PUBLICATIONS

* Shared first authorship
**Corresponding author

31. 2024 **Stiller, J., Feng, S., Chowdhury, A., Rivas-González, I., Duchêne, DA., Fang, Q., Deng, Y., Kozlov, A., Stamatakis, A., Claramunt, S., Nguyen, JMT., Ho, SYW., Faircloth, BC., Haag, J., Houde, P., Cracraft, J., Balaban, M., Mai, U., Chen, G., Gao, R., Zhou, C., Xie, Y., Huang, Z., Cao, Z., Yan, Z., Ogilvie, HA., Nakhleh, L., Lindow, B., Morel, B., Fjeldså, J., Hosner, P., Fonseca, RRda, Petersen, B., Tobias, JA., Székely, T., Kennedy, JD., Reeve, AH., Liker, A., Stervander, M., Antunes, A., Tietze, DT., Bertelsen, M., Lei, F., Rahbek, C., Graves, GR., Schierup, MH., Warnow, T., Braun, EL., Gilbert, MTP., Jarvis‚ ED., Mirarab, S., Zhang, G. Complexity of avian evolution revealed by family-level genomes. Nature (Accelerated Article Preview).

https://doi.org/10.1038/s41586-024-07323-1

30. 2024 Mirarab, S., Rivas-González, I., Feng, S., Stiller, J., Fang, Q., Mai, U., Hickey, G., Brajuka, N., Fedrigo, O., Formenti, G., Wolf, J., Howe, K., Antunes, A., Schierup, MH., Paten, B., Jarvis, ED., Zhang, G., Braun, EL. A region of suppressed recombination misleads neoavian phylogenomics. PNAS 121 (15) e2319506121.

https://doi.org/10.1073/pnas.2319506121

29. 2024 Duchêne, DA., Duchêne, S., Stiller, J., Heller, R., Ho, SYW. ClockstaRX: testing molecular clock hypotheses with genomic data. Genome Biology and Evolution evae064. https://doi.org/10.1093/gbe/evae064

28. 2023 Payne, CY., Tilic, E., Boschen-Rose, R., Gannon, A., Stiller, J., Hiley, AS., Grupe, BM., Mah, C., Rouse, GW. A new Xyloplax species (Asteroidea, Echinodermata) that is not always associated with woodfalls. Diversity 15(12): 1212.

https://doi.org/10.3390/d15121212

Impact: One of the Top 10 new marine species of 2023 of the World Register of Marine Species (WoRMS)

27. 2023 de-Dios, T., Fontsere, C., Renom, P., Stiller, J., Llovera, L., Uliano-Silva, M., Sánchez-Gracia, A., Wright, C., Lizano, E., Caballero, B., Navarro, A., Civit, S., Robbins, R., Blaxter, M., Marquès-Bonet, T., Vila, R., Lalueza-Fox, C. Whole-genomes from the extinct Xerces Blue butterfly can help identify declining insect species. eLife 12:RP87928.

https://doi.org/10.7554/eLife.87928.2

Impact: Featured in a PNAS ‘Journal Club’ article highlighting selected recent papers.

26. 2023 Koch, NM., Tilic, E., Miller, AK., Stiller, J., Rouse, GW. Confusion will be my epitaph: Genome-scale discordance stifles phylogenetic resolution of Holothuroidea. Proceedings of the Royal Society B 290: 20230988.

https://doi.org/10.1098/rspb.2023.0988

Cover article.

