Detecting macroevolutionary genotype–phenotype associations using error-corrected rates of protein convergence
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Abstract
On macroevolutionary timescales, extensive mutations and phylogenetic uncertainty mask the signals of genotype–phenotype associations underlying convergent evolution. To overcome this problem, we extended the widely used framework of non-synonymous to synonymous substitution rate ratios and developed the novel metric ω C , which measures the error-corrected convergence rate of protein evolution. While ω C distinguishes natural selection from genetic noise and phylogenetic errors in simulation and real examples, its accuracy allows an exploratory genome-wide search of adaptive molecular convergence without phenotypic hypothesis or candidate genes. Using gene expression data, we explored over 20 million branch combinations in vertebrate genes and identified the joint convergence of expression patterns and protein sequences with amino acid substitutions in functionally important sites, providing hypotheses on undiscovered phenotypes. We further extended our method with a heuristic algorithm to detect highly repetitive convergence among computationally non-trivial higher-order phylogenetic combinations. Our approach allows bidirectional searches for genotype–phenotype associations, even in lineages that diverged for hundreds of millions of years.
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Cites
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Katoh, K., & Standley, D. M. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst010 · Cited by 46,209 · see citing works
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764 · see citing works
Berman, H. M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.235 · Cited by 40,196 · see citing works
Matplotlib: a 2D graphics environment
Hunter, J. D. (2007) · Computing in Science & Engineering · doi:10.1109/mcse.2007.55 · Cited by 39,249 · see citing works
SciPy 1.0: fundamental algorithms for scientific computing in Python
Virtanen, P., Gommers, R., Oliphant, T. E., Haberland, M., Reddy, T., Cournapeau, D., Burovski, E., Peterson, P., Weckesser, W., Bright, J., et al. (2020) · Nature Methods · doi:10.1038/s41592-019-0686-2 · Cited by 38,430 · see citing works
fastp: an ultra-fast all-in-one FASTQ preprocessor
(2018) · doi:10.1093/bioinformatics/bty560 · Cited by 29,721 · see citing works
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
Nguyen, L.-T., Schmidt, H. A., von Haeseler, A., & Minh, B. Q. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msu300 · Cited by 26,046 · see citing works
Harris, C. R., Millman, K. J., van der Walt, S. J., Gommers, R., Virtanen, P., Cournapeau, D., Wieser, E., Taylor, J., Berg, S., Smith, N. J., et al. (2020) · Nature · doi:10.1038/s41586-020-2649-2 · Cited by 23,826 · see citing works
BLAST+: architecture and applications
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-421 · Cited by 22,074 · see citing works
Full-length transcriptome assembly from RNA-Seq data without a reference genome
Grabherr, M. G., Haas, B. J., Yassour, M., Levin, J. Z., Thompson, D. A., Amit, I., Adiconis, X., Fan, L., Raychowdhury, R., Zeng, Q., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.1883 · Cited by 20,770 · see citing works
Harris, C., Millman, K., van der Walt, S., Gommers, R., Virtanen, P., Cournapeau, D., Wieser, E., Taylor, J., Berg, S., Smith, N., et al. (2020) · RePEc: Research Papers in Economics · Cited by 17,844 · see citing works
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
Minh, B. Q., Schmidt, H. A., Chernomor, O., Schrempf, D., Woodhams, M. D., von Haeseler, A., & Lanfear, R. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa015 · Cited by 16,873 · see citing works
ggplot2: Elegant Graphics for Data Analysis
Wickham, H. (2009) · doi:10.1007/978-0-387-98141-3 · Cited by 14,447 · see citing works
PAML 4: Phylogenetic Analysis by Maximum Likelihood
Yang, Z. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm088 · Cited by 13,879 · see citing works
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V., & Zdobnov, E. M. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv351 · Cited by 13,344 · see citing works
Krogh, A., Larsson, B., von Heijne, G., & Sonnhammer, E. L. L. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.4315 · Cited by 12,654 · see citing works
UFBoot2: Improving the Ultrafast Bootstrap Approximation
Hoang, D. T., Chernomor, O., von Haeseler, A., Minh, B. Q., & Vinh, L. S. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msx281 · Cited by 10,881 · see citing works
SciPy 1.0: fundamental algorithms for scientific computing in Python
Virtanen, P., Gommers, R., Oliphant, T. E., Haberland, M., Reddy, T., Cournapeau, D., Burovski, E., Peterson, P., Weckesser, W., Bright, J., et al. (2019) · Apollo - University of Cambridge Repository · doi:10.17863/cam.64134 · Cited by 10,460 · see citing works
EMBOSS: the European molecular biology open software suite.
Rice, P., Longden, I., & Bleasby, A. (2000) · Trends in Genetics · doi:10.1016/s0168-9525(00)02024-2 · Cited by 9,466 · see citing works
Varadi, M., Anyango, S., Deshpande, M., Nair, S., Natassia, C., Yordanova, G., Yuan, D., Stroe, O., Wood, G., Laydon, A., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkab1061 · Cited by 7,850 · see citing works
OrthoFinder: phylogenetic orthology inference for comparative genomics
Emms, D. M., & Kelly, S. (2019) · Genome Biology · doi:10.1186/s13059-019-1832-y · Cited by 7,676 · see citing works
seaborn: statistical data visualization
Waskom, M. (2021) · Journal of Open Source Software · doi:10.21105/joss.03021 · Cited by 7,310 · see citing works
The rapid generation of mutation data matrices from protein sequences
Jones, D. T., Taylor, W. R., & Thornton, J. M. (1992) · Computer applications in the biosciences · doi:10.1093/bioinformatics/8.3.275 · Cited by 6,916 · see citing works
Darwin, C. R., Murray, J. J., Sons, W. C. A., & Evans., B. &. (1859) · doi:10.5962/bhl.title.82303 · Cited by 5,610 · see citing works
Ultrafast Approximation for Phylogenetic Bootstrap
Minh, B. Q., Nguyen, M. A. T., & von Haeseler, A. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst024 · Cited by 4,844 · see citing works
MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets
Steinegger, M., & Söding, J. (2017) · Nature Biotechnology · doi:10.1038/nbt.3988 · Cited by 4,840 · see citing works
The Pfam protein families database in 2019
El-Gebali, S., Mistry, J., Bateman, A., Eddy, S. R., Luciani, A., Potter, S. C., Qureshi, M., Richardson, L. J., Salazar, G. A., Smart, A., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky995 · Cited by 4,602 · see citing works
Evolutionary Rate at the Molecular Level
KIMURA, M. (1968) · Nature · doi:10.1038/217624a0 · Cited by 3,747 · see citing works
Emms, D. M., & Kelly, S. (2015) · Genome Biology · doi:10.1186/s13059-015-0721-2 · Cited by 3,408 · see citing works
Whelan, S., & Goldman, N. (2001) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003851 · Cited by 2,849 · see citing works
NCBI Taxonomy: a comprehensive update on curation, resources and tools
Schoch, C. L., Ciufo, S., Domrachev, M., Hotton, C. L., Kannan, S., Khovanskaya, R., Leipe, D., Mcveigh, R., O’Neill, K., Robbertse, B., et al. (2020) · Database · doi:10.1093/database/baaa062 · Cited by 2,635 · see citing works
Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection
Pond, S. L. K., & Frost, S. D. W. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi105 · Cited by 2,336 · see citing works
ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data
Huerta‐Cepas, J., Serra, F., & Peer Bork, B. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw046 · Cited by 2,239 · see citing works
Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors
Anzalone, A. V., Koblan, L. W., & Liu, D. R. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0561-9 · Cited by 2,237 · see citing works
An Automatic Method for Solving Discrete Programming Problems
Land, A. H., & Doig, A. G. (2009) · Springer eBooks · doi:10.1007/978-3-540-68279-0_5 · Cited by 2,007 · see citing works
A codon-based model of nucleotide substitution for protein-coding DNA sequences.
