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PUBLISHED WORK

Evolutionary Genetics Laboratory Findings

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PUBLICATION IN REVISION

Hypergraphs and centrality measures identifying key features in gene expression data

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

 

Mathematical Biosciences - 2023

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REPLICATED EVOLUTION IN PLANTS

Replicated Evolution in Plants

 

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

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Ann Rev Plant Biology - 2023

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List of publications

Daniel's Google Scholar page

       Preprints

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  1. 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,  bioRxiv, https://doi.org/10.1101/2020.05.26.117846.
     

  2. 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, https://doi.org/10.1101/692673.
     

  3. Jung, H., Jeon, B J., & D. Ortiz-Barrientos. easyfm : An easy software suite for file manipulation of Next Generation Sequencing data on desktops. bioRxiv, https://doi.org/10.1101/2021.09.29.4622.
     

  4. O.Brien, N.V., Holland, B., Engelstaedter,. J., and D. Ortiz-Barrientos. The distribution of fitness effects during adaptive walks using a simple genetic network, bioRxiv, https://www.biorxiv.org/content/10.1101/2023.10.26.564303v3


    Published

  5. James, M. E., and D. Ortiz-Barrientos, 2024 The genomic consequences of selection across development. Molecular Ecology.
     

  6. Rieseberg, L., E. Warschefsky, D. Ortiz-Barrientos, N. C. Kane, K. Thresher et al., 2023 Editorial 2023. Molecular Ecology 32: 1-25.
     

  7. James, M. E., T. Brodribb, I. J. Wright, L. H. Rieseberg and D. Ortiz-Barrientos, 2023 Replicated Evolution in Plants. Annual Review of Plant Biology 74: 697-725.
     

  8. James, M. E., R. N. Allsopp, J. S. Groh, A. Kaur, M. J. Wilkinson et al., 2023 Uncovering the genetic architecture of parallel evolution. Molecular Ecology 32: 5575-5589.
     

  9. Gao, L. X., M. B. Kantar, D. Moxley, D. Ortiz-Barrientos and L. H. Rieseberg, 2023 Crop adaptation to climate change: An evolutionary perspective. Molecular Plant 16: 1518-1546.
     

  10. Barton, S., Z. Broad, D. Ortiz-Barrientos, D. Donovan and J. Lefevre, 2023 Hypergraphs and centrality measures identifying key features in gene expression data. Mathematical Biosciences 366.
     

  11. Wilkinson, M. J., R. Yamashita, M. E. James, I. S. E. Bally, N. L. Dillon et al., 2022 The influence of genetic structure on phenotypic diversity in the Australian mango gene pool. Scientific Reports 12.
     

  12. Rieseberg, L., E. Warschefsky, B. O'Boyle, P. Taberlet, D. Ortiz-Barrientos et al., 2022 Editorial 2022. Molecular Ecology 31: 1-30.
     

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

  14. Ambrose, L., I. Popovic, J. Hereward, D. Ortiz-Barrientos and N. W. Beebe, 2022 Comparisons of chemosensory gene repertoires in human and non-human feeding mosquitoes link olfactory genes to anthropophily. Iscience 25.
     

  15. Wilkinson, M. J., F. Roda, G. M. Walter, M. E. James, R. Nipper et al., 2021 Adaptive divergence in shoot gravitropism creates hybrid sterility in an Australian wildflower. Proceedings of the National Academy of Sciences of the United States of America 118.
     

  16. Rieseberg, L., E. Warschefsky, B. O'Boyle, P. Taberlet, D. Ortiz-Barrientos et al., 2021 Editorial 2021. Molecular Ecology 30: 1-25.
     

  17. Narum, S., J. Kelley, N. Fountain-Jones, R. Hooper, D. Ortiz-Barrientos et al., 2021 Editorial 2021. Molecular Ecology Resources 21: 1-10.
     

  18. Marden, E., R. J. Abbott, F. Austerlitz, D. Ortiz-Barrientos, R. S. Baucom et al., 2021 Sharing and reporting benefits from biodiversity research. Molecular Ecology 30: 1103-1107.
     

  19. James, M. E., M. J. Wilkinson, D. M. Bernal, H. L. Liu, H. L. North et al., 2021 Phenotypic and genotypic parallel evolution in parapatric ecotypes of. Evolution 75: 3115-3131.
     

  20. James, M. E., H. Arenas-Castro, J. S. Groh, S. L. Allen, J. Engelstädter et al., 2021 Highly Replicated Evolution of Parapatric Ecotypes. Molecular Biology and Evolution 38: 4805-4821.
     

  21. Cooper, M., O. Powell, K. P. Voss-Fels, C. D. Messina, C. Gho et al., 2021 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.
     

  22. Butlin, R. K., M. R. Servedio, C. M. Smadja, C. Bank, N. H. Barton et al., 2021 Homage to Felsenstein 1981, or why are there so few/many species? Evolution 75: 978-988.
     

  23. Ambrose, L., D. Ortiz-Barrientos, R. D. Cooper, N. F. Lobo, T. R. Burkot et al., 2021 Gene flow between island populations of the malaria mosquito, may have contributed to the spread of divergent host preference phenotypes. Evolutionary Applications 14: 2244-2257.
     

