Distinct Phylogeographic Structures of Wild Radish (Raphanus sativus L. var. raphanistroides Makino) in Japan

Abstract

Coastal plants with simple linear distribution ranges along coastlines provide a suitable system for improving our understanding of patterns of intra-specific distributional history and genetic variation. Due to the combination of high seed longevity and high dispersibility of seeds via seawater, we hypothesized that wild radish would poorly represent phylogeographic structure at the local scale. On the other hand, we also hypothesized that wild radish populations might be geographically differentiated, as has been exhibited by their considerable phenotypic variations along the islands of Japan. We conducted nuclear DNA microsatellite loci and chloroplast DNA haplotype analyses for 486 samples and 144 samples, respectively, from 18 populations to investigate the phylogeographic structure of wild radish in Japan. Cluster analysis supported the existence of differential genetic structures between the Ryukyu Islands and mainland Japan populations. A significant strong pattern of isolation by distance and significant evidence of a recent bottleneck were detected. The chloroplast marker analysis resulted in the generation of eight haplotypes, of which two haplotypes (A and B) were broadly distributed in most wild radish populations. High levels of variation in microsatellite loci were identified, whereas cpDNA displayed low levels of genetic diversity within populations. Our results indicate that the Kuroshio Current would have contributed to the sculpting of the phylogeographic structure by shaping genetic gaps between isolated populations. In addition, the Tokara Strait would have created a geographic barrier between the Ryukyu Islands and mainland Japan. Finally, extant habitat disturbances (coastal erosion), migration patterns (linear expansion), and geographic characteristics (small islands and sea currents) have influenced the expansion and historical population dynamics of wild radish. Our study is the first to record the robust phylogeographic structure in wild radish between the Ryukyu Islands and mainland Japan, and might provide new insight into the genetic differentiation of coastal plants across islands.

Lineage isolation in the face of active gene flow in the coastal plant wild radish is reinforced by differentiated vernalisation responses

“…10–24) lineages (Fig. 2 ) agreed strongly with previous findings [ 17 ]. These populations entirely corresponded to separate geographic regions.…”

“…The multi-locus analysis demonstrated that there was robust genetic differentiation between the southern and northern groups, consistent with previous findings [ 17 ]. However, in contrast to a previous study, the present study originally suggested that the two lineages were estimated to have diverged approximately 18,000 years ago, during the LGM period.…”

“…2–3 months from germination to anthesis), it produces seeds prolifically, is easily cultivated in restricted spaces, and is closely related to Arabidopsis , to which it likely has considerable genetic homology. In coastal plants, evidence of divergence between lineages remains sparse due to the high dispersability and longevity of seeds; however, a previous study using nine microsatellites presented conclusive evidence that wild radish on Japanese islands comprises two genetically isolated lineages, namely, the southern and northern groups [ 17 ]. However, a general understanding of the relationships of divergence and the counteracting factors of coastal plant populations is still unclear.…”

High Genetic Diversity and Low Differentiation in Michelia shiluensis, an Endangered Magnolia Species in South China

“…This inconsistency may be related to the differential focus of the markers or high levels of gene flow [68]. Comparative analysis between bi-parental markers and maternally inherited markers can provide comprehensive insights into population dynamics because cpDNA mutations reflect past changes, while nSSR mutations can provide inferences for recent population events [69]. Thus, differences in genetic patterns and rates of evolution often produce large contrasts between nuclear and organelle genetic diversities under conditions of genetic differentiation [28].…”

Genetic Diversity and Population Structure of Rhododendron rex Subsp. rex Inferred from Microsatellite Markers and Chloroplast DNA Sequences

“…Various insect vectors evolved longer dispersal distance for pollen, whereas the seeds dispersed by wind traveled less than 10 m albeit in open landscapes [74]. Meanwhile, this different consequence might be related to the type and evolutionary rates of different genome sequences [76]. In general, the evolutionary rate of nuclear genomes transmitted by parents was higher than that of maternally inherited chloroplast genomes [77].…”