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Evolutionary Genetics Laboratory Findings



Hypergraphs and centrality measures identifying key features in gene expression data

Samuel Barton, Zoe C Broad, Daniel Ortiz-Barrientos, Diane Donovan, James G Lefevre


Mathematical Biosciences - 2023

2019-11-29 16.35.23.jpg


Replicated Evolution in Plants


Maddie E. James, Tim Brodribb, Ian Wriught, Loren H. RIeseberg, and Daniel Ortiz-Barrientos. 

Ann Rev Plant Biology - 2023


List of publications

Daniel's Google Scholar page



Beaman, J., Ortiz-Barrientos, Monro, K., D., Hall, M.D. & White, C.R. Metabolic scaling has diversified among species, despite an evolutionary constraint within species, in reviewbioRxiv,

James, M. E., Allsopp, R. N., Groh, J. S., Kaur, A., Wilkinson, M. J., & Ortiz-Barrientos, D. (2022). Uncovering the Genetic Architecture of Replicated Adaptation. SSRN preprint.

James, M.E., Melo, M.C., Roda, F., Bernal-Franco, D.M., Wilkinson, M.J., Liu, H., Walter, G.M., & D. Ortiz-Barrientos. Evidence for mutation-order speciation in an Australian wildflower, bioRxiv,

Jung, H., Jeon, B J., & D. Ortiz-Barrientos. easyfm : An easy software suite for file manipulation of Next Generation Sequencing data on desktops. in review, bioRxiv,



Barton, S., Broad, Z. C., Ortiz-Barrientos, D., Donovan, D., & J. G. Lefevre. (2023). Hypergraphs and centrality measures identifying key features in gene expression data. Mathematical Biosciences, Major revision. doi:

Gao, L., Kantar, M.B., Moxley, D., Ortiz-Barrientos, D., & Loren H. Rieseberg. (2023). Crop Adaptation to Climate Change: An Evolutionary Perspective. Molecular Plant, In press.

James, M. E., Allsopp, R. N., Groh, J. S., Kauur, A., Wilkinson, M. J., & D. Ortiz-Barrientos. (2023). Uncovering the genetic architecture of replicated adaptation. Molecular Ecology, Minor revision.

James, M. E., Brodribb, T., Wright, I., Rieseberg, L. H., & D. Ortiz-Barrientos. (2023). Replicated Evolution in Plants. Annual Review of Plant Biology, 74, 697–725.

Thompson, K. A., Brandvain, Y., Coughlan, J. M., Delmore, K. E., Justen, H., Linnen, C. R., Ortiz-Barrientos, D., Rushworth, C. A., Schneemann, H., Schumer, M., & Stelkens, R. (In press). The Ecology of Hybrid Incompatibilities. Cold Spring Harbour Perspectives in Biology (Speciation), in press.


Ambrose, L., Popovic, I., Hereward, J., Ortiz-Barrientos, D., & N. W. Beebe. (2022). Comparisons of chemosensory gene repertoires in human and non-human feeding Anopheles mosquitoes link olfactory genes to anthropophily. iScience, 25(7), 104521.

Munyengwa, N., Peace, C., Dillon, N. L., Ortiz-Barrientos, D., Christie, N., Myburg, A. A., & Hardner, C. (2022). SNP and haplotype-based genomic prediction of fruit quality traits in sweet cherry (Prunus avium). In XXXI International Horticultural Congress (IHC2022): International Symposium on Breeding and Effective Use of Biotechnology, 1362,173-180.


Wilkinson, M. J., Yamashita, R., James, M. E., Bally, I. S. E., Dillon, N. L., Ali, A., Hardner, C. M., & D. Ortiz-Barrientos. (2022). The influence of genetic structure on phenotypic diversity in the Australian mango (Mangifera indica) gene pool. Scientific Reports, 12, 20614.

Rieseberg, L.H., Warschefsky, E., O’Boyle, B., Taberlet, P., Ortiz‐Barrientos, D., et al. (2022) Editorial. Molecular Ecology 31 (1), 1-30.

Narum, S., Kelley, J., Fountain‐Jones, N, Hooper, R., Ortiz‐Barrientos, D., et al. (2022) Editorial. Molecular Ecology Resources 22 (1), 1-8.



Ambrose, L., Ortiz-Barrientos, D., Cooper, R.D., Ong, W., Lobo, N.F., Burkot, T.R., Russell, T.L., & N.W. Beebe. (2021) The evolution and spread of divergent human host preference traits in island populations of mosquitoes, Evolutionary applications,


Butlin, Roger K., Servedio, Maria R., Smadja, Carole M., Bank, Claudia., Barton, Nicholas H., Flaxman, Samuel M., Giraud, Tatiana., Hopkins, Robin., Larson, Erica L., Maan, Martine E., Meier, J., Merrill, R., Noor, M.A.F.,  Ortiz‐Barrientos, D,. & A.  Qvarnström. (2021) Homage to Felsenstein 1981, or why are there so few/many species? Evolution 75: 978-988.


