The repeated evolution of stripe patterns is correlated with body morphology in the adaptive radiations of East African cichlid fishes

Meristic co-evolution and genomic co-localization of lateral line scales and vertebrae in Central American cichlid fishes

Meristic traits are often treated as distinct phenotypes that can be used to differentiate and delineate recently diverged species. For instance, the number of lateral line scales and vertebrae, two traits that vary substantially among Neotropical Heroine cichlid species, have been previously suggested to co-evolve. These meristic traits could co-evolve due to shared adaptive, developmental, or genetic factors. If they were found to be genetically or developmentally non-independent, this might require a more general re-evaluation of their role in evolutionary or taxonomic studies. We expanded a previous analysis of correlated evolution of meristic traits (lateral line scales and vertebrae counts) in these fishes to include a range of phylogenetic reconstructions as well as the analyses of 13 Nicaraguan Midas cichlid species (Amphilophus spp.). Additionally, we performed qualitative traits locus (QTL) mapping in a F2 laboratory-reared hybrid population from two ecologically divergent Midas cichlid fish species to discover and evaluate whether genomic co-segregation might explain the observed patterns of meristic co-evolution. Meristic values for these traits were found to morphologically differentiate some species of the Midas cichlid adaptive radiation. Our QTL analysis pinpointed several genomic regions associated with divergence in these traits and highlighted the potential for genomic co-segregation of the lateral line and vertebrae numbers on two chromosomes. Further, our phylogenetic comparative analyses consistently recovered a significant positive evolutionary correlation between the counts of lateral line scale and vertebrae numbers in Neotropical cichlids. Hence, the findings of genomic co-segregation could partially explain the co-evolution of these two meristic traits in these species. Continuing to unravel the genetic architecture governing meristic divergence helps to better understand both trait correlations and the utility of meristic traits in taxonomic diagnoses and how traits in phenotypes might be expected to co-evolve.

Genes, Morphology, Performance, and Fitness: Quantifying Organismal Performance to Understand Adaptive Evolution

To understand the complexities of morphological evolution, we must understand the relationships between genes, morphology, performance, and fitness in complex traits. Genomicists have made tremendous progress in finding the genetic basis of many phenotypes, including a myriad of morphological characters. Similarly, field biologists have greatly advanced our understanding of the relationship between performance and fitness in natural populations. However, the connection from morphology to performance has primarily been studied at the interspecific level, meaning that in most cases we lack a mechanistic understanding of how evolutionarily relevant variation among individuals affects organismal performance. Therefore, functional morphologists need methods that will allow for the analysis of fine-grained intraspecific variation in order to close the path from genes to fitness. We suggest three methodological areas that we believe are well suited for this research program and provide examples of how each can be applied within fish model systems to build our understanding of microevolutionary processes. Specifically, we believe that structural equation modeling, biological robotics, and simultaneous multi-modal functional data acquisition will open up fruitful collaborations among biomechanists, evolutionary biologists, and field biologists. It is only through the combined efforts of all three fields that we will understand the connection between evolution (acting at the level of genes) and natural selection (acting on fitness).

Multiple paths toward repeated phenotypic evolution in the spiny-leg adaptive radiation (Tetragnatha; Hawai'i)

The repeated evolution of phenotypes provides clear evidence for the role of natural selection in driving evolutionary change. However, the evolutionary origin of repeated phenotypes can be difficult to disentangle as it can arise from a combination of factors such as gene flow, shared ancestral polymorphisms or mutation. Here, we investigate the presence of these evolutionary processes in the Hawaiian spiny-leg Tetragnatha adaptive radiation, which includes four microhabitat-specialists or ecomorphs, with different body pigmentation and size (Green, Large Brown, Maroon, and Small Brown). We investigated the evolutionary history of this radiation using 76 newly generated low-coverage, whole-genome resequenced samples, along with phylogenetic and population genomic tools. Considering the Green ecomorph as the ancestral state, our results suggest that the Green ecomorph likely re-evolved once, the Large Brown and Maroon ecomorphs evolved twice and the Small Brown evolved three times. We found that the evolution of the Maroon and Small Brown ecomorphs likely involved ancestral hybridization events, while the Green and Large Brown ecomorphs likely evolved through novel mutations, despite a high rate of incomplete lineage sorting in the dataset. Our findings demonstrate that the repeated evolution of ecomorphs in the Hawaiian spiny-leg Tetragnatha is influenced by multiple evolutionary processes.