  24. Walter, G. M., T. J. Richards, M. J. Wilkinson, M. W. Blows, J. D. Aguirre et al., 2020 Loss of ecologically important genetic variation in late generation hybrids reveals links between adaptation and speciation. Evolution Letters 4: 302-316.
     

  25. Walter, G. M., R. J. Abbott, A. C. Brennan, J. R. Bridle, M. Chapman et al., 2020 as a model system for integrating studies of genotype, phenotype and fitness. New Phytologist 226: 326-344.
     

  26. White, C. R., D. J. Marshall, L. A. Alton, P. A. Arnold, J. E. Beaman et al., 2019 The origin and maintenance of metabolic allometry in animals. Nature Ecology & Evolution 3: 598-603.
     

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

  28. Bernal, X. E., B. Rojas, M. A. Pinto, A. M. Mendoza-Henao, A. Herrera-Montes et al., 2019 Empowering Latina scientists. Science 363: 825-826.
     

  29. Walter, G. M., M. J. Wilkinson, J. D. Aguirre, M. W. Blows and D. Ortiz-Barrientos, 2018 Environmentally induced development costs underlie fitness tradeoffs. Ecology 99: 1391-1401.
     

  30. Walter, G. M., J. D. Aguirre, M. W. Blows and D. Ortiz-Barrientos, 2018 Evolution of Genetic Variance during Adaptive Radiation. American Naturalist 191: E108-E128.
     

  31. Liew, C. S., A. E. Memory, D. Ortiz-Barrientos, P. J. de Lange and P. B. Pelser, 2018 The delimitation and evolutionary history of the Australasian Lautusoid group of (Asteraceae: Senecioneae). Taxon 67: 130-148.
     

  32. Ortiz-Barrientos, D., and M. E. James, 2017 Evolution of recombination rates and the genomic landscape of speciation. Journal of Evolutionary Biology 30: 1519-1521.
     

  33. Roda, F., G. M. Walter, R. Nipper and D. Ortiz-Barrientos, 2017 Genomic clustering of adaptive loci during parallel evolution of an Australian wildflower. Molecular Ecology 26: 3687-3699.
     

  34. Littleford-Colquhoun, B. L., C. Clemente, M. J. Whiting, D. Ortiz-Barrientos and C. H. Frère, 2017 Archipelagos of the Anthropocene: rapid and extensive differentiation of native terrestrial vertebrates in a single metropolis. Molecular Ecology 26: 2466-2481.
     

  35. Reeve, J., D. Ortiz-Barrientos and J. Engelstädter, 2016 The evolution of recombination rates in finite populations during ecological speciation. Proceedings of the Royal Society B-Biological Sciences 283.
     

  36. Beekman, M., B. Nieuwenhuis, D. Ortiz-Barrientos and J. P. Evans, 2016 Sexual selection in hermaphrodites, sperm and broadcast spawners, plants and fungi. Philosophical Transactions of the Royal Society B-Biological Sciences 371.
     

  37. Richards, T. J., G. M. Walter, K. McGuigan and D. Ortiz-Barrientos, 2016 Divergent natural selection drives the evolution of reproductive isolation in an Australian wildflower. Evolution 70: 1993-2003.
     

  38. Walter, G. M., M. J. Wilkinson, M. E. James, T. J. Richards, J. D. Aguirre et al., 2016 Diversification across a heterogeneous landscape. Evolution 70: 1979-1992.
     

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

  40. Ortiz-Barrientos, D., J. Engelstädter and L. H. Rieseberg, 2016 Recombination Rate Evolution and the Origin of Species. Trends in Ecology & Evolution 31: 226-236.
     

  41. Baack, E., M. C. Melo, L. H. Rieseberg and D. Ortiz-Barrientos, 2015 The origins of reproductive isolation in plants. New Phytologist 207: 968-984.
     

  42. Matute, D. R., and D. Ortiz-Barrientos, 2014 Speciation: The Strength of Natural Selection Driving Reinforcement. Current Biology 24: R955-R957.
     

  43. Ortiz-Barrientos, D., and E. J. Baack, 2014 Species integrity in trees. Molecular Ecology 23: 4188-4191.
     

  44. Melo, M. C., A. Grealy, B. Brittain, G. M. Walter and D. Ortiz-Barrientos, 2014 Strong extrinsic reproductive isolation between parapatric populations of an Australian groundsel. New Phytologist 203: 323-334.
     

  45. Elliott, A. G., C. Delay, H. L. Liu, Z. Y. Phua, K. J. Rosengren et al., 2014 Evolutionary Origins of a Bioactive Peptide Buried within Preproalbumin. Plant Cell 26: 981-995.
     

  46. Roda, F., H. L. Liu, M. J. Wilkinson, G. M. Walter, M. E. James et al., 2013 Convergence and Divergence during the Adaptation to Similar Environments by an Australian Groundsel. Evolution 67: 2515-2529.
     