(1994) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040153 · Cited by 1,960 · see citing works
An Automatic Method of Solving Discrete Programming Problems
Land, A. H., & Doig, A. G. (1960) · Econometrica · doi:10.2307/1910129 · Cited by 1,958 · see citing works
A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process
Lartillot, N., & Philippe, H. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh112 · Cited by 1,516 · see citing works
CRISPR-Cas guides the future of genetic engineering
Knott, G. J., & Doudna, J. A. (2018) · Science · doi:10.1126/science.aat5011 · Cited by 1,410 · see citing works
Stabilizing selection and the comparative analysis of adaptation
Hansen, T. F. (1997) · Evolution · doi:10.1111/j.1558-5646.1997.tb01457.x · Cited by 1,361 · see citing works
Yanai, I., Benjamin, H., Shmoish, M., Chalifa-Caspi, V., Shklar, M., Ophir, R., Bar-Even, A., Horn-Saban, S., Safran, M., Domany, E., et al. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti042 · Cited by 1,300 · see citing works
Turning a hobby into a job: How duplicated genes find new functions
Conant, G. C., & Wolfe, K. H. (2008) · Nature Reviews Genetics · doi:10.1038/nrg2482 · Cited by 1,281 · see citing works
Yates, A. D., Akanni, W. A., Amode, M. R., Barrell, D. G., Billis, K., Carvalho‐Silva, D., Cummins, C. A., Clapham, P., Fitzgerald, S. F., Gil, L., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1157 · Cited by 1,246 · see citing works
TimeTree: A public knowledge-base of divergence times among organisms
Hedges, S. B., Dudley, J., & Kumar, S. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl505 · Cited by 1,234 · see citing works
Cython: The Best of Both Worlds
Behnel, S., Bradshaw, R., Citro, C., Dalcín, L., Seljebotn, D. S., & Smith, K. (2010) · Computing in Science & Engineering · doi:10.1109/mcse.2010.118 · Cited by 1,233 · see citing works
Computational Molecular Evolution
Yang, Z. (2006) · doi:10.1093/acprof:oso/9780198567028.001.0001 · Cited by 1,143 · see citing works
Slightly Deleterious Mutant Substitutions in Evolution
OHTA, T. (1973) · Nature · doi:10.1038/246096a0 · Cited by 1,104 · see citing works
Tree of Life Reveals Clock-Like Speciation and Diversification
Hedges, S. B., Marin, J., Suleski, M., Paymer, M., & Kumar, S. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv037 · Cited by 959 · see citing works
(1994) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040152 · Cited by 920 · see citing works
Darwin, C. R. (1888) · Springer eBooks · doi:10.1007/978-3-319-19650-3_303511 · Cited by 869 · see citing works
Origins, evolution, and phenotypic impact of new genesPreprint
Kaessmann, H. (2010) · Genome Research · doi:10.1101/gr.101386.109 · Cited by 818 · see citing works
The genetic causes of convergent evolution
Stern, D. L. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3483 · Cited by 818 · see citing works
Natural selection on protein-coding genes in the human genome
Bustamante, C. D., Fledel-Alon, A., Williamson, S., Nielsen, R., Hubisz, M. J., Glanowski, S., Tanenbaum, D. M., White, T. J., Sninsky, J. J., Hernandez, R. D., et al. (2005) · Nature · doi:10.1038/nature04240 · Cited by 788 · see citing works
ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference
Steenwyk, J. L., Buida, T. J., Li, Y., Shen, X., & Rokas, A. (2020) · PLoS Biology · doi:10.1371/journal.pbio.3001007 · Cited by 691 · see citing works
The C4 plant lineages of planet Earth
Sage, R. F., Christin, P., & Edwards, E. J. (2011) · Journal of Experimental Botany · doi:10.1093/jxb/err048 · Cited by 660 · see citing works
The Nonparametric Behrens-Fisher Problem: Asymptotic Theory and a Small-Sample Approximation
Brunner, E., & Munzel, U. (2000) · Biometrical Journal · doi:10.1002/(sici)1521-4036(200001)42:1 · Cited by 630 · see citing works
Rare variant contribution to human disease in 281,104 UK Biobank exomes
Wang, Q., Dhindsa, R. S., Carss, K., Harper, A. R., Nag, A., Tachmazidou, I., Vitsios, D., Deevi, S. V. V., Mackay, A., Muthas, D., et al. (2021) · Nature · doi:10.1038/s41586-021-03855-y · Cited by 604 · see citing works
Maximum Allowed Solvent Accessibilites of Residues in Proteins
Tien, M. Z., Meyer, A. G., Sydykova, D. K., Spielman, S. J., & Wilke, C. O. (2013) · PLoS ONE · doi:10.1371/journal.pone.0080635 · Cited by 516 · see citing works
THE LOCI OF REPEATED EVOLUTION: A CATALOG OF GENETIC HOTSPOTS OF PHENOTYPIC VARIATION
Martin, A., & Courtier‐Orgogozo, V. (2013) · Evolution · doi:10.1111/evo.12081 · Cited by 483 · see citing works
Convergent evolution of the genomes of marine mammals
Foote, A. D., Liu, Y., Thomas, G. W. C., Vinař, T., Alföldi, J., Deng, J., Dugan, S., van Elk, C. E., Hunter, M. E., Joshi, V., et al. (2015) · Nature Genetics · doi:10.1038/ng.3198 · Cited by 453 · see citing works
Phylogenomics reveals three sources of adaptive variation during a rapid radiation
Pease, J. B., Haak, D. C., Hahn, M. W., & Moyle, L. C. (2016) · PLOS Biology · doi:10.1371/journal.pbio.1002379 · Cited by 432 · see citing works
The Apostasia genome and the evolution of orchids
Zhang, G., Liu, K.-W., Li, Z., Lohaus, R., Hsiao, Y., Niu, S.-C., Wang, J., Lin, Y., Xu, Q., Chen, L., et al. (2017) · Nature · doi:10.1038/nature23897 · Cited by 406 · see citing works
Genome-wide signatures of convergent evolution in echolocating mammals
Parker, J., Tsagkogeorga, G., Cotton, J. A., Liu, Y., Provero, P., Stupka, E., & Rossiter, S. J. (2013) · Nature · doi:10.1038/nature12511 · Cited by 375 · see citing works
Adaptive evolution in the stomach lysozymes of foregut fermenters
Stewart, C.-B., Schilling, J. W., & Wilson, A. C. (1987) · Nature · doi:10.1038/330401a0 · Cited by 374 · see citing works
Determinants of the rate of protein sequence evolution
Zhang, J., & Yang, J. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3950 · Cited by 361 · see citing works
