Population genetics of an ecosystem-defining reef coral Pocillopora damicornis in the Tropical Eastern Pacific

Abstract

Background: Coral reefs in the Tropical Eastern Pacific (TEP) are amongst the most peripheral and geographically isolated in the world. This isolation has shaped the biology of TEP organisms and lead to the formation of numerous endemic species. For example, the coral Pocillopora damicornis is a minor reef-builder elsewhere in the Indo-West Pacific, but is the dominant reef-building coral in the TEP, where it forms large, mono-specific stands, covering many hectares of reef. Moreover, TEP P. damicornis reproduces by broadcast spawning, while it broods mostly parthenogenetic larvae throughout the rest of the Indo-West Pacific. Population genetic surveys for P. damicornis from across its Indo-Pacific range indicate that gene flow (i.e. larval dispersal) is generally limited over hundreds of kilometers or less. Little is known about the population genetic structure and the dispersal potential of P. damicornis in the TEP.

Methodology: Using multilocus microsatellite data, we analyzed the population structure of TEP P. damicornis among and within nine reefs and test for significant genetic structure across three geographically and ecologically distinct regions in Panama.

Principal findings/conclusions: We detected significant levels of population genetic structure (global R(ST) = 0.162), indicating restricted gene flow (i.e. larvae dispersal), both among the three regions (R(RT) = 0.081) as well as within regions (R(SR) = 0.089). Limited gene flow across a distinct environmental cline, like the regional upwelling gradient in Panama, indicates a significant potential for differential adaptation and population differentiation. Individual reefs were characterized by unexpectedly high genet diversity (avg. 94%), relatively high inbreeding coefficients (global F(IS) = 0.183), and localized spatial genetic structure among individuals (i.e. unique genets) over 10 m intervals. These findings suggest that gene flow is limited in TEP P. damicornis populations, particularly among regions, but even over meter scales within populations.

Figure 1. Map of Panama, showing the three main Pacific regions and the sampled locations.

The pie charts show the distribution of the five genetic clusters identified by STRUCTURE 2.3 in the three regional and nine reef populations. The bar plot shows each individual sample as a vertical bar with colors indicating the relative proportions of each genetic cluster. Map created on www.aquarius.ifm-geomar.de. U = Uva Island; C = Canal de Afuera Island; G = Granito de Oro Island; B  =  Bahia de Damas, Coiba Island; A  =  Achotines Bay; I  =  Iguana Island; S  =  Saboga Island; Co  =  Contadora Island; T  =  Taboga Island.

Figure 2. Principal component analysis of Pocillopora damicornis populations, constructed using GenAlEx 6.1 .

Distances between populations were analyzed as RST pairwise genetic distances. The two axes explained 90.4% of the total variation. Blue circles  =  Populations in the Gulf of Chiriqui; Red triangles  =  Azuero Peninsula; Green squares  =  Gulf of Panama.

Figure 3. Spatial correlograms of the SpaGeDi analysis of Spatial Genetic Structure (SGS) among specimen within discrete distance classes.

Black lines represent the genet dataset, excluding clones and grey lines show the results for the ramet dataset, including clones. Dashed lines are the permuted 95% confidence intervals. Error bars are 95% bootstrap errors of the genet datasets. Figure 3a ) Spatial correlogram of the average pairwise kinship F_ij as a function of distance over all populations. Figure 3b–d ) Spatial correlograms over the populations in each of the three regions, b) the Gulf of Chiriqui, c) the Azuero Peninsula and d) the Gulf of Panama.