Genetic structure and putative selective sweep in the pioneer tree, Zanthoxylum ailanthoides

Abstract

Zanthoxylum ailanthoides Siebold & Zucc. is one of the most frequently encountered pioneer trees in Japanese warm-temperate evergreen oak forests. Our previous study in one region of Japan suggested high levels of population differentiation and putative natural selection acting on one of the nuclear loci analyzed. Here, we extend our analysis to study the genetic structure of 10 populations of Z. ailanthoides across Japan using 9 simple sequence repeat (SSR) loci for a better understanding of its genetic structure. First, the southernmost population (Kagoshima) in the samples was found to have the highest genetic diversity, suggesting there was a glacial refugium at or near the location of the population. Second, relatively strong genetic differentiation was found among populations, and there was a positive correlation between genetic distances and geographic distances (Mantel test; P < 0.001). Based on this information, we analyzed nucleotide variation at the putatively selected locus homologous to the gene encoding the ADP-glucose pyrophosphorylase large subunit (agpL). Despite the strong genetic differentiation among populations suggested by the SSR loci, the agpL locus was monomorphic in almost all populations analyzed. The results of this study strongly supported the possibility of a selective sweep at or near the agpL locus.

Approximate Bayesian computation analysis of EST-associated microsatellites indicates that the broadleaved evergreen tree Castanopsis sieboldii survived the Last Glacial Maximum in multiple refugia in Japan

“…ellipticus (Aoki et al 2004b), Photinia glabra (Aoki et al 2006), Myrsine seguinii (Aoki et al 2011), and Camellia japonica (Ueno 2015) for plant species, C. hilgendorfi; a specific predator of C. sieboldii seeds (Aoki et al 2008) and Rhynchaenus dorsoplanatus; a specific leaf miner of C. sieboldii leaves (Aoki et al 2010) for insect species. Genetic boundaries between several species of warm to cool temperate zones in Japan also appear to be located in this region, for example, Pinus (Miyata and Ubukata 1994;Iwaizumi et al 2013), Cerasus (Tsuda et al 2009), Zanthoxylum (Yoshida et al 2010), Padus, Carpinus, and Magnolia (Iwasaki et al 2010(Iwasaki et al , 2012, and Acer (Yoshimaru and Matsumoto 2015) for plant species; Curculio (Aoki et al 2009) for insect species; and Cervus (Nagata et al 1999), Macaca (Kawamoto et al 2007), Petaurista (Oshida et al 2009), Ursus (Yasukochi et al 2009), and Lepus (Nunome et al 2010) for mammal species. The common geographic differentiation among multiple codistributed taxa may help efforts to elucidate the relative influence of major historical events such as climate changes during the glacial and interglacial periods (Avise 2000).…”

Genetic Differentiation and Genetic Diversity of Castanopsis (Fagaceae), the Dominant Tree Species in Japanese Broadleaved Evergreen Forests, Revealed by Analysis of EST-Associated Microsatellites

“…Wind-pollinated and wind-dispersed tree species have previously been reported to exhibit low values of G ST (0.014–0.038 in Fagus crenata ; 0.028–0.047 in Cryptomeria japonica ), as reviewed by Tsumura [12]. In contrast, insect- or animal-pollinated and animal-dispersed tree species exhibit relatively high G ST values: 0.144 in Camellia japonica [62] and 0.318 in Zanthoxylum ailanthoides [63]. The G ST values of the Castanopsis species examined in this study were relatively low even though they are insect-pollinated and animal-dispersed.…”

High gene flow and genetic diversity in three economically important Zanthoxylum Spp. of Upper Brahmaputra Valley Zone of NE India using molecular markers

“…In the past the analysis of genetic diversity in Zanthoxylum has been done comprising development and characterization of microsatellite markers in Zanthoxylum ailanthoides ( Yoshida et al, 2010 ) molecular identification of medicinally important Zanthoxylum schinifolium using ribosomal DNA internal transcribed spacers ( Sun et al, 2010a , Sun et al, 2010b ) and genetic diversity of Zanthoxylum hamiltonianum of north-east India through RAPD analysis ( Medhi et al, 2013 ) which itself depicts the need of more molecular works as per as this plant is concerned. Zanthoxylum is a complicated genus with many different, similar and not well-researched species.…”