Chloroplast and total genomic diversity in the endemic Costa Rican tree, Lonchocarpus costaricensis (J.D. Smith) Pittier (Papilionaceae).

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, FST = 0.12, although Matapalo was
strongly differentiated from all other populations (FST =
0.16–0.22), apart from Cobano (FST = 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.