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George Tiley

Molecular Evolution and Ecology

Publications

Publications

25. Fauskee B, Crowl AA, Piatkowski B, Yoder AD, Tiley GP. 2024. Ancient introgression in mouse lemurs (Microcebus: Cheirogaleidae) explains 20 tears of phylogenetic uncertainty. Accepted at Bulletin of the Society of Systematic Biologists.

24. Tiley GP, Crowl AA, Almary TOM, Luke WRQ, Solofondranohatra CL, Besnard G, Lehmann CER, Yoder AD, Vorontsova MS. 2023. Genetic variation in Loudetia simplex supports the presence of ancient grasslands in Madagascar. Plants People Planet doi: https://doi.org/10.1002/ppp3.10437

23. Shao Y, Zhou L, Li F, Zhao L, Zhang B-L, Shao F, Chen J, Chunyan C, Bi X, Zhuang X-L, Zhu H, Hu J, Sun Z, Li X, Wang D, Rivas-González I, Wang S, Wang Y-M, Chen W, Li G, Lu H-M, Liu Y, Kuderna L, Farh K, Fan P, Yu L, Li M, Liu Z, Tiley GP, Yoder AD, Roos C, Hayakawa T, Marques-Bonet T, Rogers J, Stenson P, Cooper D, Schierup M, Yao Y-G, Zhang Y-P, Wang W, Qi X-G, Zhang G, Wu D-D. 2023. Phylogenomic analyses provide insights into primate evolution. Science 380:913-924.

22. Tiley GP, Flouri T, Jiao X, Poelstra JW, Xu B, Zhu T, Rannala B, Yoder AD, Yang Z. 2023. Estimation of species divergence times in presence of cross-species gene flow. Systematic Biology 72:820-836.

21. Samonds KE, Ali JR, Huber M, Vences M, Tiley GP, Yoder AD. 2022. History of animal and plant colonization: A synopsis. In: Goodman SM, editor. The New Natural History of Madagascar. Princeton University Press. p. 73-77.

20. Crowl AA, Fritsch PW, Tiley GP, Lynch NP, Ranney TG, Ashrafi H, Manos PS. 2022. A first complete phylogenomic hypothesis for diploid blueberries (Vaccinium section Cyanococcus). American Journal of Botany 109:1596-1606.

19. Tiley GP†, van Elst T†, Teixeira H, Schüßler D, Salmona J, Blanco MB, Ralison JM, Randrianambinina B, Rasoloarison RM, Stahlke AR, Hohenlohe PA, Chikhi L, Louis Jr EE, Radespiel U, Yoder AD. 2022. Phylogeographic analysis of Goodman’s mouse lemur reveals historical interconnectivity of Madagascar’s Central Highlands and eastern rainforests. Molecular Ecology 31:4901-4918.

18. Bergeron LA, Besenbacher S, Turner T, Versoza CJ, Wang RJ, Price AL, Armstrong E, Riera M, Carlson J, Chen H-Y, Hahn MW, Harris K, Jleppe AS, López-Nandam EH, Moorjani P, Pfeifer SP, Tiley GP, Yoder AD, Zhang G, Schierup MH. 2022. The mutationathon highlights the importance of reaching standardization in the estimates of pedigree-based germline mutation rates. eLife 11:e73577.

17. Campbell CR†, Tiley GP†, Poelstra JW, Hunnicutt KE, Larsen PA, Lee H-J, Thorne JL, dos Reis M, Yoder AD. 2021. Pedigree-based and phylogenetic methods support surprising patterns of mutation rate and spectrum in the gray mouse lemur. Heredity 127:233-244.

16. Yoder AD, Tiley GP. 2021. The challenge and promise of estimating the de novo mutation rate from whole-genome comparisons among closely related individuals. Molecular Ecology 30:6087-6100.

15. Carey SB, Jenkins J, Payton AC, Shu S, Lovell JT, Maumus F, Sreedasyam A, Tiley GP, Fernandez-Pozo N, Barry K, Chen C, Wang M, Lipzen A, Daum C, Saski CA, McBreen JC, Conrad RE, Kollar LM, Olsson S, Huttunen S, Landis JB, Burleigh JB, Wickett NJ, Johnson MG, Rensing SA, Grimwood J, Schmutz J, McDaniel SF. 2021. Chromosome fusions shape an ancient UV sex chromosome system. Science Advances 7:eabh2488.

14. Breinholt JW, Carey SB, Tiley GP, Davis EC, Endara L, McDaniel SF, Neves LG, Sessa EB, von Konrat M, Chantanaorrapint S, Fawcett S, Ickert-Bond SM, Labiak PH, Larraín J, Lehnert M, Lewis LR, Nagalingum NS, Patel N, Rensing SA, Testo W, Vasco A, Villarreal JC, Williams EW, Burleigh JG. 2021. A target enrichment probe set for resolving the flagellate plant tree of life. Applications in Plant Sciences 9:e11406.

