Deforestation and abandonment of neotropical agricultural land has led to rapid exploitation by pioneer species. As recolonised populations may be founded by a limited number of individuals, there is significant potential for genetic\ud bottlenecks. Previous studies of pioneer tree dynamics have failed to consider population density interactions (by sampling populations with different densities)and the multigenerational consequences of recolonisation. In this paper we examine the genetic outcomes of a clearance / recolonisation regime for a Costa Rican long-lived pioneer species, Vochysia ferruginea, at a series of sites with\ud different densities and across multi-generational cohorts (old growth forest,secondary forest and seedlings) using variation for amplified fragment length polymorphism (AFLPs) and single sequence repeats (SSRs, microsatellites). A clearance/recolonisation phase was found to significantly increase fine-scale genetic structuring (average intensity of spatial genetic structure, Sp [SSR] = 0.0358) compared to old growth forest (Sp = 0.0126), and significantly reduces genetic diversity (Shannon’s index [AFLP] = 0.202 and 0.271–0.355 for other forest histories following density correction), which compounds over generations (e.g. at Tirimbina: old growth forest, allelic richness, RT [SSR] = 8.86; secondary forest RT = 7.95; seedlings RT = 4.76). Spatial structuring of closely related individuals suggests that V. ferruginea colonises sites via early invaders, which establish patches with half sib relationship. The variability observed between cohorts for genetic differentiation and inbreeding coefficients suggests that the presence of remnant trees can have an important impact on the genetic make up of recolonised populations. One main concern from these\ud results is that if secondary forest blocks harbour reduced genetic diversity and persist in the landscape, then species like V. ferruginea may be forced into a downward spiral of diversity loss if old growth remnants, which harbour higher diversity, are cleared and secondary blocks are used as reforestation sources
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