Phylogenomic comparative methods: Accurate evolutionary inferences in the presence of gene tree discordance

Phylogenetic comparative methods have long been a mainstay of evolutionary biology, allowing for the study of trait evolution across species while accounting for their common ancestry. These analyses typically assume a single, bifurcating phylogenetic tree describing the shared history among species. However, modern phylogenomic analyses have shown that genomes are often composed of mosaic histories that can disagree both with the species tree and with each other-so-called discordant gene trees. These gene trees describe shared histories that are not captured by the species tree, and therefore that are unaccounted for in classic comparative approaches. The application of standard comparative methods to species histories containing discordance leads to incorrect inferences about the timing, direction, and rate of evolution. Here, we develop two approaches for incorporating gene tree histories into comparative methods: one that constructs an updated phylogenetic variance-covariance matrix from gene trees, and another that applies Felsenstein's pruning algorithm over a set of gene trees to calculate trait histories and likelihoods. Using simulation, we demonstrate that our approaches generate much more accurate estimates of tree-wide rates of trait evolution than standard methods. We apply our methods to two clades of the wild tomato genus Solanum with varying rates of discordance, demonstrating the contribution of gene tree discordance to variation in a set of floral traits. Our approaches have the potential to be applied to a broad range of classic inference problems in phylogenetics, including ancestral state reconstruction and the inference of lineage-specific rate shifts.

Transcriptome analyses of betta fish (Betta splendens) provide novel insights into fin regeneration and color-related genes

The betta fish (Betta splendens), an important ornamental fish, haswell-developed and colorful fins.After fin amputation, betta fish can easily regenerate finssimilar to the originalsin terms of structureand color. The powerful fin regeneration ability and a variety of colors in the betta fish are fascinating. However, the underlying molecular mechanisms are still not fully understood. In this study, tail fin amputation and regeneration experiments were performed on two kinds of betta fish: red and white color betta fish. Then, transcriptome analyseswere conducted to screen out fin regeneration and color-relatedgenes in betta fish. Through enrichment analyses of differentially expressed genes (DEGs), we founda series of enrichment pathways and genes related to finregeneration, including cell cycle (i.e. plcg2), TGF-beta signaling pathway (i.e. bmp6), PI3K-Akt signaling pathway (i.e. loxl2aand loxl2b), Wnt signaling pathway(i.e. lef1), gap junctions (i.e. cx43), angiogenesis (i.e. foxp1), and interferon regulatory factor (i.e. irf8). Meanwhile, some fin color-related pathways and genes were identified in betta fish, especially melanogenesis (i.e. tyr, tyrp1a, tyrp1b, and mc1r) and carotenoid color genes (i.e. pax3, pax7, sox10, and ednrba). In conclusion, this studycan not only enrich the research onfish tissue regeneration, but also has a potential significance for the aquaculture and breeding of the betta fish.

East African cichlid fishes

Cichlid fishes are a very diverse and species-rich family of teleost fishes that inhabit lakes and rivers of India, Africa, and South and Central America. Research has largely focused on East African cichlids of the Rift Lakes Tanganyika, Malawi, and Victoria that constitute the biodiversity hotspots of cichlid fishes. Here, we give an overview of the study system, research questions, and methodologies. Research on cichlid fishes spans many disciplines including ecology, evolution, physiology, genetics, development, and behavioral biology. In this review, we focus on a range of organismal traits, including coloration phenotypes, trophic adaptations, appendages like fins and scales, sensory systems, sex, brains, and behaviors. Moreover, we discuss studies on cichlid phylogenies, plasticity, and general evolutionary patterns, ranging from convergence to speciation rates and the proximate and ultimate mechanisms underlying these processes. From a methodological viewpoint, the last decade has brought great advances in cichlid fish research, particularly through the advent of affordable deep sequencing and advances in genetic manipulations. The ability to integrate across traits and research disciplines, ranging from developmental biology to ecology and evolution, makes cichlid fishes a fascinating research system.