INVESTIGATING THE GENETIC BASIS OF AND PLASTICITY IN ECOLOGICALLY RELEVANT PHENOTYPES IN AFRICAN CICHLIDS

Understanding the generation of phenotypic variation by linking it to genetic variation has long been a focus of evolutionary biology; this framework has successfully been implemented in a variety of studies across the tree of life1,2. However, our understanding of the phenotype remains incomplete until we account for a myriad of interactions that influence the genotype-phenotype map, including interactions between traits (TxT), interactions between genes and the environment (GxE), as well as the ways in which various types of interactions are nested within and build upon one another (e.g., (TxT)xG). My dissertation aims to contribute to filling this gap by dissecting the interactions that influence variation in ecologically-relevant phenotypes in a model adaptive radiation: African cichlid fish. We utilize a stereotypical ecomorphological axis of variation, in which benthic fish scrape and bite prey off the rocky substrate while pelagic fish suction prey out of the water column3. Chapter 1 focuses predominantly on understanding the genetics that underlie variation across disparate anatomical units which relate to both the feeding and locomotive systems in these fish (i.e. a [[TxT]xG] interaction). We found that the genotype–phenotype map for fin shape is largely distinct from other morphological characters including body and craniofacial shape. These data suggest that key aspects of fin, body and jaw shape are genetically modular and that the coordinated evolution of these traits in cichlids is more likely due to common selective pressures than to pleiotropy or linkage. Chapter 2 dissects the genetics underlying those same anatomical units across environments, representing a more complex model of putative interactions (i.e. [[[TxT]xG]xE]). In more specific terms, this chapter aims to understand the genetic basis of phenotypic plasticity, We found a substantial degree of modularity in the plastic responses at both the morphological and genetic levels. In all, our data provide minimal support for the existence of global regulators of plasticity, serve as an important step toward further characterizing the genetic basis of plasticity in cichlids, and provide a list of candidate loci for future functional analyses. Chapter 3 delves more into a specific GxE interaction in craniofacial morphology, and for the first time in a vertebrate system tests the functional capacity of a signal transduction pathway to mediate the magnitude of a plastic response. We verify important roles for Hh signaling in this response, thus filling important gaps in the field. Together, my dissertation demonstrates how a broadly integrative approach to evolutionary biology can allow us to layer multiple lines of empirical evidence onto strong theoretical frameworks and further generate insights into the production and maintenance of real-world variation

Foraging environment determines the genetic architecture and evolutionary potential of trophic morphology in cichlid fishes

Phenotypic plasticity allows organisms to change their phenotype in response to shifts in the environment. While a central topic in current discussions of evolutionary potential, a comprehensive understanding of the genetic underpinnings of plasticity is lacking in systems undergoing adaptive diversification. Here, we investigate the genetic basis of phenotypic plasticity in a textbook adaptive radiation, Lake Malawi cichlid fishes. Specifically, we crossed two divergent species to generate an F3 hybrid mapping population. At early juvenile stages, hybrid families were split and reared in alternate foraging environments that mimicked benthic/scraping or limnetic/sucking modes of feeding. These alternate treatments produced a variation in morphology that was broadly similar to the major axis of divergence among Malawi cichlids, providing support for the flexible stem theory of adaptive radiation. Next, we found that the genetic architecture of several morphological traits was highly sensitive to the environment. In particular, of 22 significant quantitative trait loci (QTL), only one was shared between the environments. In addition, we identified QTL acting across environments with alternate alleles being differentially sensitive to the environment. Thus, our data suggest that while plasticity is largely determined by loci specific to a given environment, it may also be influenced by loci operating across environments. Finally, our mapping data provide evidence for the evolution of plasticity via genetic assimilation at an important regulatory locus, ptch1. In all, our data address long-standing discussions about the genetic basis and evolution of plasticity. They also underscore the importance of the environment in affecting developmental outcomes, genetic architectures, morphological diversity and evolutionary potential

Hedgehog signaling is necessary and sufficient to mediate craniofacial plasticity in teleosts

Phenotypic plasticity, the ability of a single genotype to produce multiple phenotypes under different environmental conditions, is critical for the origins and maintenance of biodiversity; however, the genetic mechanisms underlying plasticity as well as how variation in those mechanisms can drive evolutionary change remain poorly understood. Here, we examine the cichlid feeding apparatus, an icon of both prodigious evolutionary divergence and adaptive phenotypic plasticity. We first provide a tissue-level mechanism for plasticity in craniofacial shape by measuring rates of bone deposition within functionally salient elements of the feeding apparatus in fishes forced to employ alternate foraging modes. We show that levels and patterns of phenotypic plasticity are distinct among closely related cichlid species, underscoring the evolutionary potential of this trait. Next, we demonstrate that hedgehog (Hh) signaling, which has been implicated in the evolutionary divergence of cichlid feeding architecture, is associated with environmentally induced rates of bone deposition. Finally, to demonstrate that Hh levels are the cause of the plastic response and not simply the consequence of producing more bone, we use transgenic zebrafish in which Hh levels could be experimentally manipulated under different foraging conditions. Notably, we find that the ability to modulate bone deposition rates in different environments is dampened when Hh levels are reduced, whereas the sensitivity of bone deposition to different mechanical demands increases with elevated Hh levels. These data advance a mechanistic understanding of phenotypic plasticity in the teleost feeding apparatus and in doing so contribute key insights into the origins of adaptive morphological radiations

Wnt_Modulation_Data_MZ

Fin measures in the species, MZ, following manipulation of the Wnt pathway with small molecules

Data from: Genetic and developmental basis for fin shape variation in African cichlid fishes

Adaptive radiations are often characterized by the rapid evolution of traits associated with divergent feeding modes. For example, the evolutionary history of African cichlids is marked by repeated and coordinated shifts in skull, trophic, fin and body shape. Here, we seek to explore the molecular basis for fin shape variation in Lake Malawi cichlids. We first described variation within an F2 mapping population derived by crossing two cichlid species with divergent morphologies including fin shape. We then used this population to genetically map loci that influence variation in this trait. We found that the genotype–phenotype map for fin shape is largely distinct from other morphological characters including body and craniofacial shape. These data suggest that key aspects of fin, body and jaw shape are genetically modular and that the coordinated evolution of these traits in cichlids is more likely due to common selective pressures than to pleiotropy or linkage. We next combined genetic mapping data with population-level genome scans to identify wnt7aa and col1a1 as candidate genes underlying variation in the number of pectoral fin ray elements. Gene expression patterns across species with different fin morphologies and small molecule manipulation of the Wnt pathway during fin development further support the hypothesis that variation at these loci underlies divergence in fin shape between cichlid species. In all, our data provide additional insights into the genetic and molecular mechanisms associated with morphological divergence in this important adaptive radiation

Key

Key that provides information for each data file associated with this entry

Linkage Map_Fin

linkage map and fin traits for qtl analysi

Fin_LM_parental

x,y landmark data for fin shape in the parental specie

Parental_Fin_Data

Various fin measures for parental specie

Wnt_Modulation_Data_LF_TRC

Fin measures in TRC and LF larvae following manipulation of the Wnt pathway with small molecules