13. Poelstra JW†, Salmona J †, Tiley GP†, Schüßler D, Blanco MB, Andriambeloson JB, Bouchez O, Campbell CR, Etter PD, Hohenlohe PA, Hunnicutt KE, Iribar A, Johnson EA, Kappeler PM, Larsen PA, Manzi S, Ralison JM, Randrianambinina B, Rasoloarison RM, Rasolofoson DW, Stahlke AR, Weisrock D, Williams RC, Chikhi L, Louis Jr EE, Radespiel U, Yoder AD. 2020. Cryptic Patterns of Speciation in Cryptic Primates: Microendemic Mouse Lemurs and the Multispecies Coalescent. Systematic Biology 70:203-218.

12. Tiley GP, Poelstra JW, dos Reis M, Yang Z, Yoder AD. 2020. Molecular Clocks without Rocks: New Solutions for Old Problems. Trends in Genetics 36:845-856.

11. Tiley GP, Pandey A, Kimball RT, Braun EL, Burleigh JG. 2020. Whole genome phylogeny of Gallus: introgression and data-type efects. Avian Research 11:1-15.

10. Hunnicutt KE†, Tiley GP†, Williams RC, Larsen PA, Blanco MB, Rasoloarison RM, Campbell CR, Zhu K, Weisrock DW, Matsunami H, Yoder AD. 2020. Comparative Genomic Analysis of the Pheromone Class 1 Family (V1R) Reveals Extreme Complexity in Mouse Lemurs (Genus, Microcebus) and a Chromosomal Hotspot across Mammals. Genome Biology and Evolution 12:3562-3579.

9. Leebens-Mack et al. 2019. One thousand plant transcriptomes and the phylogenomics of green plants. Nature 574:679-685.

8. Li Z, Tiley GP, Rundell RJ, Barker MS. 2019. Reply to Nakatani and McLysaght: Analyzing deep duplication events. PNAS 116:1819-1820.

7. Yoder AD, Poelstra JW, Tiley GP, Williams R. 2018. Neutral Theory is the foundation of Conservation Genetics. Molecular Biology and Evolution 6:1322-1326.

6. Tiley GP, Barker MS, Burleigh JG. 2018. Assessing the Performance of Ks Plots for Detecting Ancient Whole Genome Duplications. Genome Biology and Evolution 10:2882-2898.

5. Li Z†,Tiley GP†, Galuska SR, Reardon CR, Kidder TI, Rundell RJ, Barker MS. 2018. Multiple large-scale gene and genome duplications during the evolution of hexapods. PNAS 115:4713-4718.

4. Tiley GP, Kimball RT, Braun EL, Burleigh JG. 2018. Comparison of the Chinese bamboo partridge and red Junglefowl genome sequences highlights the importance of demography in genome evolution. BMC Genomics 19:336.

3. Tiley GP, Ané C, Burleigh JG. 2016. Evaluating and characterizing ancient whole-genome duplications in plants with gene count data. Genome Biology and Evolution 8:1023-1037.

2. Tiley GP, Burleigh JG. 2015. The relationship of recombination rate, genome structure, and patterns of molecular evolution across angiosperms. BMC Evolutionary Biology 15:194.

1. Eserman LA, Tiley GP, Jarret RL, Leebens-Mack JH, Miller RE. 2014. Phylogenetics and diversification of morning glories (tribe Ipomoeeae, Convolvulaceae) based on whole plastome sequences. American Journal of Botany 101:92-103.

Preprints

5. Sutherland BL, Tiley GP, Li Z, McKibben MTW, Barker MS. 2024. SLEDGe: Inference of ancient whole genome duplications using machine learning. bioRxiv doi: https://doi.org/10.1101/2024.01.17.574559

4. Tiley GP, Solís-Lemus C. 2023. Extracting diamonds: Identifiability of 4-node cycles in level-1 phylogenetic networks under a pseudolikelihood coalescent model. bioRxiv doi: https://doi.org/10.1101/2023.10.25.564087

3. Almary TOM, White J, Rasaminirina F, Razanatsoa J, Lehmann CER, Rakotoarinivo M, Ralimanana H, Vorontsova MS, Tiley GP. 2023. The grass that built the Central Highland of Madagascar: environmental niches and morphological diversity of Loudetia simplex. bioRxiv doi: https://doi.org/10.1101/2023.09.25.559324

2. Tiley GP, Crowl AA, Manos PS, Sessa EB, Solís-Lemus C, Yoder AD, Burleigh JG. 2023. Benefits and Limits of Phasing Alleles for Network Inference of Allopolyploid Complexes. bioRxiv doi: https://doi.org/10.1101.2021.05.04.442457

1. Kong Y, Tiley GP, Solis-Lemus C. 2023. Unsupervised learning of phylogenetic trees via split-weight embedding. arXiv: https://doi.org/10.48550/arXiv.2312.16074


†co-first authorship