Inferring the demographic history of Japanese cedar, Cryptomeria japonica, using amplicon sequencing

Heredity
Natsuki MoriguchiJunko Kusumi

Abstract

The evolution of a species depends on multiple forces, such as demography and natural selection. To understand the trajectory and driving forces of evolution of a target species, it is first necessary to uncover that species' population history, such as past and present population sizes, subdivision and gene flow, by using appropriate genetic markers. Cryptomeria japonica is a long-lived monoecious conifer species that is distributed in Japan. There are two main lines (omote-sugi and ura-sugi), which are distinguished by apparent differences in morphological traits that may have contributed to their local adaptation. The evolution of these morphological traits seems to be related to past climatic changes in East Asia, but no precise estimate is available for the divergence time of these two lines and the subsequent population dynamics in this species. Here, we analyzed the nucleotide variations at 120 nuclear genes in 94 individuals by using amplicon sequencing in combination with high-throughput sequencing technologies. Our analysis indicated that the population on Yakushima Island, the southern distribution limit of C. japonica in Japan, diverged from the other populations 0.85 million years ago (MYA). The divergence time of ...Continue Reading

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Methods Mentioned

BETA
amplicon-sequencing
PCR
genotyping
PCA
amplicon sequencing

Software Mentioned

R package
BWA
STRUCTURE HARVESTER
fastsimcaol2
R package SNPRelate
PopGenome
fastsimcoal2
FASTX Toolkit
MEM
HKA

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