Phylogeography, colonization and population history of the Midas cichlid species complex (Amphilophus spp.) in the Nicaraguan crater lakes

Abstract

Background: Elucidation of the mechanisms driving speciation requires detailed knowledge about the phylogenetic relationships and phylogeography of the incipient species within their entire ranges as well as their colonization history. The Midas cichlid species complex Amphilophus spp. has been proven to be a powerful model system for the study of ecological specialization, sexual selection and the mechanisms of sympatric speciation. Here we present a comprehensive and integrative phylogeographic analysis of the complete Midas Cichlid species complex in Nicaragua (> 2000 individuals) covering the entire distributional range, using two types of molecular markers (the mitochondrial DNA control region and 15 microsatellites). We investigated the majority of known lake populations of this species complex and reconstructed their colonization history in order to distinguish between alternative speciation scenarios.

Results: We found that the large lakes contain older and more diverse Midas Cichlid populations, while all crater lakes hold younger and genetically less variable species assemblages. The large lakes appear to have repeatedly acted as source populations for all crater lakes, and our data indicate that faunal exchange among crater lakes is extremely unlikely. Despite their very recent (often only a few thousand years old) and common origin from the two large Nicaraguan lakes, all crater lake Midas Cichlid radiations underwent independent, but parallel, evolution, and comprise distinct genetic units. Indeed several of these crater lakes contain multiple genetically distinct incipient species that most likely arose through sympatric speciation. Several crater lake radiations can be traced back to a single ancestral line, but some appear to have more than one founding lineage. The timing of the colonization(s) of each crater lake differs, although most of them occurred more (probably much more) recently than 20,000 years ago.

Conclusion: The genetic differentiation of the crater lake populations is directly related to the number of founding lineages, but independent of the timing of colonization. Interestingly, levels of phenotypic differentiation, and speciation events, appeared independent of both factors.

Figure 1

Map of the Pacific coast of Nicaragua and Costa Rica. Labeled localities correspond to sampling sites. Fish were collected from several sites in the large Nicaraguan lakes (Managua, Nicaragua), and from several volcanic crater lakes (Asososca León, Apoyeque, Xiloá, Asososca Managua, Masaya, Apoyo), Tisma Pond, Las Canoas reservoir, and the rivers Tipitapa, Malacatoya and San Juan.

Figure 2

Bayesian population assignment test based on 15 microsatellite loci with the software STRUCTURE. Seven to eight genetically distinct populations are uncovered that might be considered to be species.

Figure 3

Plot of the two first axes of the Principal coordinate analyses (PCoA). Each circle represents a single individual and colors reflect species and lake of origin. A. Analysis including all sampled populations (PCoA1 = 44.71%, PCoA2 = 16.54%). B. Analysis excluding the populations from crater Lake Apoyo (PCoA1 = 27.49%, PCoA2 = 20.39%). C. Analysis excluding samples from crater lakes Apoyo, Apoyeque and Asososca León (PCoA1 = 24.67%, PCoA2 = 19.65%). D. Analysis including the samples from the large lakes and Tisma Pond (PCoA1 = 24.04%, PCoA2 = 19.03%).

Figure 4

Unrooted haplotype networks of the complete mtDNA control region of cichlids of the Midas Cichlid species complex from six crater lakes in Nicaragua. Circles represent unique DNA sequences, and their size reflects the number of individuals sharing a particular haplotype (see scale; note that scale is different for crater Lake Xiloá). Colors refer to different lakes, light blue represents in each case fish from elsewhere outside the given crater lake. Connections between haplotypes represent mutational steps. The central haplotype 'C', is the most common haplotype that is found in the large lakes and some of the crater lake populations.

Figure 5

Mismatch analysis showing the inferred demographic histories of individuals from each species in each of the Nicaraguan lakes. Colored lines represent observed data, black lines represent the best-fit model, and in grey are the upper and lower boundaries.