Ballatori, N., Christian, W. V., Lee, J., Dawson, P. A., Soroka, C. J., Boyer, J. L., Madejczyk, M. S., & Li, N. (2005) · Hepatology · doi:10.1002/hep.20961 · Cited by 336 · see citing works
Near-neutrality in evolution of genes and gene regulation
Ohta, T. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.252626899 · Cited by 333 · cited 17× · see citing works
“For example, because there are 861 branch pairs in the species tree, on average, 62.5 cases of protein convergence will be obtained in our genome-scale dataset for any particular analysis of two groups of species, although the numbers of analysable branch pairs and hence of detected convergence depend on several facto…”
BackgroundInfluentialThe Earth BioGenome Project 2020: Starting the clock
Lewin, H. A., Richards, S., Aiden, E. L., Allende, M. L., Archibald, J. M., Bálint, M., Barker, K. B., Baumgartner, B. L., Belov, K., Bertorelle, G., et al. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2115635118 · Cited by 330 · see citing works
Evidence for an ancient adaptive episode of convergent molecular evolution
Castoe, T. A., de Koning, A. P. J., Kim, H., Gu, W., Noonan, B. P., Naylor, G. J. P., Jiang, Z. J., Parkinson, C. L., & Pollock, D. D. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0900233106 · Cited by 326 · see citing works
Self-citationCauses of molecular convergence and parallelism in protein evolution
Storz, J. F. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.11 · Cited by 321 · see citing works
Up to date on cholesterol 7 alpha-hydroxylase (CYP7A1) in bile acid synthesis
Chiang, J. Y. L., & Ferrell, J. M. (2020) · Liver Research · doi:10.1016/j.livres.2020.05.001 · Cited by 303 · see citing works
Darwin, C. R. (1860) · J. Murray eBooks · doi:10.5962/bhl.title.162283 · Cited by 273 · see citing works
Detection of convergent and parallel evolution at the amino acid sequence level
Zhang, J., & Kumar, S. (1997) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025789 · Cited by 271 · see citing works
Dobler, S., Dalla, S., Wagschal, V., & Agrawal, A. A. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1202111109 · Cited by 271 · see citing works
Parallel Molecular Evolution in an Herbivore Community
Zhen, Y., Aardema, M. L., Medina, E. M., Schumer, M. E., & Andolfatto, P. (2012) · Science · doi:10.1126/science.1226630 · Cited by 268 · see citing works
X-ray structure of the DNase I-d(GGTATACC)2 complex at 2·3Å resolution
Weston, S. A., Lahm, A., & Suck, D. (1992) · Journal of Molecular Biology · doi:10.1016/0022-2836(92)91064-v · Cited by 248 · see citing works
Fast and accurate detection of evolutionary shifts in Ornstein–Uhlenbeck models
Khabbazian, M., Kriebel, R., Rohe, K., & Ané, C. (2016) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.12534 · Cited by 245 · see citing works
Convergent sequence evolution between echolocating bats and dolphins
Liu, Y., Cotton, J. A., Shen, B., Han, X., Rossiter, S. J., & Zhang, S. Y. (2010) · Current Biology · doi:10.1016/j.cub.2009.11.058 · Cited by 241 · see citing works
Predictable convergence in hemoglobin function has unpredictable molecular underpinnings
Natarajan, C., Hoffmann, F. G., Weber, R. E., Fago, A., Witt, C. C., & Storz, J. F. (2016) · Science · doi:10.1126/science.aaf9070 · Cited by 241 · see citing works
C4 Photosynthesis Evolved in Grasses via Parallel Adaptive Genetic Changes
Christin, P., Salamin, N., Savolainen, V., Duvall, M. R., & Besnard, G. (2007) · Current Biology · doi:10.1016/j.cub.2007.06.036 · Cited by 223 · see citing works
Role of aldo-keto reductase family 1 (AKR1) enzymes in human steroid metabolism
Rižner, T. L., & Penning, T. M. (2014) · Steroids · doi:10.1016/j.steroids.2013.10.012 · Cited by 217 · see citing works
Parallel adaptive origins of digestive RNases in Asian and African leaf monkeys
Zhang, J. (2006) · Nature Genetics · doi:10.1038/ng1812 · Cited by 200 · see citing works
Genome editing retraces the evolution of toxin resistance in the monarch butterfly
Karageorgi, M., Groen, S. C., Sumbul, F., Pelaez, J. N., Verster, K. I., Aguilar, J. M., Hastings, A. P., Bernstein, S. L., Matsunaga, T., Astourian, M., et al. (2019) · Nature · doi:10.1038/s41586-019-1610-8 · Cited by 195 · see citing works
Amino acid coevolution induces an evolutionary Stokes shift
Pollock, D. D., Thiltgen, G., & Goldstein, R. A. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1120084109 · Cited by 193 · see citing works
Self-citationAn Empirical Codon Model for Protein Sequence Evolution
Kosiol, C., Holmes, I. H., & Goldman, N. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm064 · Cited by 186 · see citing works
Widespread convergence in toxin resistance by predictable molecular evolution
Újvári, B., Casewell, N. R., Sunagar, K., Arbuckle, K., Wüster, W., Lo, N. C., O’Meally, D., Beckmann, C., King, G. F., Deplazes, E., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1511706112 · Cited by 180 · see citing works
Huerta-Cepas, J., Dopazo, H., Dopazo, J., & Gabaldón, T. (2007) · Genome Biology · doi:10.1186/gb-2007-8-6-r109 · Cited by 176 · see citing works
Chandler, C. H., Chari, S., & Dworkin, I. M. (2013) · Trends in Genetics · doi:10.1016/j.tig.2013.01.009 · Cited by 174 · see citing works
Contingency and entrenchment in protein evolution under purifying selection
Shah, P., McCandlish, D. M., & Plotkin, J. B. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1412933112 · Cited by 172 · see citing works
Besnard, G., Muasya, A. M., Russier, F., Roalson, E. H., Salamin, N., & Christin, P. (2009) · Molecular Biology and Evolution · doi:10.1093/molbev/msp103 · Cited by 163 · see citing works
Morel, B., Kozlov, A. M., Stamatakis, A., & Szöllősi, G. J. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa141 · Cited by 161 · see citing works
Historical contingency and the purported uniqueness of evolutionary innovations.
