On the origin of Lake Malawi cichlid species: A population genetic analysis of divergence

Abstract

The cichlid fishes of Lake Malawi are famously diverse. However, phylogenetic and population genetic studies of their history have been difficult because of the great amount of genetic variation that is shared between species. We apply a recently developed method for fitting the ''isolation with migration'' divergence model to a data set of specially designed compound loci to develop portraits of cichlid species divergence. Outgroup sequences from a cichlid from Lake Tanganyika permit model parameter estimates in units of years and effective population sizes. Estimated speciation times range from 1,000 to 17,000 years for species in the genus Tropheops. These exceptionally recent dates suggest that Malawi cichlids as a group experience a very active and dynamic diversification process. Current effective population size estimates range form 2,000 to near 40,000, and to >120,000 for estimates of ancestral population sizes. It appears that very recent speciation and gene flow are among the reasons why it has been difficult to discern the phylogenetic history of Malawi cichlids.divergence population genetics ͉ isolation with migration

Age of Cichlids: New Dates for Ancient Lake Fish Radiations

“…Using this rate, haplochromine radiations of the Lake Victoria region and Lake Malawi were estimated at 200,000 years and 700,000 years, respectively, whereas the divergence of the Haplochromini and Lamprologini was dated to ;4.5 MYA (Meyer et al 1990). Subsequently, divergence dates have been calculated employing assumptions that the basal radiations of the Lake Tanganyika endemic cichlid tribes occurred between 6 and 12 MYA based on evidence that during this period deep lacustrine conditions began to form in Lake Tanganyika (Sturmbauer et al 1994;Duftner et al 2005;Koblmüller et al 2005;Won et al 2005Won et al , 2006. Additionally, the basal radiation of the Lake Malawi haplochromine flock has commonly been used for calibration with the assumptions that it occurred between 0.7 and 4 MYA (Sturmbauer and Meyer 1993;Nagl et al 1998Nagl et al , 2000Nagl et al , 2001Salzburger et al 2005).…”

A northern glacial refugium for bank voles ( Clethrionomys glareolus )

“…For credibility intervals we recorded for each parameter the 90% highest posterior density (HPD) interval, i.e., the shortest span that includes 90% of the probability density of a parameter. The analysis was done using several independent runs, each with 4 to 15 chains under the Metropolis coupling to improve mixing (36). Each chain was initiated with a burn-in period of 100,000 updates, and the total length of each analysis was between 5 and 30 million updates.…”

“…1). We used the IM program (34) to run the MCMC simulations assuming the HKY model of sequence evolution and uniform prior distributions of parameter ranges, which were empirically determined to ensure that the posterior distributions fell completely within the prior distributions (36). The peaks of the posterior distributions were thus taken as maximum likelihood estimates of the parameters (33,37).…”

Parallel life history evolution in mouthbrooding cichlids from the African Great Lakes

“…An estimated 660-1,319 species of cichlid fishes have been recorded from Lakes Malawi, Tanganyika, and Victoria, most endemic to a single lake catchment (12). These species flocks are so rich that, collectively, they provide the best example of rapid adaptive radiation in vertebrates (13)(14)(15)(16). The independent radiations (14,15) in the three lakes have produced very similar communities.…”