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opencc-zeroDec 2020View details →

The genetic basis of coordinated plasticity across functional units in a Lake Malawi cichlid mapping population

Adaptive radiations are often stereotypical, as populations repeatedly specialize along conserved environmental axes. Phenotypic plasticity may be similarly stereotypical, as individuals respond to environmental cues. These parallel patterns of variation, which are often consistent across traits, have led researchers to propose that plasticity can facilitate predictable patterns of evolution along environmental gradients. This "flexible stem" model of evolution raises questions about the genetic nature of plasticity, including: How complex is the genetic basis for plasticity? Is plasticity across traits mediated by many distinct loci, or few "global" regulators? To address these questions, we reared a hybrid cichlid mapping population on alternate diet regimes mimicking an important environmental axis. We show that plasticity across an array of ecologically relevant traits is generally morphologically integrated, such that traits respond in a coordinated manner, especially those with overlapping function. Our genetic data are more ambiguous. While our mapping experiment provides little evidence for global genetic regulators of plasticity, these data do contain a genetic signal for the integration of plasticity across traits. Overall, our data suggest a compromise between genetic modularity, whereby plasticity may evolve independently across traits, and low-level but widespread genetic integration, establishing the potential for plasticity to experience coordinated evolution.

opencc-zeroFeb 2022View details →

Between a rock and a hard polytomy: phylogenomics of the rock-dwelling mbuna cichlids of Lake Malawi

Whole genome sequences are beginning to revolutionise our understanding of phylogenetic relationships. Yet, even whole genome sequences can fail to resolve the evolutionary history of the most rapidly radiating lineages, where incomplete lineage sorting, standing genetic variation, introgression, and other factors obscure the phylogenetic history of the group. To overcome such challenges, one emerging strategy is to integrate results across different methods. Most such approaches have been implemented on reduced representation genomic datasets, but whole genomes should provide the maximum possible evidence approach. Here, we test the ability of SNPs extracted from whole genome resequencing data, implemented in an integrative genomic approach, to resolve key nodes in the phylogeny of the mbuna, rock-dwelling cichlid fishes of Lake Malaŵi, which epitomise the phylogenetic intractability that often accompanies explosive lineage diversification. This monophyletic radiation has diversified at an unparalleled rate into several hundred species in less than two million years. Using an array of phylogenomic methods, we consistently recovered four major clades of mbuna, but a large basal polytomy among them. Although introgression between clades apparently contributed to the challenge of phylogenetic reconstruction, reduction of the dataset to non-introgressed sites still did not help to resolve the basal polytomy. On the other hand, relationships among six congeneric species pairs were resolved without ambiguity, even in one case where existing data led us to predict that resolution would be difficult. We conclude that the bursts of diversification at the earliest stages of the mbuna radiation may be phylogenetically unresolvable, but other regions of the tree are phylogenetically clearly supported. Integration of multiple phylogenomic approaches will continue to increase confidence in relationships inferred from these and other whole-genome datasets.

publicFeb 2022View details →

Between a rock and a hard polytomy: phylogenomics of the rock-dwelling mbuna cichlids of Lake Malawi

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publicApr 2021View details →

The genetic basis of coordinated plasticity across functional units in a Lake Malawi cichlid mapping population

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opencc-zeroDec 2018View details →

Data from: Pleiotropic jaw morphology links the evolution of mechanical modularity and functional feeding convergence in Lake Malawi Cichlids

Complexity in how mechanistic variation translates into ecological novelty could be critical to organismal diversification. For instance, when multiple distinct morphologies can generate the same mechanical or functional phenotype this could mitigate tradeoffs and/or provide alternative ways to meet the same ecological challenge. To investigate how this type of complexity shapes diversity in a classic adaptive radiation, we tested several evolutionary consequences of the anterior jaw four-bar linkage for Lake Malawi cichlid trophic diversification. Using a novel phylogenetic framework, we demonstrated that different mechanical outputs of the same four jaw elements are evolutionarily associated with both jaw protrusion distance and jaw protrusion angle. However, these two functional aspects of jaw protrusion have evolved independently. Additionally, although four-bar morphology showed little evidence for attraction to optima, there was substantial evidence of adaptive peaks for emergent four-bar linkage mechanics and jaw protrusion abilities among Malawi feeding guilds. Finally, we highlighted a clear case of "cryptic convergence" in which two cichlid species that have independently evolved to graze algae in less than two million years, have converged on similar jaw protrusion abilities as well as four-bar linkage mechanics, but have evolved these similarities via non-convergent four-bar morphologies.

opencc-zeroDec 2014View details →

Data from: A genetic demographic analysis of Lake Malawi rock-dwelling cichlids using spatio-temporal sampling