Vermeij, G. (2006) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.0508724103 · Cited by 157 · see citing works
Zou, Z., & Zhang, J. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv091 · Cited by 148 · see citing works
Genome of the pitcher plant Cephalotus reveals genetic changes associated with carnivory
Fukushima, K., Fang, X., Alvarez‐Ponce, D., Cai, H., Carretero‐Paulet, L., Chen, C., Chang, T.-H., Farr, K. M., Fujita, T., Hiwatashi, Y., et al. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-016-0059 · Cited by 146 · see citing works
Self-citationHiller, M., Schaar, B. T., Indjeian, V. B., Kingsley, D. M., Hagey, L. R., & Bejerano, G. (2012) · Cell Reports · doi:10.1016/j.celrep.2012.08.032 · Cited by 144 · see citing works
Phylogenetics is the New Genetics (for Most of Biodiversity)
Smith, S., Pennell, M. W., Dunn, C. W., & Edwards, S. V. (2020) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2020.01.005 · Cited by 136 · see citing works
Adaptive Evolution and Functional Redesign of Core Metabolic Proteins in Snakes
Castoe, T. A., Jiang, Z. J., Gu, W., Wang, Z. O., & Pollock, D. D. (2008) · PLoS ONE · doi:10.1371/journal.pone.0002201 · Cited by 135 · see citing works
Self-citationRERconverge: an R package for associating evolutionary rates with convergent traits
Kowalczyk, A. M., Meyer, W. K., Partha, R., Mao, W., Clark, N. L., & Chikina, M. D. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz468 · Cited by 134 · see citing works
Lateral transfers of large DNA fragments spread functional genes among grasses
Dunning, L. T., Olofsson, J. K., Parisod, C., Choudhury, R. R., Moreno-Villena, J. J., Yang, Y., Dionora, J., Quick, W. P., Park, M., Bennetzen, J. L., et al. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1810031116 · Cited by 125 · see citing works
Thomas, G. W. C., & Hahn, M. W. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv013 · Cited by 124 · see citing works
Bläsing, O. E., Westhoff, P., & Svensson, P. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.m909832199 · Cited by 112 · see citing works
Pervasive contingency and entrenchment in a billion years of Hsp90 evolution
Starr, T. N., Flynn, J. M., Mishra, P., Bolon, D. N. A., & Thornton, J. W. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1718133115 · Cited by 111 · see citing works
Sirikantaramas, S., Yamazaki, M., & Saito, K. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0801038105 · Cited by 111 · see citing works
Digestion, absorption and transport of lipids in ruminant animals
Noble, R. C. (1978) · Progress in Lipid Research · doi:10.1016/0079-6832(78)90005-8 · Cited by 110 · see citing works
Liu, Z., Qi, F.-Y., Zhou, X., Ren, H.-Q., & Shi, P. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu194 · Cited by 110 · see citing works
Convergent horizontal gene transfer and cross-talk of mobile nucleic acids in parasitic plants
Yang, Z., Wafula, E. K., Kim, G., Shahid, S., McNeal, J. R., Ralph, P. E., Timilsena, P. R., Yu, W., Kelly, E. A., Zhang, H., et al. (2019) · Nature Plants · doi:10.1038/s41477-019-0458-0 · Cited by 110 · see citing works
No Genome-Wide Protein Sequence Convergence for Echolocation
Zou, Z., & Zhang, J. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv014 · Cited by 99 · see citing works
Kleene, K. C. (2004) · Developmental Biology · doi:10.1016/j.ydbio.2004.09.031 · Cited by 99 · see citing works
Idiosyncratic epistasis creates universals in mutational effects and evolutionary trajectories
Lyons, D. M., Zou, Z., Xu, H., & Zhang, J. (2020) · Nature Ecology & Evolution · doi:10.1038/s41559-020-01286-y · Cited by 99 · see citing works
Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies
Spielman, S. J., & Wilke, C. O. (2015) · PLoS ONE · doi:10.1371/journal.pone.0139047 · Cited by 88 · see citing works
Prudent, X., Parra, G., Schwede, P., Roscito, J. G., & Hiller, M. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw098 · Cited by 71 · see citing works
Accurate Detection of Convergent Amino-Acid Evolution with PCOC
Rey, C., Guéguen, L., Sémon, M., & Boussau, B. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy114 · Cited by 71 · see citing works
Fukushima, K., & Pollock, D. D. (2020) · Nature Communications · doi:10.1038/s41467-020-18090-8 · Cited by 70 · see citing works
Self-citationBayesian Detection of Convergent Rate Changes of Conserved Noncoding Elements on Phylogenetic Trees
Hu, Z., Sackton, T. B., Edwards, S. V., & Liu, J. S. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz049 · Cited by 69 · see citing works
Nonadaptive Amino Acid Convergence Rates Decrease over Time
Goldstein, R. A., Pollard, S. T., Shah, S. D., & Pollock, D. D. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv041 · Cited by 69 · see citing works
Self-citationGene Tree Discordance Can Generate Patterns of Diminishing Convergence over Time
Mendes, F. K., Hahn, Y., & Hahn, M. W. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw197 · Cited by 66 · see citing works