  47. Roda, F., L. Ambrose, G. M. Walter, H. L. L. Liu, A. Schaul et al., 2013 Genomic evidence for the parallel evolution of coastal forms in the Senecio lautus complex. Molecular Ecology 22: 2941-2952.
     

  48. Ortiz-Barrientos, D., 2013 The Color Genes of Speciation in Plants. Genetics 194: 39-42.
     

  49. Sambatti, J. B. M., J. L. Strasburg, D. Ortiz-Barrientos, E. J. Baack and L. H. Rieseberg, 2012 Reconciling Extremely Strong Barriers with High Levels of Gene Exchange in Annual Sunflowers. Evolution 66: 1459-1473.
     

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

  51. David, G. K., R. S. Wilson and D. Ortiz-Barrientos, 2011 Diving in soccer: When does it pay to be dishonest? Integrative and Comparative Biology 51: E30-E30.
     

  52. Cameron, S. F., D. Ortiz-Barrientos and R. W. Wilson, 2011 Sexual dimorphism of morphology and functional traits of the introduced Asian house gecko (Hemidactylus frenatus) across a latitudinal cline. Integrative and Comparative Biology 51: E20-E20.
     

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

  54. David, G., D. Ortiz-Barrientos, M. Smith and R. Wilson, 2010 I can score more than you! Investigating the importance of skill on whole organism performance in a complex environment. Integrative and Comparative Biology 50: E39-E39.
     

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

  56. Ortiz-Barrientos, D., A. Grealy and P. Nosil, 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.
     

  57. Sambatti, J. B. M., D. Ortiz-Barrientos, E. J. Baack and L. H. Rieseberg, 2008 Ecological selection maintains cytonuclear incompatibilities in hybridizing sunflowers. Ecology Letters 11: 1082-1091.
     

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

  59. Etges, W. J., C. C. de Oliveira, E. Gragg, D. Ortíz-Barrientos, M. A. F. Noor et al., 2007 Genetics of incipient speciation in Male courtship song, mating success, and genotype x environment interactions. Evolution 61: 1106-1119.
     

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

  61. Ortiz-Barrientos, D., and L. H. Rieseberg, 2006 Speciation - Splitting when together. Heredity 97: 2-3.
     

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

  63. Ortiz-Barrientos, D., S. C. Audrey and M. A. F. Noor, 2006 A recombinational portrait of the Drosophila pseudooscura genome. Genetics Research 87: 23-31.
     

  64. Ortíz-Barrientos, D., and M. A. F. Noor, 2005 Evidence for a one-allele assortative mating locus. Science 310: 1467-1467.
     

  65. Richards, S., Y. Liu, B. R. Bettencourt, P. Hradecky, S. Letovsky et al., 2005 Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution. Genome Research 15: 1-18.
     

  66. Ortiz-Barrientos, D., B. A. Counterman and M. A. F. Noor, 2004 The genetics of speciation by reinforcement. Plos Biology 2: 2256-2263.
     

  67. Counterman, B. A., D. Ortíz-Barrientos and M. A. F. Noor, 2004 Using comparative genomic data to test for fast-x evolution. Evolution 58: 656-660.
     

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

  69. Mesa, N. R., M. C. Mondragón, I. D. Soto, M. V. Parra, C. Duque 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.
     

  70. Carvajal-Carmona, L. G., I. D. Soto, N. Pineda, D. Ortíz-Barrientos, C. Duque 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.
     

  71. Ospina-Duque, J., C. Duque, L. Carvajal-Carmona, D. Ortiz-Barrientos, I. Soto 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.
     

  72. Ospina-Duque, J., C. Duque, L. Carvajal-Carmona, D. Ortiz-Barrientos, I. Soto et al., 2000 Lack of association between a serotonin transporter promoter polymorphism and bipolar disorder in Antioquia, Colombia. American Journal of Human Genetics 67: 339-339.
     

  73. Carvajal-Carmona, L. G., J. Ospina-Duque, J. Calle, C. Lopez, L. Ochoa et al., 2000 A search for genetic loci involved in predisposition to bipolar mood disorder in the population of Antioquia, Colombia. American Journal of Human Genetics 67: 309-309.
     

  74. Mesa, N., M. C. Mondragon, I. D. Soto, M. V. Parra, C. Duque et al., 2000 A comparison of autosomal, mtDNA and Y-chromosome diversity in Native South Americans. American Journal of Human Genetics 67: 230-230.
     

  75. Torres, M. M., D. Ortiz-Barrientos, I. D. Soto, L. G. Carvajal, C. Duque et al., 2000 mtDNA diversity of Colombian Amerind populations. American Journal of Human Genetics 67: 216-216.
     

  76. Ospina-Duque, J., L. Carvajal-Carmona, J. Calle, C. López, L. Ochoa 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.
     

  77. Ospina-Duque, J., C. Duque, L. Carvajal-Carmona, M. Cuartas, D. Ortiz-Barrientos 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.
     

  78. Ruiz-Linares, A., D. Ortíz-Barrientos, M. Figueroa, N. Mesa, J. G. Múnera et al., 1999 Microsatellites provide evidence for Y chromosome diversity among the founders of the New World. Proceedings of the National Academy of Sciences of the United States of America 96: 6312-6317.

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