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Jonathan Chang

evolutionary biologist

Vita

Jonathan Chang’s CV (pdf)

Education

Appointments

Honors & Awards

Grants & Fellowships

Publications

Google Scholar profile: 2171 citations; h-index: 14; i10-index: 17

Peer-reviewed manuscripts

  1. (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

  2. (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

  3. (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

  4. (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]

  5. (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

  6. (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

  7. (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

  8. (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

  9. (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]

  10. (2018) SV Liu, B Frédérich, S Lavoué, J Chang, MV Erdmann, GN Mahardika, PH Barber. Buccal venom gland associates with increased of diversification rate in the fang blenny fish Meiacanthus (Blenniidae; Teleostei). Molecular Phylogenetics and Evolution 125:138-146 doi:10.1016/j.ympev.2018.03.027

  11. (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

  12. (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

  13. (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

  14. (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

  15. (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

  16. (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

Other manuscripts

  1. (2012) BC Faircloth, J Chang, ME Alfaro. TAPIR enables high-throughput estimation and comparison of phylogenetic informativeness incorporating locus-specific substitution models. [arXiv:1202.1215]

Presentations

Invited presentations

Contributed presentations

Older presentations

  • (2020) J Chang, MD McGee. Tree thinking for comparative genomics: lessons from whole genome sequencing in killifishes. Systematic Biology, January 3–6, Gainesville, FL

  • (2019) J Chang. A macroevolutionary perspective on the distribution of commercially exploited fish species. Australian Society for Fish Biology, October 14–18, Canberra, Australia

  • (2019) J Chang, MD McGee. Comparative genomics and the evolution of lifespan in ray-finned fishes. Australian Academy of Sciences Boden Research Conference, August 2–4, Melbourne, Australia

  • (2019) J Chang, MD McGee. Comparative genomics and the evolution of lifespan in ray-finned fishes. Evolution, June 21–25, Providence, RI

  • (2019) ME Alfaro, EA Karan, J Chang, LK Woo. High throughput phenoscaping for comparative studies. Integrative and Comparative Biology, January 3–7, Tampa, FL

  • (2019) J Chang, ME Alfaro, DL Rabosky. Extending and remixing the complete ray-finned fish tree of life via fishtreeoflife.org. Integrative and Comparative Biology, January 3–7, Tampa, FL

  • (2018) JW Lynch Alfaro, MG Lima, D Černý, J Chang, J Zheng, JC Buckner, ME Alfaro, A Martins, J de Sousa e Silva-Júnior, A Aleixo. Phylogenomics and population genomic analyses for the Neotropical robust capuchin monkey radiation: UCEs reveal extensive population admixture within Sapajus. International Primatological Society, August 19–25, Nairobi, Kenya

  • (2018) J Chang, DL Rabosky, ME Alfaro. Incomplete sampling in phylogenies: when likelihoods go flat. Systematic Biology, June 1–4, Columbus, OH

  • (2018) J Chang, ME Alfaro. Building the complete ray-finned fish tree of life. Integrative and Comparative Biology, January 3–7, San Francisco, CA

  • (2017) JA Sime, J Chang, ME Alfaro, L Sallan. Does the ecology of clade imbalance explain the “living fossil” phenomenon within a mega-phylogeny of ray-finned (actinopterygian) fishes?. Geological Society of America, October 22–25, Seattle, WA

  • (2017) JA Sime, J Chang, ME Alfaro, L Sallan. Pervasive diversity imbalance among sister clades of ray-fin fishes. Evolution, June 23–27, Portland, OR

  • (2017) J Chang, ME Alfaro. A complete ray-finned fish phylogeny using taxonomy and birth-death models. Evolution, June 23–27, Portland, OR (Poster)

  • (2017) J Chang, PF Cowman, M Friedman, LC Sallan, JT Clarke, ME Alfaro. A complete ray-finned fish phylogeny using taxonomy and birth-death models. Systematic Biology, January 8–10, Baton Rogue, LA

  • (2017) J Chang, K Roy, JK Baum, PF Cowman, M Friedman, LC Sallan, JT Clarke, ME Alfaro. Size-selective harvesting and the macroevolutionary implications of an “anthropogenic filter” in ray-finned fishes. Integrative and Comparative Biology, January 4–8, New Orleans, LA

  • (2016) J Chang, K Roy, JK Baum, ME Alfaro. Size-selective harvesting and the macroevolutionary impacts of the “anthropogenic filter” in ray-finned fishes. Southwest Organismal Biologists, November 19, Fullerton, CA (Poster)

  • (2016) J Chang, K Roy, JK Baum, ME Alfaro. Size-selective harvesting and the macroevolutionary impacts of the “anthropogenic filter” in ray-finned fishes. Luskin Inaugural Symposium, October 19, Los Angeles, CA (Poster)

