Research

Why do some taxa have more species than others? One hypothesis to explain this phenomenon is “evolvability”: lineages with an intrinsic ability to evolve novel morphologies also have an increased ability to speciate. Several key predictions can be made based on differential evolvability across clades. More evolvable lineages should have higher richness and diversification rates, and have more phenotypic disparity and rates of phenotypic evolution. Lineages that enjoy fast phenotypic evolution should also diversify into a larger variety of ecological niches. Finally, key innovations leading to adaptive radiations may actually be traits that also promote evolvability through an increase in morphological and functional diversity.

My dissertation tests these macroevolutionary predictions within the ray-finned fishes (Actinopterygii), which comprise about half of vertebrate diversity, with over 30,000 described species across nearly 500 families. Fishes are an excellent study system due to their high species richness as well as exceptional phenotypic and ecological diversity, which are distributed unevenly across the fish tree of life. Fishes are also intensively harvested for human consumption, leading to potentially disastrous impacts on their diversity and their ability to serve as ecological role players and as a human food source.

What processes drive the rate of lineage origination and the rate of phenotypic (body shape) evolution? Is there a correlation between speciation rates and rates of character evolution? Are certain environments (e.g., coral reefs) associated with increased rates of phenotypic evolution? How have mass extinction events (e.g., the Cretaceous-Paleogene) altered the trajectory of fish morphological evolution?

Relevant publications:

(2021) BF Melo, BL Sidlauskas, TJ Near, FF Roxo, A Ghezelayagh, LE Ochoa, MLJ Stiassny, J Arroyave, J Chang, BC Faircloth, DJ MacGuigan, RC Harrington, RC Benine, MD Burns, K Hoekzema, NC Sanches, JA Maldonado Ocampo, RMC Castro, F Foresti, ME Alfaro, C Oliveira. Accelerated diversification explains the exceptional species richness of tropical characoid fishes. Systematic Biology 71(1):78-92 doi:10.1093/sysbio/syab040

(2020) LE Ochoa, A Datovo, C DoNascimiento, FF Roxo, MH Sabaj, J Chang, BF Melo, GSC Silva, F Foresti, ME Alfaro, C Oliveira. Phylogenomic analysis of trichomycterid catfishes (Teleostei: Siluriformes) inferred from ultraconserved elements. Scientific Reports 10(1):2697 doi:10.1038/s41598-020-59519-w

(2020) E Gjesfjeld, D Silvestro, J Chang, B Koch, JG Foster, ME Alfaro. A quantitative workflow for modeling diversification in material culture. PLOS ONE 15(2):e0227579 doi:10.1371/journal.pone.0227579

(2019) J Chang, DL Rabosky, ME Alfaro. Estimating diversification rates on incompletely sampled phylogenies: theoretical concerns and practical solutions. Systematic Biology 69(3):602-611 doi:10.1093/sysbio/syz081 [link]

(2019) J Chang, DL Rabosky, SA Smith, ME Alfaro. An R package and online resource for macroevolutionary studies using the ray-finned fish tree of life. Methods in Ecology and Evolution 10(7):1118-1124 doi:10.1111/2041-210X.13182

(2018) DL Rabosky, J Chang, PO Title, PF Cowman, L Sallan, M Friedman, K Kaschner, C Garilao, TJ Near, M Coll, ME Alfaro. An inverse latitudinal gradient in speciation rate for marine fishes. Nature 559(7714):392-395 doi:10.1038/s41586-018-0273-1

(2018) G Burin, LRV de Alencar, J Chang, ME Alfaro, TB Quental. How well can we estimate diversity dynamics for clades in diversity decline?. Systematic Biology 68(1):47-62 doi:10.1093/sysbio/syy037 [link]

(2017) DL Rabosky, JS Mitchell, J Chang. Is BAMM flawed? Theoretical and practical concerns in the analysis of multi-rate diversification models. Systematic Biology 66(4):477-498 doi:10.1093/sysbio/syx037

(2016) E Gjesfjeld, J Chang, D Silvestro, C Kelty, ME Alfaro. Competition and extinction explain the evolution of diversity in American automobiles. Palgrave Communications 2(1):16019 doi:10.1057/palcomms.2016.19

(2013) DL Rabosky, F Santini, JM Eastman, SA Smith, BL Sidlauskas, J Chang, ME Alfaro. Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation. Nature Communications 4:1958 doi:10.1038/ncomms2958

How can researchers overcome general problems in high-throughput collection and analysis of phenotypic data?

Relevant publications:

(2015) J Chang, ME Alfaro. Crowdsourced geometric morphometrics enable rapid large-scale collection and analysis of phenotypic data. Methods in Ecology and Evolution 7(4):472-482 doi:10.1111/2041-210x.12508

Ultraconserved elements (UCEs) are highly conserved regions of genomes shared among taxa, including birds, fishes, and humans. Recently they have been used in a number of different publications reconstructing the evolutionary history of many challenging groups.

Relevant publications:

(2019) FF Roxo, LE Ochoa, MH Sabaj, NK Lujan, R Covain, GSC Silva, BF Melo, JS Albert, J Chang, F Foresti, ME Alfaro, C Oliveira. Phylogenomic reappraisal of the Neotropical catfish family Loricariidae (Teleostei: Siluriformes) using ultraconserved elements. Molecular Phylogenetics and Evolution 135:148-165 doi:10.1016/j.ympev.2019.02.017

(2018) JD DiBattista, ME Alfaro, L Sorenson, JH Choat, JA Hobbs, TH Sinclair-Taylor, LA Rocha, J Chang, OJ Luiz, PF Cowman, M Friedman, ML Berumen. Ice ages and butterflyfishes: Phylogenomics elucidates the ecological and evolutionary history of reef fishes in an endemism hotspot. Ecology and Evolution 8(22):10989-11008 doi:10.1002/ece3.4566

(2018) MGM Lima, J de Sousa e Silva-Júnior, D Černý, JC Buckner, A Aleixo, J Chang, J Zheng, ME Alfaro, A Di Fiore, JP Boubli, JW Lynch Alfaro. A phylogenomic perspective on the robust capuchin monkey (Sapajus) radiation: First evidence for extensive population admixture across South America. Molecular Phylogenetics and Evolution 214:137-150 doi:10.1016/j.ympev.2018.02.023

(2015) PS Gilbert, J Chang, E Sobel, JS Sinsheimer, BC Faircloth, ME Alfaro. Genome-wide ultraconserved elements exhibit higher phylogenetic informativeness than traditional gene markers for the fish series Percomorpha. Molecular Phylogenetics and Evolution 92:140-146 doi:10.1016/j.ympev.2015.05.027

You may also be interested in the website ultraconserved.org.

How pervasive is commercial exploitation of fishes across phenotypes? Are there fish with certain body shapes that are disproportionately exploited? What is the association between exploitation, body shape, and environment?

Jonathan Chang

Research