NSF DEB-2225130 (R. Betancur-R.). Collaborative Research: Investigating the factors shaping marine-derived freshwater fish radiations in tropical rivers of Australia and New Guinea

Project overview: The goal of this project is to investigate the evolutionary history of marine-derived freshwater fish groups in Australia and New Guinea (AU-NG), an area that offers a unique set of conditions for understanding the historical factors regulating adaptive radiations at regional scales. Unlike riverine fish communities in other continents that mostly include salt intolerant groups of freshwater origins, the primary freshwater ichthyofauna in AU-NG is depauperate and most lineages are marine-derived, including ~500 species in 28 families spread across the Fish Tree of Life. This assemblage includes seven or more putative adaptive radiations that took place as invading marine lineages encountered open niche space with low pre-existing diversity upon colonization of novel habitat regimes. This project aims to identify the factors that promoted or constrained diversification, phenotypic, and genomic evolution of marine-derived groups in the region. We propose an innovative integration of phylogenomics, phylogenetic comparative methods, and comparative genomics (PhyloG2P) applied to a suite of morphological, paleontological, dietary, and habitat affiliation data layers to examine two core aspects: adaptive radiations stemming from marine-to-freshwater transitions and ecomorphological convergences associated with transitions along the benthic-to-pelagic axis. We will use time-calibrated trees to explore diversification patterns and unravel the chronological sequence of transitions into the region. We will test whether the tempo and mode of habitat transitions influenced the outcome of freshwater radiations, the effect of ecological regimes on diversification and morphological disparity, and the extent to which unrelated groups occupying similar habitats have converged ecomorphologically. PhyloG2P approaches will be used to identify loci related to functional adaptations, including signatures of molecular adaptation and convergence as well as gene family expansions and contractions.  

Total budget approved: $1,126,532 for 48 months ($695,571 for lead PI R. Betancur). Start date 02/01/2023.

NSF DEB-2144325 (D. Arcila). CAREER: Integrating genomic, paleoclimatic, and morphological approaches to unravel the evolutionary history of fossil and extant marine fishes. 

Project overview: This project proposes the implementation of an integrative macroevolutionary investigation of morphological diversity using whole-genome sequencing data coupled with state-of-the-art approaches for the study of morphological, paleoclimatic, and paleontological data to elucidate the drivers of phenotypic diversification in a mostly marine fish clade (tetraodontiforms). This study will address three main questions: (i) are ancient climatic events associated with an increase in rates of morphological evolution? (ii) is genome size evolution correlated with higher rates of morphological and lineage diversification? and (iii) is phenotypic convergence in body size correlated with patterns of molecular convergence? Results will ultimately establish new directions to understand how other marine groups have evolved and adapted to abrupt climatic changes. It will also enhance our understanding of the relationships between phenotypic and genotypic predictability using whole-genome sequencing and morphological data in a macroevolutionary context and create new ways of exploring evolution through novel comparative analyses based on a variety of rich layers of data. The educational plan of this proposal includes a new ichthyology course, coding summer workshops, and a variety of museum exhibitions and outreach activities, presenting fishes as an excellent system to understand morphological evolution.  

Total budget approved $1,231,653 for 60 months (PI D.Arcila). Start date 01/20/2022.

NSF DEB-2015404 (D. Arcila). Exploring the genomics of convergent snout elongations in deep-sea fishes 

