Baoqing Ding

Evolution of body shape in differently coloured sympatric congeners and allopatric populations of Lake Malawi's rock-dwelling cichlids

The cichlid fishes of Lake Malawi represent one of the most diverse adaptive radiations of vertebrates known. Among the rock‐dwelling cichlids (mbuna), closely related sympatric congeners possess similar trophic morphologies (i.e. cranial and jaw structures), defend overlapping or adjacent territories, but can be easily distinguished based on male nuptial coloration. The apparent morphological similarity of congeners, however, leads to an ecological conundrum: theory predicts that ecological competition should lead to competitive exclusion. Hence, we hypothesized that slight, yet significant, ecological differences accompanied the divergence in sexual signals and that the divergence of ecological and sexual traits is correlated. To evaluate this hypothesis, we quantified body shape, a trait of known ecological importance, in populations of Maylandia zebra, a barred, widespread mbuna, and several sympatric nonbarred congeners. We found that the barred populations differ in body shape from their nonbarred sympatric congeners and that the direction of shape differences was consistent across all barred vs. nonbarred comparisons. Barred populations are generally deeper bodied which may be an adaptation to the structurally complex habitat they prefer, whereas the nonbarred species have a more fusiform body shape, which may be adaptive in their more open microhabitat. Furthermore, M. zebra populations sympatric with nonbarred congeners differ from populations where the nonbarred phenotype is absent and occupy less morphospace, indicating potential ecological character displacement. Mitochondrial DNA as well as published AFLP data indicated that the nonbarred populations are not monophyletic and therefore may have evolved multiple times independently. Overall our data suggest that the evolution of coloration and body shape may be coupled as a result of correlational selection. We hypothesize that correlated evolution of sexually selected and ecological traits may have contributed to rapid speciation as well as the maintenance of diversity in one of the most diverse adaptive radiations known.

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.

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.

Isolation and characterization of 11 polymorphic microsatellite loci for the Saurogobio dabryi (Teleostei: Cyprinidae)

Eleven polymorphic microsatellite loci for the Saurogobio dabryi were isolated from three repeat-enriched genomic libraries. Characterization of these loci were developed in 24 individuals with the number of alleles ranged from 2 to 14. Observed heterozygosity ranged from 0.17 to 1.00 and expected heterozygosity was from 0.16 to 0.93. Three loci significantly deviated from Hardy–Weinberg equilibrium after Bonferroni correction, and all pairwise tests for linkage disequilibrium among loci were nonsignificant. These novel loci will be used to investigate the population genetics and geographic differentiation in Saurogobio dabryi.

Body shape differences in a pair of closely related Malawi cichlids and their hybrids: Effects of genetic variation, phenotypic plasticity, and transgressive segregation

Abstract Phenotypic differences may have genetic and plastic components. Here, we investigated the contributions of both for differences in body shape in two species of Lake Malawi cichlids using wild‐caught specimens and a common garden experiment. We further hybridized the two species to investigate the mode of gene action influencing body shape differences and to examine the potential for transgressive segregation. We found that body shape differences between the two species observed in the field are maintained after more than 10 generations in a standardized environment. Nonetheless, both species experienced similar changes in the laboratory environment. Our hybrid cross experiment confirmed that substantial variation in body shape appears to be genetically determined. The data further suggest that the underlying mode of gene action is complex and cannot be explained by simple additive or additive‐dominance models. Transgressive phenotypes were found in the hybrid generations, as hybrids occupied significantly more morphospace than both parentals combined. Further, the body shapes of transgressive individuals resemble the body shapes observed in other Lake Malawi rock‐dwelling genera. Our findings indicate that body shape can respond to selection immediately, through plasticity, and over longer timescales through adaptation. In addition, our results suggest that hybridization may have played an important role in the diversification of Lake Malawi cichlids through creating new phenotypic variation.

Testing the utility of fluorescent proteins in Mimulus lewisii by an Agrobacterium-mediated transient assay.

Key messageTheAgrobacterium-mediated transient expression assay by leaf infiltration inMimulus lewisiiis robust. Fluorescent proteins EGFP, EYFP and DsRed give bright fluorescence signals in the infiltrated tissue.AbstractMimulus lewisii is an emerging developmental genetic model system. Recently developed genomic and genetic resources and a stable transformation protocol have greatly facilitated the identification and functional characterization of genes controlling the development of ecologically important floral traits using this species. To further expedite gene and protein function analyses in M. lewisii, we adopted and simplified the Agrobacterium-mediated transient gene expression method routinely used in tobacco plants. With the validated transient assay, we examined the performance of fluorescent proteins EGFP, EYFP and DsRed in M. lewisii. All three proteins gave bright fluorescence signals when transiently expressed in agroinfiltrated leaves. Furthermore, we demonstrated the utility of fluorescent proteins in M. lewisii by showing the nuclear localization of Reduced Carotenoid Pigmentation 1 (RCP1), a recently discovered R2R3-MYB transcription factor that regulates carotenoid pigmentation during flower development. Both the transient assay and the fluorescent proteins are valuable additions to the M. lewisii toolbox, making this emerging genetic and developmental model system even more powerful.

