phylogeny was inferred with Bayesian inference (BI) and Maximum likelihood (ML) for concatenated alignments. Bayesian inference was conducted in MrBayes v3.2.2 on XSEDE (Huelsenbeck & Ronquist 2001;Ronquist & Huelsenbeck 2003), on the CIPRES webserver (Miller et al. 2010) with the BIC selected substitution model (nst=2). ...