  • (2016) EJ Gjesfjeld, J Chang, D Silvestro, ME Alfaro. Modeling diversification dynamics in the pharmaceutical industry. Human Behavior and Evolution, June 28–July 2, Vancouver, BC (Poster)

  • (2016) J Chang, K Roy, JK Baum, PF Cowman, M Friedman, LC Sallan, JT Clarke, ME Alfaro. Eating away the fish tree of life: the phylogenetic distribution of human exploitation. Evolution, June 17–21, Austin, TX

  • (2016) ME Alfaro, J Chang, PF Cowman, M Friedman, LC Sallan, JT Clarke, DL Rabosky, TJ Near. An evolutionary timescale for the diversification of ray-finned fishes. Evolution, June 17–21, Austin, TX

  • (2016) EJ Gjesfjeld, J Chang, D Silvestro, C Kelty, ME Alfaro. A quantitative macroevolutionary approach to exploring the pharmaceutical drug innovation crisis. Evolution, June 17–21, Austin, TX

  • (2016) J Chang, ME Alfaro. The tempo of body shape evolution in ray-finned fishes: bringing morphology into the “phenomic era” with crowdsourced morphometrics. Integrative and Comparative Biology, January 3–7, Portland, OR (Won David and Marvalee Wake Award for Best Student Presentation)

  • (2016) ME Alfaro, DL Rabosky, J Chang, P Title, M Venzon. Global patterns of diversification across the ray-finned fish tree of life. Integrative and Comparative Biology, January 3–7, Portland, OR

  • (2016) MB Balisi, J Chang. Hypercarnivory and extinction risk in North American fossil dogs. Integrative and Comparative Biology, January 3–7, Portland, OR (Poster)

  • (2015) EJ Gjesfjeld, J Chang, D Silvestro, C Kelty, ME Alfaro. Investigating the diversification of car models using macroevolutionary methods. Evolution, June 26–30, Guarujá, Brazil

  • (2015) J Chang, ME Alfaro. Patterns of shape diversity across ray-finned fishes with crowdsourced morphometrics. Evolution, June 26–30, Guarujá, Brazil (Ernst Mayr Symposium)

  • (2015) EJ Gjesfjeld, J Chang, D Silvestro, ME Alfaro. Investigating the diversification of car models using macroevolutionary methods. Human Behavior and Evolution, May 27–30, Columbia, MO (Poster)

  • (2015) J Chang, ME Alfaro. Crowdsourced morphometrics for large-scale analysis of phenotypic data. Systematic Biology, May 20–22, Ann Arbor, MI

  • (2015) J Chang, ME Alfaro. Crowdsourced morphometric data are as accurate as traditionally collected data in 7 ray-finned fish families. Integrative and Comparative Biology, January 3–7, West Palm Beach, FL

  • (2015) MD McGee, SR Borstein, J Chang, ME Alfaro, PC Wainwright. Progressive functional innovation in cichlid adaptive radiations. Integrative and Comparative Biology, January 3–7, West Palm Beach, FL

  • (2014) J Zheng, J Chang, ME Alfaro. Novel approach measures the topological accuracy of large phylogenetic reconstruction. UCLA Biology Research Symposium., May 17, Los Angeles, CA (Jimmy won Best Student Presentation)

  • (2014) J Chang, DL Rabosky, ME Alfaro. Crowdsourced morphometrics: a method to overcome bottlenecks in collecting phenotype data. Integrative and Comparative Biology, January 3–7, Austin, TX

  • (2013) J Chang, DL Rabosky, ME Alfaro. Morphology and exploitation in ray-finned fishes using crowdsourced data. Evolution, June 21–25, Snowbird, UT

  • (2013) J Chang, JM Eastman, ME Alfaro. Family-level analysis of exploited and at-risk ray-finned fish species shows high potential loss of biodiversity. Integrative and Comparative Biology, January 3–7, San Francisco, CA

  • (2012) J Chang, K Roy, JM Eastman, SA Smith, F Santini, JK Baum, PA Hastings, BL Sidlauskas, ME Alfaro. Phylogenetic clustering of commercially exploited fish species. Integrative and Comparative Biology, January 3–7, Charleston, SC

  • (2012) ME Alfaro, BC Faircloth, L Sorenson, J Chang, F Santini. A 500-locus phylogenomic study of ray-finned fishes. Integrative and Comparative Biology, January 3–7, Charleston, SC

  • (2012) PS Gilbert, J Chang, BC Faircloth, ME Alfaro. Genome-wide ultraconserved elements exhibit higher phylogenetic informativeness than traditional fish markers. Integrative and Comparative Biology, January 3–7, Charleston, SC (Poster)

  • (2011) ME Alfaro, K Roy, J Chang, JM Eastman, SA Smith, F Santini, JK Baum, PA Hastings, BL Sidlauskas. Phylogenetic distribution of commercially exploited fish species: How many times has ‘tastiness’ evolved?. Evolution, June 17–21, Norman, OK

Teaching

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Travel awards