Concha, C., Wallbank, R. W. R., Hanly, J. J., Fenner, J. L., Livraghi, L., Rivera, E. S., Paulo, D. F., Arias, C. F., Vargas, M., Sanjeev, M., et al. (2019) · Current Biology · doi:10.1016/j.cub.2019.10.010 · Cited by 66 · see citing works
DNA Conformation Induces Adaptable Binding by Tandem Zinc Finger Proteins
Patel, A. B., Yang, P., Tinkham, M., Pradhan, M., Sun, M., Wang, Y., Hoang, D., Wolf, G., Horton, J. R., Zhang, X., et al. (2018) · Cell · doi:10.1016/j.cell.2018.02.058 · Cited by 65 · see citing works
Hermans, J., & Westhoff, P. (1992) · Molecular and General Genetics MGG · doi:10.1007/bf00283848 · Cited by 64 · see citing works
Konečná, V., Bray, S., Vlček, J., Bohutínská, M., Požárová, D., Choudhury, R. R., Bollmann‐Giolai, A., Flis, P., Salt, D. E., Parisod, C., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-25256-5 · Cited by 61 · see citing works
Sato, K., Inazu, A., Yamaguchi, S., Nakayama, T., Deyashiki, Y., Sawada, H., & Hara, A. (1993) · Archives of Biochemistry and Biophysics · doi:10.1006/abbi.1993.1591 · Cited by 61 · see citing works
DIGESTION, ABSORPTION AND TRANSPORT OF LIPIDS IN RUMINANT ANIMALS
Noble, R. C. (1981) · Elsevier eBooks · doi:10.1016/b978-0-08-023789-3.50007-6 · Cited by 59 · see citing works
MYADM regulates Rac1 targeting to ordered membranes required for cell spreading and migration
Aranda, J. F., Reglero-Real, N., Kremer, L., Marcos‐Ramiro, B., Ruiz-Sáenz, A., Calvo, M., Enrich, C., Correas, I., Millán, J., & Alonso, M. A. (2011) · Molecular Biology of the Cell · doi:10.1091/mbc.e10-11-0910 · Cited by 55 · see citing works
Multiple cDNAs of phosphoenolpyruvate car☐ylase in the C4 dicotFlaveria trinervia
Poetsch, W., Hermans, J., & Westhoff, P. (1991) · FEBS Letters · doi:10.1016/0014-5793(91)80850-3 · Cited by 54 · see citing works
Marcovitz, A., Turakhia, Y., Chen, H. I., Gloudemans, M. J., Braun, B. A., Wang, H., & Bejerano, G. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1818532116 · Cited by 54 · see citing works
“Reverse genomics” predicts function of human conserved noncoding elements
Marcovitz, A., Jia, R., & Bejerano, G. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw001 · Cited by 53 · see citing works
Mechanism of 53BP1 activity regulation by RNA-binding TIRR and a designer protein
Botuyan, M. V., Cui, G., Drané, P., Oliveira, C., Detappe, A., Brault, M. E., Parnandi, N., Chaubey, S., Thompson, J. R., Bragantini, B., et al. (2018) · Nature Structural & Molecular Biology · doi:10.1038/s41594-018-0083-z · Cited by 51 · see citing works
Sequence entropy of folding and the absolute rate of amino acid substitutions
Goldstein, R. A., & Pollock, D. D. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0338-9 · Cited by 51 · see citing works
Self-citationWang, L., Ma, G., Wang, H., Cheng, C., Mu, S., Quan, W., Jiang, L., Zhao, Z., Zhang, Y., Zhang, K., et al. (2019) · GigaScience · doi:10.1093/gigascience/giz116 · Cited by 43 · see citing works
Predictability in the evolution of Orthopteran cardenolide insensitivity
Yang, L., Ravikanthachari, N., Mariño‐Pérez, R., Deshmukh, R., Wu, M., Rosenstein, A., Kunte, K. K., Song, H., & Andolfatto, P. (2019) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2018.0246 · Cited by 43 · see citing works
Nishikawa, A., Gregory, W. T., Frenz, J. H., Cacia, J., & Kornfeld, S. A. (1997) · Journal of Biological Chemistry · doi:10.1074/jbc.272.31.19408 · Cited by 39 · see citing works
Taverner, A. M., Yang, L., Barile, Z. J., Lin, B., Peng, J., Pinharanda, A., Rao, A., Roland, B. P., Talsma, A. D., Wei, D. H., et al. (2019) · eLife · doi:10.7554/elife.48224 · Cited by 39 · see citing works
Couture, J., Legrand, P., Cantin, L., Labrie, F., Luu-The, V., & Breton, R. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.03.035 · Cited by 38 · see citing works
Nudix Hydrolase NUDT16 Regulates 53BP1 Protein by Reversing 53BP1 ADP-Ribosylation
Zhang, F., Lou, L., Peng, B., Song, X., Reizes, O., Almasan, A., & Gong, Z. (2020) · Cancer Research · doi:10.1158/0008-5472.can-19-2205 · Cited by 37 · see citing works
The perils of intralocus recombination for inferences of molecular convergence
Mendes, F. K., Livera, A. P., & Hahn, M. W. (2019) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2018.0244 · Cited by 36 · see citing works
Engelmann, S., Bläsing, O. E., Westhoff, P., & Svensson, P. (2002) · FEBS Letters · doi:10.1016/s0014-5793(02)02975-7 · Cited by 35 · see citing works
An N-acyl glycyltaurine conjugate of deoxycholic acid in the biliary bile acids of the rabbit
Hagey, L. R., Schteingart, C. D., Rossi, S. S., Ton-Nu, H.-T., & Hofmann, A. F. (1998) · Journal of Lipid Research · doi:10.1016/s0022-2275(20)32466-4 · Cited by 32 · see citing works
DiMario, R. J., & Cousins, A. B. (2018) · Journal of Experimental Botany · doi:10.1093/jxb/ery403 · Cited by 28 · see citing works
Structural and functional features of dimeric dihydrodiol dehydrogenase
Carbone, V., Hara, A., & El-Kabbani, O. A. L. (2008) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-008-7508-5 · Cited by 27 · see citing works
The effects of increasing the number of taxa on inferences of molecular convergence