We estimated the effective population sizes (Ne) and tested for short-term temporal demographic stability of populations of two Lake Malawi cichlids: Maylandia benetos, a micro-endemic, and Maylandia zebra, a widespread species found across the lake. We sampled a total of 351 individuals, genotyped them at 13 microsatellite loci and sequenced their mitochondrial D-loop to estimate genetic diversity, population structure, demographic history and effective population sizes. At the microsatellite loci, genetic diversity was high in all populations. Yet, genetic diversity was relatively low for the sequence data. Microsatellites yielded mean Ne estimates of 481 individuals (±99 SD) for M. benetos and between 597 (±106.3 SD) and 1524 (±483.9 SD) individuals for local populations of M. zebra. The microsatellite data indicated no deviations from mutation–drift equilibrium. Maylandia zebra was further found to be in migration–drift equilibrium. Temporal fluctuations in allele frequencies were limited across the sampling period for both species. Bayesian Skyline analyses suggested a recent expansion of M. zebra populations in line with lake-level fluctuations, whereas the demographic history of M. benetos could only be estimated for the very recent past. Divergence time estimates placed the origin of M. benetos within the last 100 ka after the refilling of the lake and suggested that it split off the sympatric M. zebra population. Overall, our data indicate that micro-endemics and populations in less favourable habitats have smaller Ne, indicating that drift may play an important role driving their divergence. Yet, despite small population sizes, high genetic variation can be maintained.

opencc-zeroDec 2012View details →

Data from: Morphological stasis in an ongoing gastropod radiation from Lake Malawi

Evolutionary processes leading to adaptive radiation regularly occur too fast to be accurately recorded in the fossil record but too slowly to be readily observed in living biota. The study of evolutionary radiations is thereby confronted with an epistemological gap between the timescales and approaches used by neontologists and paleontologists. Here we report on an ongoing radiation of extant Bellamya species (n = 4) from the African Rift Lake Malawi that provides an unusual opportunity to bridge this gap. The substantial molecular differentiation in this monophyletic Bellamya clade has arisen since Late Pleistocene megadroughts in the Malawi Basin caused by climate change. Morphological time-series analysis of a high-resolution, radiocarbon-dated sequence of 22 faunas spanning the Holocene documents stasis up to the middle Holocene in all traits studied (shell height, number of whorls, and two variables obtained from geometric morphometrics). Between deposition of the last fossil fauna (∼5 ka) and the present day, a drastic increase in morphological disparity was observed (3.7–5.8 times) associated with an increase in species diversity. Comparison of the rates of morphological evolution obtained from the paleontological time-series with phylogenetic rates indicates that the divergence in two traits could be reconstructed with the slow rates documented in the fossils, that one trait required a rate reduction (stabilizing selection), and the other faster rates (divergent selection). The combined paleontological and comparative approach taken here allows recognition that morphological stasis can be the dominant evolutionary pattern within species lineages, even in very young and radiating clades.

opencc-zeroDec 2014View details →

Data from: Quantitative genetic analyses of male color pattern and female mate choice in a pair of cichlid fishes of Lake Malawi, East Africa

The traits involved in sexual selection, such as male secondary sexual characteristics and female mate choice, often co-evolve which can promote population differentiation. However, the genetic architecture of these phenotypes can influence their evolvability and thereby affect the divergence of species. The extraordinary diversity of East African cichlid fishes is often attributed to strong sexual selection and thus this system provides an excellent model to test predictions regarding the genetic architecture of sexually selected traits that contribute to reproductive isolation. In particular, theory predicts that rapid speciation is facilitated when male sexual traits and female mating preferences are controlled by a limited number of linked genes. However, few studies have examined the genetic basis of male secondary sexual traits and female mating preferences in cichlids and none have investigated the genetic architecture of both jointly. In this study, we artificially hybridized a pair of behaviorally isolated cichlid fishes from Lake Malawi and quantified both melanistic color pattern and female mate choice. We investigated the genetic architecture of both phenotypes using quantitative genetic analyses. Our results suggest that 1) many non-additively acting genetic factors influence melanistic color patterns, 2) female mate choice may be controlled by a minimum of 1–2 non-additive genetic factors, and 3) F2 female mate choice is not influenced by male courting effort. Furthermore, a joint analysis of color pattern and female mate choice indicates that the genes underlying these two traits are unlikely to be physically linked. These results suggest that reproductive isolation may evolve rapidly owing to the few genetic factors underlying female mate choice. Hence, female mate choice likely played an important role in the unparalleled speciation of East African cichlid fish.

opennotspecifiedDec 2006View details →

FIGURES 1–3. Astiotrema turneri n in Astiotrema turneri n. sp. (Digenea: Plagiorchiidae) from cichlid fishes (Cichlidae: Perciformes) of Lake Malawi, southeastern Africa

FIGURES 1–3. Astiotrema turneri n. sp. 1. 1. Ventral view of holotype specimen from Pseudotropheus zebra, uterus in bold outline. 2. Ventral view of flattened specimen from Labeotropheus trewavasae, uterus in bold outline. 3. Terminal genitalia of specimen from P. z e b r a. Scale bars 1, 2 = 500 μm, 3 = 100μm.

FIGURE 16 in An endemic species flock of Cypridopsinae (Crustacea, Ostracoda) from the ancient Lake Malawi (Africa), with the description of a new genus and three new species

FIGURE 16. Limbs of Malawidopsis antoniae gen. et sp. nov., female—A. A1, Allotype (INV.159033). B. MdCox, Paratype (INV.159040). C. Md palp, Paratype. (INV.159052). D. A2, Paratype (INV.159052). E. A2, detail of terminal part, Paratype. (INV.159052). Scales: all 50 µm.