25. 2023 **Stiller, J., Wilson, NG. Rouse, GW. Range-wide population structure of common seadragons (Syngnathidae) shows secondary contact over a former barrier and insights on illegal capture. BMC Biology 21:129.

https://doi.org/10.1186/s12915-023-01628-9

24. 2023 Bergeron, LA., Besenbacher, S., Zheng, J., Li, P., Bertelsen, MF., Quintard, B., Hoffman, IJ., Li, Z., St. Leger, J., Shao, C., Stiller, J., Gilbert, MTP., Schierup, MH., Zhang, G. Evolution of the germline mutation rate across vertebrates. Nature 614:285–291.

https://doi.org/10.1038/s41586-023-05752-y

23. 2023 Grealy, A., Miller, GH., Phillips, MJ., Clarke, SJ., Fogel, M., Patalwala, D., Rigby, P., Hubbard, A., Demarchi, B., Collins, M., Mackie, M., Sakalauskaite, J., Stiller, J., Clarke, JA., Legendre, LJ., Douglass, K., Hansford, J., Haile, J., Bunce, M. Molecular exploration of fossil eggshell uncovers hidden lineage of giant extinct bird. Nature Communications 14:914.

https://doi.org/10.1038/s41467-023-36405-3

22. 2022 Mohammadi, S., Özdemir, Hİ., Ozbek, P., Stiller, J., Deng, Y., Crawford, AJ., Rowland, H., Storz, J., Andolfatto, P., Dobler, S. Epistatic effects between amino acid insertions and substitutions mediate toxin-resistance of vertebrate Na+,K+-ATPases. Molecular Biology and Evolution 39:1-13.

https://doi.org/10.1093/molbev/msac258

21. 2022 **Stiller, J., Short, G., Healy, H., Saarman, N., Longo, S., Wainwright, P., Rouse, GW., Simison, WB. Phylogenomic analysis of Syngnathidae reveals novel relationships, origins of endemic diversity and variable diversification rates. BMC Biology 20:75.

https://doi.org/10.1186/s12915-022-01271-w

20. 2022 Demarchi, B., Stiller, J., Grealy, A., Mackie, M., Deng, Y., Gilbert, T., Clarke, J., Legendre, LJ., Boano, R., Sicheritz-Pontén, T., Magee, J., Zhang, G., Bunce, M., Collins, MJ., Miller, G. Ancient proteins resolve controversy over the identity of Genyornis eggshell. PNAS e2109326119.

https://doi.org/10.1073/pnas.2109326119

Impact: Featured in a short film by Google’s DeepMind a piece in The Conversation, and media coverage in Washington Post and Videnskab.dk.

19. 2021 Herranz, M., Stiller, J., Worsaae, K. & Sørensen, MV. Phylogenomic analyses of mud dragons (Kinorhyncha). Molecular Phylogenetics and Evolution 168:107375.

https://doi.org/10.1016/j.ympev.2021.107375

18. 2021 Tilic, E., Stiller, J., Campos, E., Pleijel, F. & Rouse, GW. Phylogenomics resolves ambiguous relationships within Aciculata (Errantia, Annelida). Molecular Phylogenetics and Evolution 166:107339.

https://doi.org/10.1016/j.ympev.2021.107339

17. 2021 **Stiller, J., Fonseca, RRd., Alfaro, ME., Faircloth, BC., Wilson, NG., Rouse, GW. Using UCEs to track the influence of shifting coastlines on leafy seadragon populations. Molecular Ecology 30:1364-1380.

https://doi.org/10.1111/mec.15744

Impact: Published with an independent News & Views Perspective.

16. 2021 Andreu-Sánchez, S., Chen, W., Stiller, J., Zhang, G. Multiple origins of a frameshift insertion in a mitochondrial gene in birds and turtles. GigaScience 10:1–11.

https://doi.org/10.1093/gigascience/giaa161

15. 2020 Armstrong, J., Hickey, G., Diekhans, M., Deran, A., Fang, Q., Feng, S., Stiller, J., Genereux, D., Johnson, J., Marinescu, V., Haussler, D., Alfoldi, J., Lindblad-Toh, K., Karlsson, E., Jarvis, E., Xie, D., Zhang, G., Paten, B. Progressive alignment with Cactus: a multiple-genome aligner for the thousand-genome era. Nature 587:246–251.