James, M. E., Arenas-Castro, H., Groh, J. S., Engelstädter, J. & D. Ortiz-Barrientos (2021). Highly replicated evolution of parapatric ecotypes. Molecular Biology and Evolution,

James, M. E., Wilkinson, M.J., North, H., Engelstädter, J., & D. Ortiz-Barrientos. Phenotypic and genotypic parallel evolution in parapatric ecotypes of Senecio. Evolution, in press,


Wilkinson, M.C., Roda, F., Walter, G.M., James, M.E., Nipper, R., Walsh, J., Liu, H., Beveridge, C.B., & D. Ortiz-Barrientos. (2021) Divergence in hormone signalling links local adaptation and hybrid failure. PNAS in press, 





Cooper, M., Powell, O., Voss-Fels, K.P., Messina, C., Gho, C., Podlich, D., Technow, F., Chapman, S., Beveridge, C.A., & D. Ortiz-Barrientos (2020) Modelling selection response in plant breeding programs using crop models as mechanistic gene-to-phenotype (CGM-G2P) multi-trait link functions. In silico plants 3: 1, .


Walter, G.M., Abbott, R.J., Brennan, A.C., Bridle, J.R., Chapman, M., Filatov, D., Nevado, B., Ortiz-Barrientos, D. & S.J. Hiscock (2020) Tansley Review: Senecio as a model system for integrating studies of genotype, phenotype and fitness, New Phytologist 226: 326-344.


Walter, G.M., Richards, T., Wilkinson, M.J., Aguirre, D., Blows, M.W.,  & D. Ortiz-Barrientos. Loss of ecologically important genetic variation in late-generation hybrids reveals links between adaptation and speciation, Evolution Letters 4: 302-316.




Arenas-Castro, H., Brittain, B.M., Matute, D.R., & D. Ortiz-Barrientos (2019). Reinforcement.  Oxford Bibliographies in Evolutionary Biology.  Ed. EIC Name. New York: Oxford University Press, DOI: 10.1093/OBO/9780199941728-0120.


Bernal, Ximena E., Rojas, Bibiana., Pinto, Maria Alejandra., Mendoza-Henao, Ángela M., Herrera-Montes, Adriana., Herrera-Montes, Maria Isabel., Franco, ADC., Ceron-Souza, Ivania., Paz, Andrea., Vergara, Daniela., et al. (2018) Empowering Latina scientists, Science 363: 825-826.


Richards, T., Ortiz-Barrientos, D & K., McGuigan. (2019) Natural selection drives leaf divergence in experimental populations of Senecio lautus under natural conditions, Ecology and Evolution 9: 6959-6967.


White, C.R., Marshall, D.J., Alton, L., et al. & D. Ortiz-Barrientos. (2019) The origin and maintenance of metabolic allometry in animals, Nature Ecology & Evolution 3: 598-603.




Lieu, C-S., Memory, A., Ortiz-Barrientos, D., Thompson, I.R., de Lange P.J., & P.B. Pelser (2018) The delimitation and evolutionary history of the Australasian Lautusoid group of Senecio (Asteraceae; Senecioneae), Taxon 62:127-140. 


Walter, G.M., Aguirre, D., Blows, M.W. & D. Ortiz-Barrientos. (2018) Evolution of genetic variance during adaptive radiation. American Naturalist 191, 4: E108-E128. 


Walter, G.M., Wilkinson, M,. Aguirre, D., Blows, M.W. & D. Ortiz-Barrientos. Environmentally-induced developmental rates drive the origin of fitness trade-offs, Ecology 99:1391-1401. 




Littleford-Colquhoun, B.L., Clemente, C., Whiting, M.J., Ortiz-Barrientos, D. & C.H. Frere. (2017) Rapid and extensive diversification of a native vertebrate in city parks. Molecular Ecology 9:2466-2481. 


Ortiz-Barrientos, D. & James, M.E. The evolution of recombination rates and the genomic landscape of speciation. Journal of Evolutionary Biology 30: 1519–1521. 


Roda, F.,  Walter, G.M., Nipper, R. & D. Ortiz-Barrientos. (2017). Genomic clustering of adaptive loci during parallel evolution of an Australian wildflower. Molecular Ecology 14: 3687–3699. 