Developmental genetics of corolla tube formation: role of the tasiRNA-ARF pathway

More than 80,000 angiosperm species produce flowers with petals fused into a corolla tube. As an important element of the tremendous diversity of flower morphology, the corolla tube plays a critical role in many specialized interactions between plants and animal pollinators (e.g., beeflies, hawkmoths, hummingbirds, nectar bats), which in turn drives rapid plant speciation. Despite its clear significance in plant reproduction and evolution, the corolla tube remains one of the least understood plant structures from a developmental genetics perspective. Through mutant analyses and transgenic experiments, here we show that the tasiRNA-ARF pathway is required for corolla tube formation in the monkeyflower species Mimulus lewisii. Loss-of-function mutations in the M. lewisii orthologs of ARGONAUTE7 and SUPPRESSOR OF GENE SILENCING 3 cause a dramatic decrease in abundance of TAS3-derived small RNAs and a moderate up-regulation of AUXIN RESPONSE FACTOR 3 (ARF3) and ARF4, which lead to inhibition of lateral expansion of the bases of petal primordia and complete arrest of the upward growth of the inter-primordial regions, resulting in unfused corollas. By using an auxin reporter construct, we discovered that auxin distribution is continuous along the petal primordium base and the inter-primordial region during the critical stage of corolla tube formation in the wild-type, and that this auxin distribution is much weaker and more restricted in the mutant. Together, these results suggest a new conceptual model highlighting the central role of auxin directed synchronized growth of the petal primordium base and the inter-primordial region in corolla tube formation.

Formation of periodic pigment spots by the reaction-diffusion mechanism

Many organisms exhibit visually striking spotted or striped pigmentation patterns. Turing’s reaction-diffusion model postulates that such periodic pigmentation patterns form when a local autocatalytic feedback loop and a long-range inhibitory feedback loop interact. At its simplest, this network only requires one self-activating activator that also activates a repressor, which inhibits the activator and diffuses to neighboring cells. However, the molecular activators and repressors fully fitting this versatile model remain elusive. Here, we characterize an R2R3-MYB activator and an R3-MYB repressor in monkeyflowers that correspond to Turing’s model and explain how periodic anthocyanin spots form. Notably, disrupting this pattern impacts pollinator visitation. Thus, subtle changes in simple reaction-diffusion networks are likely essential contributors to the evolution of the remarkable diversity of periodic pigmentation patterns in flowers.

Saurogobio punctatus sp. nov., a new cyprinid gudgeon (Teleostei: Cypriniformes) from the Yangtze River, based on both morphological and molecular data

A new cyprinid gudgeon, Saurogobio punctatus sp. nov., is described based on specimens collected from the Yangtze River, China. The new species can be distinguished from its congeners by differences in both morphology and the cytochrome b (cytb) gene sequence. Numerous minute blackish spots are scattered on dorsal and caudal fins in S. punctatus sp. nov. v. absent in the other seven valid Saurogobio species. The new species can be further distinguished from its congeners by the following unique combination of characters: a dorsal fin with eight branched rays; absence of scales in chest area before pectoral origin; upper and lower lips thick, covered with papillae; and a papillose mental pad approximately triangular. Morphologically, the new species most resembles the Chinese lizard gudgeon Saurogobio dabryi, but the new species lays yellowish adhesive eggs v. white pelagic eggs in S. dabryi. A phylogenetic analysis of all Saurogobio species based on cytb gene sequences indicated that S. punctatus sp. nov was distinctly separated from its congeners, with mean sequence divergence ranging from 12·6 to 21·0%. Therefore, molecular data further supported the distinctiveness of the new species.

Complex patterns of genetic and phenotypic divergence in populations of the Lake Malawi cichlid Maylandia zebra

Ecological speciation, which relies heavily on selection driving the emergence of new species, has become the primary paradigm through which rapid species radiations are understood. In this way, selection, particularly ecological selection, is assumed to be the driver of most species radiations. However, in many radiations, such as the radiation of Lake Malawi’s cichlids, the assumption of selection as the driver of speciation has rarely been explicitly tested, and drift, often, has completely been ignored as potential factor. In order to understand the forces driving the divergence of Lake Malawi cichlids at the microevolutionary level, we studied the genetic and phenotypic divergence of ten allopatric populations of Maylandia zebra. We estimated effective population sizes as proxy for drift. Further, we compared neutral genetic differentiation to divergence in three phenotypic traits: body size, body shape, and melanophore counts. We found small, yet significant, population differentiation in all the studied traits across most populations. Population sizes were small rendering the potential for drift to be high. However, phenotypic differentiation exceeded neutral expectations for all traits suggesting divergent local selection. Our data suggest that natural, and potentially also sexual, selection may be the dominant force driving population differentiation in Lake Malawi’s rock-dwelling cichlids, despite the potential for drift in small populations.