https://doi.org/10.1038/s41586-020-2871-y

14. 2020 (*equal contribution) Feng, S.*, Stiller, J.*, Deng, Y.*, Armstrong, J.*, Fang, Q., Reeve, A., Xie, D., Chen, G., Guo, C., Faircloth, B., Petersen, B., Wang, Z., Zhou, Q., Diekhans, M., Chen, W., Andreu-Sánchez, S., Margaryan, A., Howard, J., Pacheco, G., Mikkel-Sinding, H., Puetz, L., Cavill, E., Ribeiro, Â., Fjeldså, J., Hosner, P., Brumfield, R., Christidis, L., Bertelsen, M., Tietze, DT., Robertson, B., Song, G., Borgia, G., Claramunt, S., Lovette, I., Cowen, S., Njoroge, P., Dumbacher, J., Ryder, O., Fuchs, J., Bunce, M., Burt, D., Cracraft, J., Meng, G., Hackett, S., Ryan, P., Jønsson, K., Spencer, H., da Fonseca, R., Braun, E., Houde, P., Mirarab, S., Suh, A., Stervander, M., Hansson, B., Sigeman, H., Ponnikas, S., Frandsen, P., Van der Zwan, H., Balakrishnan, C., Clark, A., Fitzpatrick, J., Bowman, R., Chen, N., Cloutier, A., Sackton, T., Foote, D., Shakya, S., Sheldon, F., Vignal, A., Soares, A., Shapiro, B., Solís, J., Ferrer-Obiol, J., Rozas, J., Riutort, M., Tigano, A., Friesen, V., Dalen, L., Urrutia, A., Szekely, T., Liu, Y., Campana, M., Corvelo, A., Fleischer, RC., Rutherford, K., Gemmell, N., Dussex, N., Mouritsen, H., Thiele, N., Delmore, K., Liedvogel, M., Franke, A., Höppner, M., Krone, O., Fudickar, A., Mila, B., Ketterson, E., Fidler, A., Friis, G., Parody-Merino, A., Battley, P., Cox, M., Lima, N., Prosdocimi, F., Parchman, T., Schlinger, B., Loiselle, B., Blake, J., Lim, H., Day, L., Fuxjager, M., Baldwin, M., Braun, M., Wirthlin, M., Dikow, R., Ryder, T., Camenisch, G., Keller, L., DaCosta, J., Hauber, M., Louder, M., Witt, C., McGuire, J., Mudge, J., Megna, L., Carling, M., Wang, B., Taylor, S., Del-Rio , G., Aleixo, A., Vasconcelos, AT., Mello, C., Weir, J., Haussler, D., Li, Q., Yang, H., Wang, J., Lei, F., Rahbek, C., Gilbert, MPT., Graves, G., Jarvis, E., Paten, B., Zhang, G.

Densely sampling genomes across the diversity of birds increases power of comparative genomics analyses. Nature 587:252–257.

https://doi.org/10.1038/s41586-020-2873-9

Impact: Featured in 42 news outlets, including an interview for Videnskab.dk. I designed material for a Twitter campaign, resulting in 884 tweets.

13. 2020 Tilic, E., Sayyari, E., Stiller, J., Mirarab, S., Rouse, GW. More is needed — Thousands of loci are required to elucidate the relationships of the ‘flowers of the sea’ (Sabellida, Annelida).