Thomas, G. W. C., Hahn, M. W., & Hahn, Y. (2017) · Genome Biology and Evolution · doi:10.1093/gbe/evw306 · Cited by 27 · see citing works
Gunaratne, J., Goh, M. X., Swa, H. L. F., Lee, F. Y., Sanford, E., Wong, L. M., Hogue, K. A., Blackstock, W. P., & Okumura, K. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.221184 · Cited by 26 · see citing works
Sun, L., Bai, Y., Zhao, R., Sun, T., Cao, R., Wang, F., He, G., Zhang, W., Chen, Y., Ye, P., et al. (2016) · Arteriosclerosis Thrombosis and Vascular Biology · doi:10.1161/atvbaha.115.307412 · Cited by 24 · see citing works
Comparative biochemical properties of vertebrate deoxyribonuclease I
Fujihara, J., Yasuda, T., Ueki, M., Iida, R., & Takeshita, H. (2012) · Comparative Biochemistry and Physiology Part B Biochemistry and Molecular Biology · doi:10.1016/j.cbpb.2012.07.002 · Cited by 20 · see citing works
Cloning and sequencing of the cDNA species for mammalian dimeric dihydrodiol dehydrogenases
Arimitsu, E., Aoki, S., Ishikura, S., NAKANISHI, K., Matsuura, K., & Hara, A. (1999) · Biochemical Journal · doi:10.1042/0264-6021:3420721 · Cited by 19 · see citing works
Mulchande, J., Martins, L. M. D. R. S., Moreira, R., Archer, M., Oliveira, T. F., & Iley, J. (2007) · Organic & Biomolecular Chemistry · doi:10.1039/b706622h · Cited by 18 · see citing works
Thirawatananond, P., McPherson, R. L., Malhi, J. K., Nathan, S., Lambrecht, M. J., Brichacek, M. P., Hergenrother, P. J., Leung, A. K. L., & Gabelli, S. B. (2019) · Scientific Reports · doi:10.1038/s41598-019-39491-w · Cited by 16 · see citing works
Muñoz‐Clares, R. A., González‐Segura, L., Juárez‐Díaz, J. A., & Mújica‐Jiménez, C. (2020) · Biochemical Journal · doi:10.1042/bcj20200304 · Cited by 15 · see citing works
Distribution of Dimeric Dihydrodiol Dehydrogenase in Pig Tissues and its Role in Carbonyl Metabolism
Nakayama, T., Sawada, H., Deyashiki, Y., Kanazu, T., Hara, A., Shinoda, M., Matsuura, K., Bunai, Y., & Ohya, I. (1990) · Advances in experimental medicine and biology · doi:10.1007/978-1-4684-5901-2_21 · Cited by 13 · see citing works
Purification and Characterization of Dimeric Dihydrodiol Dehydrogenase from Dog Liver
Sato, K., Nakanishi, M., Deyashiki, Y., Hara, A., Matsuura, K., & Ohya, I. (1994) · The Journal of Biochemistry · doi:10.1093/oxfordjournals.jbchem.a124585 · Cited by 12 · see citing works
Nakagawa, M., Matsuura, K., Hara, A., Sawada, H., Bunai, Y., & Ohya, I. (1989) · The Journal of Biochemistry · doi:10.1093/oxfordjournals.jbchem.a122973 · Cited by 11 · see citing works
Zou, Z., & Zhang, J. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx109 · Cited by 10 · see citing works
Carbone, V., Endo, S., Sumii, R., Chung, R. P. ‐., Matsunaga, T., Hara, A., & El-Kabbani, O. A. L. (2007) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21566 · Cited by 10 · see citing works
Dy, A. B. C., Langlais, P. R., Barker, N. K., Addison, K. J., Tanyaratsrisakul, S., Boitano, S. A., Christenson, S. A., Kraft, M., Meyers, D. A., Bleecker, E. R., et al. (2021) · Scientific Reports · doi:10.1038/s41598-021-02869-w · Cited by 8 · see citing works
Accurate detection of convergent amino-acid evolution with PCOCPreprint
Rey, C., Guéguen, L., Sémon, M., & Boussau, B. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/247296 · Cited by 7 · see citing works
Parallel and Convergent Molecular Evolution
Pollock, D. D., & Pollard, S. T. (2016) · Elsevier eBooks · doi:10.1016/b978-0-12-800049-6.00173-6 · Cited by 2 · see citing works
Self-citationFukushima, K., & Pollock, D. D. (2022) · Zenodo (CERN European Organization for Nuclear Research) · doi:10.5061/dryad.tx95x6b0v · Cited by 1 · see citing works
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Subgenome dominance shapes novel gene evolution in the decaploid pitcher plant Nepenthes gracilis
Saul, F., Scharmann, M., Wakatake, T., Rajaraman, S., Marques, A., Freund, M., Bringmann, G., Channon, L., Becker, D., Carroll, E., et al. (2023) · Nature Plants · doi:10.1038/s41477-023-01562-2 · Cited by 33 · see citing works
Self-citationOno, E., & Murata, J. (2023) · Plant and Cell Physiology · doi:10.1093/pcp/pcad057 · Cited by 30 · see citing works
Cai, L., Liu, D., Yang, F., Zhang, R., Yun, Q., Dao, Z., Ma, Y., & Sun, W. (2024) · GigaScience · doi:10.1093/gigascience/giad110 · Cited by 27 · see citing works
Convergence in hearing-related genes between echolocating birds and mammals
Sadanandan, K. R., Ko, M., Low, G. W., Gahr, M. L., Edwards, S. V., Hiller, M., Sackton, T. B., Rheindt, F. E., Sin, S. Y. W., & Baldwin, M. W. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2307340120 · Cited by 19 · see citing works
Convergent acquisition of disulfide-forming enzymes in malodorous flowers
Okuyama, Y., Fukushima, K., Kakishima, S., Valchanova, A. K., Takano, K. T., Ito‐Inaba, Y., Nakazato, T., & Nagano, A. J. (2025) · Science · doi:10.1126/science.adu8988 · Cited by 17 · see citing works
Self-citationConvergent and lineage-specific genomic changes shape adaptations in sugar-consuming birds.
