| Summary: | Rear-edge populations are of significant scientific interest because they can contain allelic variation not found in core-range populations. However, such populations can differ in their level of genetic diversity and divergence reflecting variation in life-history traits, demographic histories and human impacts. Using 13 EST-microsatellites, we investigated the genetic diversity and differentiation of rear-edge populations of the Japanese endemic conifer <i>Thuja standishii </i>(Gordon) Carr. in southwest Japan from the core-range in northeast Japan. Range-wide genetic differentiation was moderate (<i>Fst</i> = 0.087), with northeast populations weakly differentiated (<i>Fst</i> = 0.047), but harboring high genetic diversity (average population-level <i>Ar</i> = 4.76 and<i> Ho </i>= 0.59). In contrast, rear-edge populations were genetically diverged (<i>Fst</i> = 0.168), but contained few unique alleles with lower genetic diversity (<i>Ar</i> = 3.73, <i>Ho</i> = 0.49). The divergence between rear-edge populations exceeding levels observed in the core-range and results from ABC analysis and species distribution modelling suggest that these populations are most likely relicts of the Last Glacial Maximum. However, despite long term persistence, low effective population size, low migration between populations and genetic drift have worked to promote the genetic differentiation of southwest Japan populations of <i>T. standishii</i> without the accumulation of unique alleles.
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