Molecular Phylogenetics and Evolution 151:106892.

https://doi.org/10.1016/j.ympev.2020.106892

12. 2020 Zhang, P., Zhao, y., Li, C., Lin, M., Dong, L., Zhang, R., Liu, M., Li, K., Zhang, H., Liu, X., Zhang, Y., Yuan, Y., Liu, H., Seim, I., Chang, Y., Li, F., Liu, S., Lee., S.M.-Y. Wang, K., Qiu, Q., Wang, D., Wang, X., McGowen, M., Jefferson, T., Olsen, M., Stiller, J., Zhang, G., Xu, X., Yang, H., Fan, G., Liu, X., Li, S. Indo-Pacific humpback dolphin genome reveals insights into chromosome evolution and the historical demography of a vulnerable species. iScience 23:101640.

https://doi.org/10.1016/j.isci.2020.101640

11. 2020 **Stiller, J., Tilic, E., Rousset, V., Pleijel, F., Rouse, GW. Spaghetti to a tree: A robust phylogeny for Terebelliformia (Annelida) based on transcriptomes, molecular and morphological data. Biology 9:73.

https://doi.org/10.3390/biology9040073

Cover article.

10. 2020 Gelabert, P., Sandoval-Velasco, M., Serres, A., de Manuel, M., Renom, P., Margaryan, A., Stiller, J., de Dios, T., Fang, Q., Feng, S., Mañosa, S., Pacheco, G., Ferrando-Bernal, M., Shi, G., Hao, F., Chen, X., Petersen, B., Olsen, R.-A., Navarro, A., Deng, Y., Dalén, L., Marquès-Bonet, T., Zhang, G., Antunes, A., Gilbert, MTP., Lalueza-Fox, C. Evolutionary history, genomic adaptation to toxic diet and extinction of the Carolina parakeet. Current Biology 30:108–114. — 2020.

https://doi.org/10.1016/j.cub.2019.10.066

Cover article. Impact: Featured in the New York Times, Forbes and BBC.

9. 2019 Stiller, J., Zhang, G. Comparative phylogenomics, a stepping stone for bird biodiversity studies. Diversity 11:115.

https://doi.org/10.3390/d11070115

8. 2017 Eilertsen, MH., Kongsrud, JA., Alvestad, T., Stiller, J., Rouse, GW., & Rapp, HT. Do ampharetids take sedimented steps between vents and seeps? Phylogeny and habitat-use of Ampharetidae (Annelida, Terebelliformia) in chemosynthesis-based ecosystems. BMC Evolutionary Biology 17:222.

https://doi.org/10.1186/s12862-017-1065-1

7. 2017 Forrest, MJ., Stiller, J., King, TL., Rouse, GW. Between hot rocks and dry places: The status of the Dixie Valley Toad. Western North American Naturalist 77:162-175.

https://doi.org/10.3398/064.077.0204

6. 2017 Stiller, J., Wilson, NG., Donnellan, S., Rouse, GW. The leafy seadragon, Phycodurus eques, a flagship species with low but structured genetic variability. Journal of Heredity 108:152-162.

https://doi.org/10.1093/jhered/esw075

5. 2017 Rouse, GW., Stiller, J., Wilson, NG. First live records of the ruby seadragon (Phyllopteryx dewysea, Syngnathidae). Marine Biodiversity Records 10:2.

https://doi.org/10.1186/s41200-016-0102-x

Impact: Featured in 800 news outlets, including New York Times, Washington Post, National Geographic.

4. 2017 (*equal contribution) Wilson, NG.*, Stiller, J.*, Rouse, GW. Barriers to gene flow in common seadragons (Syngnathidae: Phyllopteryx taeniolatus). Conservation Genetics 18:53.

https://doi.org/10.1007/s10592-016-0881-y

3. 2015 Stiller, J.**, Wilson, NG., Rouse, GW. A spectacular new species of seadragon (Syngnathidae). Royal Society Open Science 2:140458.

https://doi.org/10.1098/rsos.140458

Impact: Widely covered by media, announced by the Western Australian Parliament, interview for a book chapter in Christopher Kemp’s book “The Lost Species”, voted one of Top 10 New Species 2016.