Osipova, E., Ko, M.-C., Petricek, K. M., Sin, S., Brown, T., Winkler, S., Pippel, M., Jarrells, J., Weiche, S., Mosbech, M.-B., et al. (2026) · Science · doi:10.1126/science.adt1522 · Cited by 5 · see citing works
Distinct Genes with Similar Functions Underlie Convergent Evolution in Myotis Bat Ecomorphs
Morales, A. E., Burbrink, F. T., Segall, M., Meza, M. A., Munegowda, C., Webala, P. W., Patterson, B. D., Thong, V. D., Rüedi, M., Hiller, M., et al. (2024) · Molecular Biology and Evolution · doi:10.1093/molbev/msae165 · Cited by 16 · see citing works
Redlich, R. W., Kowalczyk, A. M., Tene, M., Sestili, H. H., Foley, K., Saputra, E. C., Clark, N. L., Chikina, M. D., Meyer, W. K., & Pfenning, A. R. (2024) · Molecular Biology and Evolution · doi:10.1093/molbev/msae210 · Cited by 13 · see citing works
Genomic signatures of convergent shifts to plunge-diving behavior in birds
Eliason, C. M., Mellenthin, L. E., Hains, T., McCullough, J. M., Pirro, S., Andersen, M. J., & Hackett, S. J. (2023) · Communications Biology · doi:10.1038/s42003-023-05359-z · Cited by 11 · see citing works
Physicochemical Perspective of Biological Heterogeneity
Kwapiszewska, K. (2024) · ACS Physical Chemistry Au · doi:10.1021/acsphyschemau.3c00079 · Cited by 11 · see citing works
Zhao, R., Zhang, I. H., Jayakumar, A., Ward, B. B., & Babbin, A. R. (2024) · ISME Communications · doi:10.1093/ismeco/ycae060 · Cited by 10 · see citing works
Evolutionary sparse learning reveals the shared genetic basis of convergent traits
Allard, J. B., Sharma, S., Patel, R., Sanderford, M. D., Tamura, K., Vučetić, S., Gerhard, G. S., & Kumar, S. (2025) · Nature Communications · doi:10.1038/s41467-025-58428-8 · Cited by 11 · see citing works
Amaral, D. T., Bonatelli, I. A. S., Romeiro‐Brito, M., Telhe, M. C., Moraes, E. M., ZAPPI, D. C., Taylor, N. P., & Franco, F. F. (2024) · Planta · doi:10.1007/s00425-024-04442-x · Cited by 9 · see citing works
Borstein, S. R., Hammer, M. P., O’Meara, B. C., & McGee, M. D. (2024) · Nature Communications · doi:10.1038/s41467-024-53141-4 · Cited by 9 · see citing works
Joseph, J. (2024) · Molecular Biology and Evolution · doi:10.1093/molbev/msae107 · Cited by 9 · see citing works
Matsuda, Y., & Makino, T. (2024) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2024.1068 · Cited by 9 · see citing works
Comparative genomics uncovers evolutionary drivers of locust migratory adaptation
Dong, S., Li, X., Liu, Q., Zhu, Τ., Tian, A., Chen, N., Tu, X., & Ban, L. (2025) · BMC Genomics · doi:10.1186/s12864-025-11376-5 · Cited by 8 · see citing works
Cao, Z., Zhang, H., & Zou, Z. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2418254122 · Cited by 9 · see citing works
The genetic foundations of convergent traits
Allard, J. B., & Kumar, S. (2026) · Nature Reviews Genetics · doi:10.1038/s41576-026-00933-7 · Cited by 9 · see citing works
Convergent evolution of noncoding elements associated with short tarsus length in birds
Shakya, S. B., Edwards, S. V., & Sackton, T. B. (2025) · BMC Biology · doi:10.1186/s12915-025-02156-4 · Cited by 8 · see citing works
Accurate Detection of Convergent Mutations in Large Protein Alignments With ConDor
Morel, M. H., Zhukova, A., Lemoine, F., & Gascuel, O. (2024) · Genome Biology and Evolution · doi:10.1093/gbe/evae040 · Cited by 7 · see citing works
Park, H., Bae, E., Jung, J. G., Kim, J., Choi, B. Y., Lee, G., Kim, C., & Shim, D. (2025) · The Plant Genome · doi:10.1002/tpg2.70070 · Cited by 5 · see citing works
Convergent genetic adaptation of Escherichia coli in minimal media leads to pleiotropic divergence
Venkataraman, P., Nagendra, P., Ahlawat, N., Brajesh, R. G., & Saini, S. (2024) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2024.1286824 · Cited by 5 · see citing works
From Trees to Traits: A Review of Advances in PhyloG2P Methods and Future Directions
MacDonald, A. A. M., James, M. E., Mitchell, J. D., & Holland, B. R. (2025) · Genome Biology and Evolution · doi:10.1093/gbe/evaf150 · Cited by 5 · see citing works
Convergent Evolution and Predictability of Gene Copy Numbers Associated with Diets in Mammals
Wilhoit, K., Yamanouchi, S., Chen, B., Yamasaki, Y. Y., Ishikawa, A., Inoue, J. G., Iwasaki, W., & Kitano, J. (2025) · Genome Biology and Evolution · doi:10.1093/gbe/evaf008 · Cited by 4 · see citing works
Cicconardi, F., McLellan, C. F., Séguret, A. C., McMillan, W. O., & Montgomery, S. H. (2025) · Molecular Biology and Evolution · doi:10.1093/molbev/msaf179 · Cited by 4 · see citing works
Sodium Channel β Subunits—An Additional Element in Animal Tetrodotoxin Resistance?