Beekman, M., Nieuwenhuis, B., Ortiz-Barrientos, D. & J. Evans. (2016) Sexual selection in hermaphrodites, plants, fungi and broadcast spawners. Philosophical Transactions B 371: 20150541. 


Ortiz-Barrientos D., Engelstädter, J. & L.H. Rieseberg. (2016) Recombination rate evolution and the origin of species. Trends in Ecology & Evolution 3:226 - 236. 


Ortiz-Barrientos, D. (2016) Species Concepts and speciation, in Encyclopaedia of Evolutionary Biology: Speciation. Chief Editor R. Kliman, Section Editor D. Ortiz-Barrientos, Elsevier, Oxford UK pages 216-227. 


Reeve, J., Ortiz-Barrientos, D. & J. Engelstädter. The evolution of recombination rates in finite populations during ecological speciation. Proceedings Royal Society B Oct 26; 283. pii: 20161243. 


Richards, T. & D. Ortiz-Barrientos. (2016) Immigrant inviability produces a strong barrier to gene flow between parapatric ecotypes of Senecio lautus. Evolution 70: 1239-1248. 


Richards, T., Walter, G.M., McGuigan, K. & D. Ortiz-Barrientos. (2016) Divergent natural selection drives the evolution of extrinsic post zygotic isolation in an Australian wildflower. Evolution 70: 1993-2003. 


Walter, G.M., Wilkinson M., James, M.E., Richards, T., Aguirre, D. & D. Ortiz-Barrientos. (2016). Diversification across a heterogeneous landscape. Evolution 70: 1079-1992.  




Baack, E.J., Melo, M.C., Rieseberg, L.H. & Ortiz-Barrientos, D. (2015) Tansley Review: The origins of reproductive isolation in plants. New Phytologist  207: 968–984. 




Elliott, A.G., Delay, C., Liu, H., Phua, Z., ,Rosengren, K.J., Benfield, A.H., Panero, J.L., Colgare  M.L., Jayasena, A.S., Dunse, K.M., Anderson, M.A., Schilling, E.E., Ortiz-Barrientos, D., Craik, D.J. & Mylne, J.S. (2014). Evolutionary origins of a bioactive peptide buried within preproalbumin. Plant Cell 26: 981-995. 


Matute D., & Ortiz-Barrientos D. (2014). Speciation: The strength of natural selection driving reinforcement. Current Biology 24: R955-R957. 


Melo, M.C., Grealy, A., Brittain, B., Walter, G.M. & D. Ortiz-Barrientos. (2014). Strong extrinsic reproductive isolation between parapatric populations of an Australian groundsel. New Phytologist 203: 232-334. 


Ortiz-Barrientos, D. & Back, E.J. (2014). Species integrity in trees. Molecular Ecology 23: 4188-4191. 




Ortiz-Barrientos, D. (2013). The color genes of speciation. Genetics 194:39-42. 


Roda, F., Ambrose, L., Walter, G. M., Liu, H. L., Schaul, A., Lowe, A., Pelser, P. B., Prentis, P., Rieseberg, L. H. & Ortiz-Barrientos, D. (2013). Genomic evidence for the parallel evolution of coastal forms in the Senecio lautus complex. Molecular Ecology 22: 2941–2952. 


Roda, F., Wilkinson, M., Liu, H., Walter, G.M., James, M., Bernal, D.M., Melo, M.C., Lowe, A., Rieseberg, L.H., Prentis, P. & D. Ortiz-Barrientos. (2013). Convergence and divergence during the adaptation to similar environments by an Australian groundsel. Evolution 67: 2515-2529. 




Sambatti J.B.M., Strasburg, J.L., Ortiz-Barrientos D., Baack E.J. & Rieseberg L.H. (2012). Reconciling extremely strong barriers with high levels of gene exchange in annual sunflowers. Evolution 66, 1459-1473. 




David G.K., Condon C.H., Bywater C.L., Ortiz-Barrientos D. & Wilson R.S. (2011). Receivers Limit the Prevalence of Deception in Humans: Evidence from Diving Behaviour in Soccer Players. PLoS One 6: e26017. 




Prentis P.J., Woolfit M., Thomas-Hall S.R., Ortiz-Barrientos D., Pavasovic A., Lowe A.J. & Schenk P.M. (2010). Massively parallel sequencing and analysis of expressed sequence tags in a successful invasive plant. Annals of Botany 106: 1009-1017. 




Nosil P., Funk D.J. & Ortiz-Barrientos D. (2009). Divergent selection and heterogeneous genomic divergence. Molecular Ecology 18: 375-402. 


Ortiz-Barrientos D., Grealy A. & Nosil P. (2009). The Genetics and Ecology of Reinforcement Implications for the Evolution of Prezygotic Isolation in Sympatry and Beyond. Year in Evolutionary Biology 2009 1168: 156-182. 