Project overview: Explaining how similar traits have independently evolved in distantly related organisms is a central goal of evolutionary biology. Fishes are one of the few evolutionary systems that provide repeated cases of adaptation to deep-sea marine environments, one of the most extreme and underexplored environments on earth. Habitat colonizations from shallow to deep-sea habitats have occurred multiple times resulting in a variety of remarkable adaptations from the presence of bioluminescence and small body size to a diverse array of morphological specializations. However, detailed comparative studies investigating the origin and genomic bases of specialized phenotypic novelties that have repeatedly appeared in the deep-sea continue to be poorly understood. This project aims to develop a comparative approach to study convergent morphological evolution and its underlying ecological and genomic bases in the deep-sea spikefishes (Triacanthodidae, Tetraodontiformes), which are distributed around the tropical and temperate upper slopes of the world’s oceans. Spikefishes provide an outstanding system for investigating convergent evolution as lineages in the group have independently evolved at least twice the most extreme tubular snout elongation in the Fish Tree of Life, have some of the smallest vertebrate genomes, and included well-preserved fossil species from the Eocene and Oligocene. The integration of state-of-the-art genomic and morphological data with the study of extant and fossil species will allow new ways of exploring convergent morphological evolution in a genomic and ecological framework. Moreover, understanding the determinants of deep-sea convergence at the molecular level has the potential to inform general principles of adaptation and morphological predictivity along ocean depth gradients.

Total budget approved $300,062 for 36 months (PI D.Arcila; CoPI K. Bemis, Smithsonian NMNH). Start date 05/30/2020.

NSF-DEB-1541491 (GoLife program; R. Betancur-R.) Collaborative Research: FishLife: genealogy and traits of living and fossil vertebrates that never left the water

Project overview: Completing the Tree of Life is a grand challenge in science, on the same intellectual scale as investigating the nature of matter or the origin of the universe; it is fundamental to understanding our world. As we make progress with this challenge, biology is being transformed by the integration of complete phylogenetic trees with rich pools of data that empower us to address large-scale questions about life. Our knowledge of the tree of life for vertebrates, and in particular the species-rich branches of fishes among which sprung a branch that gave rise to tetrapods, have undergone a dramatic transformation in the last two years due to AToL projects on teleosts and cartilaginous fishes. Increased phylogenetic resolution has led to identification of new clades among poorly resolved groups of bony fishes but still other groups remain poorly sampled and in dire need of resolution. Likewise, relationships among sharks, rays, and chimaeras are becoming clearer but an integrative and comprehensive phylogeny including cartilaginous and bony fishes has never been resolved. Here we propose such integrative analysis to elucidate the evolutionary history of all fishes and their connection to tetrapods, to complete the ongoing VertLife-terrestrial project by combining genomic, paleontological, anatomical, functional, ecological, and comparative approaches. The research team blends strengths in collection-based research for all groups of fishes, molecular and morphological phylogenetics, bioinformatics, and comparative analyses to synthesize massive data sets to resolve the phylogeny of all described fish species and perform evolutionary analysis of key traits. 

Total budget approved $2,447,345 for 60 months ($383,717 for PI R. Betancur-R.). Start date 10/01/2015.

NSF-DEB-1457184 (R. Betancur-R.) Collaborative Research: The role of habitat transitions in parallel marine fish radiations 

Project overview: recent advances in fish phylogenetics are steadily resolving long-lasting uncertainties on the phylogeny of the most diverse percomorph groups and opening up exciting and unprecedented opportunities to study mechanisms that may explain the extraordinary diversity of marine fishes. We take advantage of newly revealed percomorph clades that include disparate forms such as tunas, seahorses, flounders, and billfishes to propose an integrated research approach combining phylogenomics and phenomics. In brief, we will infer a time-calibrated phylogeny based on specifically designed genome-wide exon markers to provide the evolutionary framework for comparing parallel radiations that split lineages along similar ecological gradients. We will also assemble a large phenotypic dataset consisting of specimen photographs. Using state-of-the-art comparative methodologies, we will test for the effect of habitat shifts along the benthic-pelagic axis on the rate of morphological and lineage diversification. The combination of well-resolved, strongly-supported molecular phylogenies, the fossil record, trait and ecological data, and comparative methodologies will provide new insights into our understanding of organismal diversification. Results of this project will be readily available for comparison with ongoing research on other taxonomic groups.

Total budget approved $773,092 for 36 months ($375,196 for PI R. Betancur-R.; $397,896 for PI G. Orti). Start date 05/15/2015.