Chloroplast and Total Genomic Diversity in the Endemic Costa Rican Tree Lonchocarpus costaricensis (J. D. Smith) Pittier (Papilionaceae)

Abstract

In Mesoamerica, tropical dry forest is a highly threatened habitat, and species endemic to this environment are under extreme pressure. The tree species, Lonchocarpus costaricensis is endemic to the dry northwest of Costa Rica and southwest Nicaragua. It is a locally important species but, as land has been cleared for agriculture, populations have experienced considerable reduction and fragmentation. To assess current levels and distribution of genetic diversity in the species, a combination of chloroplast-specific (cpDNA) and whole genome DNA markers (amplified fragment length polymorphism, AFLP) were used to fingerprint 121 individual trees in 6 populations. Two cpDNA haplotypes were identified, distributed among populations such that populations at the extremes of the distribution showed lowest diversity. A large number (487) of AFLP markers were obtained and indicated that diversity levels were highest in the two coastal populations (Cobano, Matapalo, H = 0.23, 0.28 respectively). Population differentiation was low overall, F ST = 0.12, although Matapalo was strongly differentiated from all other populations (F ST = 0.16-0.22), apart from Cobano (F ST = 0.11). Spatial genetic structure was present in both datasets at different scales: cpDNA was structured at a range-wide distribution scale, whilst AFLP data revealed genetic neighbourhoods on a population scale. In general, the habitat degradation of recent times appears not to have yet impacted diversity levels in mature populations. However, although no data on seed or saplings were collected, it seems likely that reproductive mechanisms in the species will have been affected by land clearance. It is recommended that efforts should be made to conserve the extant genetic resource base and further research undertaken to investigate diversity levels in the progeny generation.

Long‐distance seed and pollen dispersal inferred from spatial genetic structure in the very low–density rainforest tree, Baillonella toxisperma Pierre, in Central Africa

“…Nowadays, long‐distance seed dispersal may not be ensured in many regions of Central Africa where hunting has drastically decreased populations of large frugivores. Finally, our results support the idea that the range of diversity levels in some rare tree species may resemble those of dense widespread tree species and that very low density is not a good predictor of the level of gene diversity (Gitzendanner & Soltis 2000; Navarro et al. 2005).…”