TL;DR: 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 is applied.
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.
TL;DR: A large deletion in the microsatellite sequence observed in the three rock-dwelling species Pseudotropheus lucerna, PseudOTropheus (Tropheops) 'band,' and Pseudosodium 'rust' and the midwater-feeding species Copadichromis sp.
Abstract: Recent studies have suggested that size homoplasy is a prevalent feature of microsatellites and is expected to increase with time of divergence among populations and taxa. In this study, we performed sequence analysis of alleles from a complex microsatellite locus (Pzeb4, initially isolated from Pseudotropheus (Maylandia) zebra) from 1 midwater-feeding and 10 rock-dwelling cichlid fish species from Lake Malawi, East Africa, to investigate how widespread size homoplasy is among closely related taxa at this locus. All cichlid fishes endemic to this lake are believed to have originated within the last 700,000 years, and some species may be less than 200 years old. The number of eletromorphs found per species varied from 3 to 13. Sequence analysis of 95 cloned Pzeb4 PCR products (representing 18 electromorphs) revealed 13 new alleles. Ten of the 13 electromorphs (77%) were found to show size homoplasy due to either single nucleotide substitutions/indels or large indels. To investigate how well this locus fits the single-step mutation model (SMM), the minimum number of mutations required to explain the length differences between pairs of alleles was plotted against their size differences. Of the 300 comparisons, 166 (55.3%) corresponded to SMM expectations and 86 (28.7%) required a smaller number of mutations, and for 48 (16.0%) pairwise comparisons, a larger number of mutations were required to explain the length differences as compared with SMM expectations. Finally, a large deletion in the microsatellite sequence observed in the three rock-dwelling species Pseudotropheus lucerna, Pseudotropheus (Tropheops) 'band,' and Pseudotropheus (Tropheops) 'rust' and the midwater-feeding species Copadichromis sp. is believed to represent a shared ancestral polymorphism.
TL;DR: Comparisons between the highly specialized and species-poor genus Labeotropheus and Tropheops are focused on, which suggests that a specialized foraging mode has not constrained cranial variability in this genus, and magnitudes of integration and patterns of modularity are lineage specific, and do not directly correspond to ecology.
Abstract: Lake Malaŵi cichlids have evolved rapidly, extensively, and in some cases iteratively to fill an array of ecological niches; however, neither species richness nor trophic diversity is distributed equally across lineages. In the context of evolutionary theory, such differences offer predictions about the magnitudes and patterns of morphological variation within lineages. In this paper, we use geometric morphometrics in three prevalent rock-dwelling genera to address questions related to morphological diversity, disparity, integration, and modularity. In particular, we focus on comparisons between the highly specialized and species-poor genus, Labeotropheus (Ahl in Sitzungsberichte der Berlinische Gesellschaft Naturforschender Freunde zu Berlin 1926:51–62, 1927), and the more ecologically diverse and species-rich genus, Tropheops (Trewavas in Revue Francaise d’Aquariologie Herpetologie 10:97–106, 1984), as well as between species with lake-wide versus more limited distributions. We find that Labeotropheus exhibits comparable levels of morphological disparity to Tropheops, which suggests that a specialized foraging mode has not constrained cranial variability in this genus. We also find that species with a lake-wide distribution exhibit levels of disparity three times greater than that in a species with a limited distribution. Finally, we show that magnitudes of integration and patterns of modularity are lineage specific, and do not directly correspond to ecology. In sum, these data provide insights into the complex relationship between ecology, morphological variability, and evolvability.
TL;DR: In this paper, the authors measured locomotor activity across the circadian cycle in 11 Lake Malawi cichlid species and identified a single species, Tropheops sp.'red cheek', that is nocturnal.
Abstract: Animals display remarkable diversity in rest and activity patterns that are regulated by endogenous foraging strategies, social behaviors and predator avoidance. Alteration in the circadian timing of activity or the duration of rest-wake cycles provide a central mechanism for animals to exploit novel niches. The diversity of the >3000 cichlid species throughout the world provides a unique opportunity to examine variation in locomotor activity and rest. Lake Malawi alone is home to over 500 species of cichlids that display divergent behaviors and inhabit well-defined niches throughout the lake. These species are presumed to be diurnal, though this has never been tested systematically. Here, we measured locomotor activity across the circadian cycle in 11 Lake Malawi cichlid species. We documented surprising variability in the circadian time of locomotor activity and the duration of rest. In particular, we identified a single species, Tropheops sp. 'red cheek', that is nocturnal. Nocturnal behavior was maintained when fish were provided shelter, but not under constant darkness, suggesting that it results from acute response to light rather than an endogenous circadian rhythm. Finally, we showed that nocturnality is associated with increased eye size after correcting for evolutionary history, suggesting a link between visual processing and nighttime activity. Together, these findings identify diversity of locomotor behavior in Lake Malawi cichlids and provide a system for investigating the molecular and neural basis underlying variation in nocturnal activity.