FIGURE 4 in An endemic species flock of Cypridopsinae (Crustacea, Ostracoda) from the ancient Lake Malawi (Africa), with the description of a new genus and three new species

FIGURE 4. Limbs of Malawidopsis stellae gen. et sp. nov., male—A. A1, Holotype (INV.159010). B. MdCox, Paratype (INV.159012). C. Md palp, Paratype (INV.159013). D. A2, Holotype. E. A2, detail of terminal part, Holotype. Scales: all 50 µm.

FIGURE 2 in An endemic species flock of Cypridopsinae (Crustacea, Ostracoda) from the ancient Lake Malawi (Africa), with the description of a new genus and three new species

FIGURE 2. Bathymetry of Lake Malawi, with an indication of the sampled localities (Modified from Lyons et al., 2011 and Park & Cohen, 2011)

FIGURE 17 in An endemic species flock of Cypridopsinae (Crustacea, Ostracoda) from the ancient Lake Malawi (Africa), with the description of a new genus and three new species

FIGURE 17. Limbs of Malawidopsis antoniae gen. et sp. nov., female—A. T2, Paratype (INV.159052). B. T3, Paratype (INV.159042). C. Mx1, respiratory plate not shown, Paratype (INV.159039). D. T1, Paratype (INV.159042). E & F. CR, Allotype (INV.159033). Scales: all 50 µm.

FIGURE 8 in An endemic species flock of Cypridopsinae (Crustacea, Ostracoda) from the ancient Lake Malawi (Africa), with the description of a new genus and three new species

FIGURE 8. Malawidopsis ruwaydae gen. et sp. nov.—A. Paratype, LVi (INV.159028, male). B. Holotype, RVi (INV.159019, male). C. Allotype, LVi (INV.159020, female). D. Allotype, RVi (INV.159020, female). E. Paratype, CpLL (INV.159029, male). F. Holotype, RVi, MSc (INV.159019, male). G. Paratype, CpD (INV.159030, female). H. Paratype, CpV (INV.159031, female). I. Paratype, CpD, detail of anterior (INV.159030, female). J. Paratype, CpV, detail of anterior (INV.159031, female). Scales: A–E, G–H = 300µm; F = 50µm; I–J = 100µm.

FIGURE 12 in An endemic species flock of Cypridopsinae (Crustacea, Ostracoda) from the ancient Lake Malawi (Africa), with the description of a new genus and three new species

FIGURE 12. Limbs of Malawidopsis ruwaydae gen. et sp. nov., female—A. T2, Allotype (INV.159020). B. T3, Paratype (INV.159025). C. Mx1, respiratory plate not show, Allotype (INV.159020). D. T1, Allotype (INV.159020). E & F. CR, Paratype (INV.159022). Scales: all 50 µm.

FIGURE 5 in An endemic species flock of Cypridopsinae (Crustacea, Ostracoda) from the ancient Lake Malawi (Africa), with the description of a new genus and three new species

FIGURE 5. Limbs of Malawidopsis stellae gen. et sp. nov., male—A. T3, Paratype (INV.159013). B. Rake like organ, Paratype (INV.159013). C. T2, Holotype (INV.159010). D. Mx1, respiratory plate not shown, Paratype (INV.159014). E. T1, Holotype. F. Lpp, Holotype. G. Rpp, Paratype (INV.159068). H. Hp, Holotype. I. Zenker's organ, Paratype (INV.159012). Scales: A, C–I = 50 µm; B = 10 µm.

FIGURE 15 in An endemic species flock of Cypridopsinae (Crustacea, Ostracoda) from the ancient Lake Malawi (Africa), with the description of a new genus and three new species

FIGURE 15. Limbs of Malawidopsis antoniae gen. et sp. nov., male—A. T3 Holotype (INV.159032). B. T2, Paratype (INV.159043). C. Mx1, Holotype (INV.159032) D. Respiratory plate, Holotype (INV.159032). E. Lpp, Paratype (INV.159034). F. Rpp, Paratype (INV.159034). G. T1, Paratype (INV.159034). H. Hp, Holotype. I. Zenker's organ, Paratype (INV.159038). Scales: all 50 µm.

FIGURE 1 in An endemic species flock of Cypridopsinae (Crustacea, Ostracoda) from the ancient Lake Malawi (Africa), with the description of a new genus and three new species

FIGURE 1. Location of Lake Malawi in the East African Rift System. Source: https://en.wikipedia.org/wiki/African_Great_Lakes (CC BY-SA 4.0)

FIGURE 14 in An endemic species flock of Cypridopsinae (Crustacea, Ostracoda) from the ancient Lake Malawi (Africa), with the description of a new genus and three new species

FIGURE 14. Limbs of Malawidopsis antoniae gen. et sp. nov., male—A. A1, Paratype (INV.159037). B. A2, Paratype (INV.159036). C. A2, detail of terminal part, Paratype (INV.159036). D. MdCox, Holotype (INV.159032). E. Md palp, Paratype (INV.159044). Scales: all 50 µm.