2. 2013 Stiller, J., Rousset, V., Chevaldonne, P., Pleijel, F., Vrijenhoek, R., Rouse, GW. Phylogeny, biogeography and systematics of hydrothermal vent and methane seep Amphisamytha (Ampharetidae, Annelida), with descriptions of three new species. Systematics and Biodiversity 11:35-65.

https://doi.org/10.1080/14772000.2013.772925

1. 2011 Beyaert, I., Köpke, D., Stiller, J., Hammerbacher, A., Schmidt, A., Gershenzon, J., Hilker, M. Can insect egg deposition “warn” a plant of future feeding damage by herbivorous larvae? Proceedings of the Royal Society B 279:101–108.

https://doi.org/10.1098/rspb.2011.0468

Stiller, J.

PUBLICATIONS

* Shared first authorship **Corresponding author

​

29. 2024 Duchêne, DA., Duchêne, S., Stiller, J., Heller, R., Ho, SYW. ClockstaRX: testing molecular clock hypotheses with genomic data. Genome Biology and Evolution evae064. https://doi.org/10.1093/gbe/evae064

​

28. 2023 Payne, CY., Tilic, E., Boschen-Rose, R., Gannon, A., Stiller, J., Hiley, AS., Grupe, BM., Mah, C., Rouse, GW. A new Xyloplax species (Asteroidea, Echinodermata) that is not always associated with woodfalls. Diversity 15(12): 1212.

Impact: One of the Top 10 new marine species of 2023 of the World Register of Marine Species (WoRMS)

​

Impact: Featured in a PNAS ‘Journal Club’ article highlighting selected recent papers.

26. 2023 Koch, NM., Tilic, E., Miller, AK., Stiller, J., Rouse, GW. Confusion will be my epitaph: Genome-scale discordance stifles phylogenetic resolution of Holothuroidea. Proceedings of the Royal Society B 290: 20230988.

Cover article.

25. 2023 **Stiller, J., Wilson, NG. Rouse, GW. Range-wide population structure of common seadragons (Syngnathidae) shows secondary contact over a former barrier and insights on illegal capture. BMC Biology 21:129.

24. 2023 Bergeron, LA., Besenbacher, S., Zheng, J., Li, P., Bertelsen, MF., Quintard, B., Hoffman, IJ., Li, Z., St. Leger, J., Shao, C., Stiller, J., Gilbert, MTP., Schierup, MH., Zhang, G. Evolution of the germline mutation rate across vertebrates. Nature 614:285–291.

​

21. 2022 **Stiller, J., Short, G., Healy, H., Saarman, N., Longo, S., Wainwright, P., Rouse, GW., Simison, WB. Phylogenomic analysis of Syngnathidae reveals novel relationships, origins of endemic diversity and variable diversification rates. BMC Biology 20:75.

​

20. 2022 Demarchi, B., Stiller, J., Grealy, A., Mackie, M., Deng, Y., Gilbert, T., Clarke, J., Legendre, LJ., Boano, R., Sicheritz-Pontén, T., Magee, J., Zhang, G., Bunce, M., Collins, MJ., Miller, G. Ancient proteins resolve controversy over the identity of Genyornis eggshell. PNAS e2109326119.

Impact: Featured in a short film by Google’s DeepMind a piece in The Conversation, and media coverage in Washington Post and Videnskab.dk.

19. 2021 Herranz, M., Stiller, J., Worsaae, K. & Sørensen, MV. Phylogenomic analyses of mud dragons (Kinorhyncha). Molecular Phylogenetics and Evolution 168:107375.

​

18. 2021 Tilic, E., Stiller, J., Campos, E., Pleijel, F. & Rouse, GW. Phylogenomics resolves ambiguous relationships within Aciculata (Errantia, Annelida). Molecular Phylogenetics and Evolution 166:107339.

17. 2021 **Stiller, J., Fonseca, RRd., Alfaro, ME., Faircloth, BC., Wilson, NG., Rouse, GW. Using UCEs to track the influence of shifting coastlines on leafy seadragon populations. Molecular Ecology 30:1364-1380.

Impact: Published with an independent News & Views Perspective.

​

* Shared first authorship
**Corresponding author