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AFLP diversity and spatial structure of Calycophyllum candidissimum (Rubiaceae), a dominant tree species of Nicaragua's critically endangered seasonally dry forest - PubMed

AFLP diversity and spatial structure of Calycophyllum candidissimum (Rubiaceae), a dominant tree species of Nicaragua's critically endangered seasonally dry forest

A Dávila-Lara et al. Heredity (Edinb). 2017 Oct.

Abstract

The Central American seasonally dry tropical (SDT) forest biome is one of the worlds' most endangered ecosystems, yet little is known about the genetic consequences of its recent fragmentation. A prominent constituent of this biome is Calycophyllum candidissimum, an insect-pollinated and wind-dispersed canopy tree of high socio-economic importance, particularly in Nicaragua. Here, we surveyed amplified fragment length polymorphisms across 13 populations of this species in Nicaragua to elucidate the relative roles of contemporary vs historical factors in shaping its genetic variation. Genetic diversity was low in all investigated populations (mean HE=0.125), and negatively correlated with latitude. Overall population differentiation was moderate (ΦST=0.109, P<0.001), and Bayesian analysis of population structure revealed two major latitudinal clusters (I: 'Pacific North'+'Central Highland'; II: 'Pacific South'), along with a genetic cline between I and II. Population-based cluster analyses indicated a strong pattern of 'isolation by distance' as confirmed by Mantel's test. Our results suggest that (1) the low genetic diversity of these populations reflects biogeographic/population history (colonisation from South America, Pleistocene range contractions) rather than recent human impact; whereas (2) the underlying process of their isolation by distance pattern, which is best explained by 'isolation by dispersal limitation', implies contemporary gene flow between neighbouring populations as likely facilitated by the species' efficient seed dispersal capacity. Overall, these results underscore that even tree species from highly decimated forest regions may be genetically resilient to habitat fragmentation due to species-typical dispersal characteristics, the necessity of broad-scale measures for their conservation notwithstanding.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1

(a) Simplified map of the geographical distribution of C. candidissimum in Central America, the Greater Antilles and northern South America based on geo-referenced specimen records (N=595) available at TROPICOS (

http://www.tropicos.org/Name/27903157

(accessed 20 October 2016)) and the Global Biodiversity Facility (GBIF.org (6th September 2016) GBIF Occurrence Download

http://doi.org/10.15468/dl.wc19nm)

. (b) Geographical locations of 13 populations of C. candidissimum in Nicaragua represented in this study for AFLP analysis (red circles), plus additional specimen records (N=90) according to TROPICOS/GBIF (small white circles). The light-brown areas represent the original distribution of seasonal dry forest derived from the World Wildlife Fund (WWF) ecoregion dataset (modified from Olson et al. (2001)). The dashed lines delimitate the physiographic regions of Nicaragua (Pacific, Central Highland, Atlantic) according to Taylor (1963). See Table 1 for identification of population codes.

Figure 2
Figure 2

Distribution of the two major AFLP gene pool clusters (I and II) within and among 13 populations (220 individuals) of C. candidissimum from Nicaragua as identified by

STRUCTURE

based on the ad hoc statistic ΔK (see also Supplementary Figure S1). The bar-plot displays the assignment of individuals to the two clusters, with the smallest vertical bar representing one individual. The y axis presents the estimated membership coefficient (Q) for each individual in the two clusters. The x axis corresponds to population codes as identified in Table 1. The pie charts at the top represent the average proportion of cluster membership computed across individuals per site. Populations are ordered from left to right according to decreasing latitude (see also Table 1 and Figure 1b).

Figure 3
Figure 3

Principal coordinates analysis (PCoA) for 13 populations of C. candidissimum from Nicaragua based on pairwise ΦPT values of AFLP data. Plots of (a) the first and second, and (b) the first and third coordinates. Percentages of total variance explained by each coordinate are noted in parentheses. Population symbols and colours indicate, respectively, regional affiliation (Table 1; Figure 1b) and gene pool (I–III) structure (black, I; grey, II; grey/black, I and II; see Figure 2; and white, III; see Supplementary Figure S2). Note in (b) the subdivision between ‘Central Highland’ and ‘Pacific North’ populations. Population codes are identified in Table 1.

Figure 4
Figure 4

Midpoint-rooted Neighbour-Joining (NJ) phenogram depicting AFLP-derived Nei’s (1987) unbiased genetic distances between 13 populations of C. candidissimum from Nicaragua. Numbers above branches indicate bootstrap values (⩾70%) based on 9999 replicates. Populations are labelled according to their geographic origin. Population codes are identified in Table 1.

Figure 5
Figure 5

Regression of AFLP-derived ΦPT/(1−ΦPT) values against the logarithm (log10) of geographic distance (km) for 78 pairwise comparisons of 13 Nicaraguan populations of C. candidissimum (r=0.651, R2=0.425; Mantel probability (9999 permutations) P<0.001).

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