Seneci, L., & Mikheyev, A. S. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25031478 · Cited by 4 · see citing works
Transcriptomic prey‐capture responses in convergently evolved carnivorous pitcher plants
Wakatake, T., & Fukushima, K. (2025) · New Phytologist · doi:10.1111/nph.70848 · Cited by 3 · see citing works
Self-citationChen, S., & Zou, Z. (2025) · Molecular Ecology Resources · doi:10.1111/1755-0998.70052 · Cited by 3 · see citing works
BUSTED-PH: Isolating the genomic signatures of convergent phenotypesPreprint
Selberg, A., Clark, N. L., Nekrutenko, A., Chikina, M. D., & Pond, S. L. K. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.01.29.702612 · Cited by 3 · see citing works
Tribble, C. M., & Stilio, V. S. D. (2026) · Integrative and Comparative Biology · doi:10.1093/icb/icag003 · Cited by 2 · see citing works
Berger, C. A., Stoilova, M. I., Varney, R., Abrams, S. C., Miglietta, M. P., Cartwright, P., & Oakley, T. H. (2026) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2616248123 · Cited by 2 · see citing works
Dong, Z., Wang, C., & Qu, Q. (2024) · Bioinformatics Advances · doi:10.1093/bioadv/vbae070 · Cited by 2 · see citing works
Cicconardi, F., Morris, B. J., Martelossi, J., Ray, D. A., & Montgomery, S. H. (2024) · Genome Biology and Evolution · doi:10.1093/gbe/evae218 · Cited by 2 · see citing works
Salve, B. G., Sharma, S., & Vijay, N. (2024) · Immunogenetics · doi:10.1007/s00251-024-01357-5 · Cited by 2 · see citing works
Integrating Intermediate Traits in Phylogenetic Genotype-to-Phenotype Studies
Clark, N. L., Hittinger, C. T., Li‐Byarlay, H., Rokas, A., Sackton, T. B., & Unckless, R. L. (2025) · Integrative and Comparative Biology · doi:10.1093/icb/icaf037 · Cited by 2 · see citing works
De Novo Genome Assembly and Phylogenetic Analysis of Cirsium nipponicum
Choi, B. Y., Kim, J., Park, H., Kim, J.-C., Han, S., Jo, I.-H., & Shim, D. (2024) · Genes · doi:10.3390/genes15101269 · Cited by 1 · see citing works
Estimates of molecular convergence reveal multiple genes with adaptive variation across teleost fish
Barua, A., Srivastava, M., Beinsteiner, B., Laudet, V., & Robinson‐Rechavi, M. (2026) · Molecular Biology and Evolution · doi:10.1093/molbev/msag015 · Cited by 1 · see citing works
Li, X., He, Z., Liu, A., Meng, F., Zhang, X., Li, N., Liu, H., Lu, Y., Wu, Z., Fan, H., et al. (2026) · Communications Biology · doi:10.1038/s42003-026-09523-z · Cited by 1 · see citing works
Origin, age, and metabolisms of dominant anammox bacteria in the global oxygen deficient zonesPreprint
Zhao, R., Zhang, I. H., Jayakumar, A., Ward, B. B., & Babbin, A. R. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.10.31.564962 · Cited by 1 · see citing works
Barua, A., Srivastava, M., Beinsteiner, B., Laudet, V., & Robinson‐Rechavi, M. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.06.24.600426 · Cited by 1 · see citing works
Convergent molecular evolution of viviparity across squamate reptilesPreprint
Xie, H., Hunter, D. C., Smout, J. L., Gaggiotti, O. E., & Elmer, K. R. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.09.26.678543 · Cited by 1 · see citing works
Convergent Emergence of Glucomannan β-Galactosyltransferase Activity in Asterids and Rosids
Ishida, K., Penner, M., Fukushima, K., Yoshimi, Y., Wilson, L. F. L., Echevarría‐Poza, A., Yu, L., & Dupree, P. (2024) · Plant and Cell Physiology · doi:10.1093/pcp/pcae118
Self-citationAllard, J. B., Sharma, S., Patel, R., Sanderford, M. D., Tamura, K., Vučetić, S., Gerhard, G. S., & Kumar, S. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.01.08.631987
Roles and Future Opportunities for Genomic Architecture in Understanding Repeated Evolution
Kellermeyer, R., Alvarez‐Ponce, D., Arsuaga, J., Chain, F. J. J., Dennis, M. Y., Margres, M. J., Meisel, R. P., Meyer, W. K., Moon, T. S., Smith, K. N., et al. (2025) · Integrative and Comparative Biology · doi:10.1093/icb/icaf040
Novel genomics insights into the molecular evolution of long-distance migratory mammals
Yuan, H., Xu, D., Xu, G., & Yang, G. (2025) · BMC Genomics · doi:10.1186/s12864-025-12022-w
A phylogenetic protein-coding genome-phenome map of complex traits across 224 primate speciesPreprint
Valenzuela, A., Barteri, F., Vasallo, C., Orkin, J. D., Kuderna, L. F. K., Boubli, J. P., Melin, A. D., Laayouni, H., Farh, K. K., Rogers, J., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.09.08.674744
Feng, Y., Zheng, R., Kong, L., Zhang, Z. Y., Chen, B., & Liu, S. (2026) · Water Research · doi:10.1016/j.watres.2026.125714
Xiao, Y., Zhao, R., Zhao, W., Wang, P., Xiao, X., Peng, X., & Jing, H. (2026) · ISME Communications · doi:10.1093/ismeco/ycag011
The interplay between recombination hotspots, GC-biased gene conversion and natural selection
Joseph, J. (2023) · theses.fr (ABES) · doi:10.70675/99f388fezf548z434az8ca0ze321e7c030e6
Convergence, stability, and thermal adaptation of the rubisco large subunit in plants
Leung, A., Chang, B. S. W., & Sage, R. F. (2026) · Evolution · doi:10.1093/evolut/qpag093
Emergence and divergence of blood cell lineages in the history of animal evolution
Nagahata, Y., & Kawamoto, H. (2026) · International Immunology · doi:10.1093/intimm/dxag039
Comparative Genomics and Functional Evidence for Convergent Adaptation to Hypoxia in Mammals
Dong, H., Wang, C., Pei, E., Zhao, L., Chai, S., & Tian, R. (2026) · Integrative Zoology · doi:10.1111/1749-4877.70158
- Authors
- Fukushima, K., & Pollock, D. D.
- Affiliations
- University of Würzburg (DE)
- Pacific Northwest National Laboratory (US)
- Corresponding author
- Fukushima, Kenji
- Venue
- Nature Ecology & Evolution
- Published
- 2023-01-05
- Volume
- 7
- Issue
- 1
- Pages
- 155-170
- ISSN
- 2397-334X (ISSN-L)
- PMC
- PMC9834058
- OpenAlex
- W4313561177
- Cited by
- 55
- References
- 163
- Citations by year
- 2026: 12 · 2025: 17 · 2024: 18 · 2023: 8
- FWCI
- 9.12
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Nature Ecology & Evolution (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- Research Square (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by-nc-sa)
- PubMed (publishedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion, cc-by-nc-sa)
- Funders
- MEXT | Japan Society for the Promotion of Science (18J00178)
- Alexander von Humboldt-Stiftung (Sofja Kovalevskaja programme 2018)
- Human Frontier Science Program (RGY0082/2021)
- U.S. Department of Health & Human Services | National Institutes of Health (GM083127)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
- Keywords
- genotype-phenotype correlation, convergent evolution, gene expression evolution, phylogenetic uncertainty
- MeSH terms
- Phenotype, Phylogeny, Genome, Evolution, Molecular, Genetic Association Studies
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