Jasinska A.J., et al. (2009). A narrow and highly significant linkage signal for severe bipolar disorder in the chromosome 5q33 region in Latin American pedigrees. American Journal of Medical Genetics, B Neuropsychiatry Genetics. 150B:998-1006. 




Sambatti J.B.M.*, Ortiz-Barrientos D.*, Baack E.J. & Rieseberg L.H. (2008). Ecological selection maintains cytonuclear incompatibilities in hybridizing sunflowers. Ecology Letters 11: 1082-1091. * Equally contributed to this work. 




Etges W.J., de Oliveira C.C., Gragg E., Ortiz-Barrientos D., Noor M.A.F. & Ritchie M.G. (2007). Genetics of incipient speciation in Drosophila mojavensis. I. Male courtship song, mating success, and genotype x environment interactions. Evolution 61: 1106-1119. 


Ortiz-Barrientos D., Counterman B.A. & Noor M.A.F. (2007). Gene expression divergence and the origin of hybrid dysfunctions. Genetica, 129: 71-81. 


Ortiz-Barrientos D. & Kane N.C. (2007). Meeting review: American genetics association symposium on the genetics of speciation. Molecular Ecology 16: 2852-2854. 




Herzberg I., et al. (2006). Convergent linkage evidence from two Latin-American population isolates supports the presence of a susceptibility locus for bipolar disorder in 5q31-34. Human Molecular Genetics. 15:3146-53. 


Noor M.A.F. & Ortiz-Barrientos D. (2006). Simulating natural conditions in the laboratory: A re-examination of sexual isolation between sympatric and allopatric populations of Drosophila pseudoobscura and D. persimilis. Behavior Genetics 36: 322-327. 

Ortiz-Barrientos D. & Rieseberg L.H. (2006). Speciation - Splitting when together. Heredity 97: 2-3. 


Ortiz-Barrientos D., Audrey S.C. & Noor M.A.F. (2006). A recombinational portrait of the Drosophila pseudoobscura genome. Genetical Research 87: 23-31. 


Torres M.M. et al. (2006). A revertant of the major founder Native American haplogroup C common in populations from northern South America. American Journal of Human Biology 18:59-65. 




Ortiz-Barrientos D. & Noor M.A.F. (2005). Evidence for a one-allele assortative mating locus. Science, 310: 1467-1467. 


Richards S., Liu Y., et al  (2005). Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution. Genome Research 15: 1-18. 




Counterman B.A.*, Ortiz-Barrientos D.* & Noor M.A.F. (2004). Using comparative genomic data to test for fast-x evolution. Evolution 58: 656-660. * co-first author. 


Ortiz-Barrientos D., Counterman B.A. & Noor M.A.F. (2004). The genetics of speciation by reinforcement. PLoS Biology 2: 2256-2263. 




Ortiz-Barrientos D., Reiland J., Hey J. & Noor M.A.F. (2002). Recombination and the divergence of hybridizing species. Genetica, 116: 167-178. 




Carvajal-Carmona L.G., Soto I.D., et al. (2000). Strong Amerind/white sex bias and a possible sephardic contribution among the founders of a population in northwest Colombia.  American Journal of Human Genetics 67: 1287-1295. 


Mesa N.R., Mondragon M.C., et al. (2000). Autosomal, mtDNA, and Y-chromosome diversity in Amerinds: Pre- and post-Columbian patterns of gene flow in South America. American Journal of Human Genetics 67: 1277-1286. 


Ospina-Duque J., Carvajal-Carmona L., et al. (2000). A search for genetic loci involved in predisposition to bipolar mood disorder in the population of Antioquia, Colombia. American Journal of Medical Genetics 96: 507-507. 


Ospina-Duque J., Duque C., et al.  (2000). An association study of bipolar mood disorder (type I) with the 5-HTTLPR serotonin transporter polymorphism in a human population isolate from Colombia. Neuroscience Letters 292, 199-202. 


Ospina-Duque J., Duque C., et al.  (2000). Lack of association between a serotonin transporter promoter polymorphism and BP1 in Antioquia, Colombia. American Journal of Medical Genetics 96: 490-491. 


Torres M.M., Ortiz-Barrientos D., Soto I.D., Carvajal L.G., Duque C., Bedoya G., de Restrepo H.G. & Ruiz-Linares A. (2000). mtDNA diversity of Colombian Amerind populations. American Journal of Human Genetics 67: 216-216. 




Ruiz-Linares A., Ortiz-Barrientos D., et al. (1999). Microsatellites provide evidence for Y chromosome diversity among the founders of the New World. PNAS, 96: 6312-6317. 

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