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1. Dense sampling of bird diversity increases power of comparative genomics (vol 587, pg 252, 2020)

Author

Feng, S, Stiller, J, Deng, Y, Armstrong, J, Fang, Q, Reeve, AH, Xie, D, Chen, G, Guo, C, Faircloth, BC, Petersen, B, Wang, Z, Zhou, Q, Diekhans, M, Chen, W, Andreu-Sanchez, S, Margaryan, A, Howard, JT, Parent, C, Pacheco, G, Sinding, M-HS, Puetz, L, Cavill, E, Ribeiro, AM, Eckhart, L, Fjeldsa, J, Hosner, PA, Brumfield, RT, Christidis, L, Bertelsen, MF, Sicheritz-Ponten, T, Tietze, DT, Robertson, BC, Song, G, Borgia, G, Claramunt, S, Lovette, IJ, Cowen, SJ, Njoroge, P, Dumbacher, JP, Ryder, OA, Fuchs, J, Bunce, M, Burt, DW, Cracraft, J, Meng, G, Hackett, SJ, Ryan, PG, Jonsson, KA, Jamieson, IG, da Fonseca, RR, Braun, EL, Houde, P, Mirarab, S, Suh, A, Hansson, B, Ponnikas, S, Sigeman, H, Stervander, M, Frandsen, PB, van der Zwan, H, van der Sluis, R, Visser, C, Balakrishnan, CN, Clark, AG, Fitzpatrick, JW, Bowman, R, Chen, N, Cloutier, A, Sackton, TB, Edwards, SV, Foote, DJ, Shakya, SB, Sheldon, FH, Vignal, A, Soares, AER, Shapiro, B, Gonzalez-Solis, J, Ferrer-Obiol, J, Rozas, J, Riutort, M, Tigano, A, Friesen, V, Dalen, L, Urrutia, AO, Szekely, T, Liu, Y, Campana, MG, Corvelo, A, Fleischer, RC, Rutherford, KM, Gemmell, NJ, Dussex, N, Mouritsen, H, Thiele, N, Delmore, K, Liedvogel, M, Franke, A, Hoeppner, MP, Krone, O, Fudickar, AM, Mila, B, Ketterson, ED, Fidler, AE, Friis, G, Parody-Merino, AM, Battley, PF, Cox, MP, Lima, NCB, Prosdocimi, F, Parchman, TL, Schlinger, BA, Loiselle, BA, Blake, JG, Lim, HC, Day, LB, Fuxjager, MJ, Baldwin, MW, Braun, MJ, Wirthlin, M, Dikow, RB, Ryder, TB, Camenisch, G, Keller, LF, DaCosta, JM, Hauber, ME, Louder, MIM, Witt, CC, McGuire, JA, Mudge, J, Megna, LC, Carling, MD, Wang, B, Taylor, SA, Del-Rio, G, Aleixo, A, Vasconcelos, ATR, Mello, CV, Weir, JT, Haussler, D, Li, Q, Yang, H, Wang, J, Lei, F, Rahbek, C, Gilbert, MTP, Graves, GR, Jarvis, ED, Paten, B, Zhang, G, Feng, S, Stiller, J, Deng, Y, Armstrong, J, Fang, Q, Reeve, AH, Xie, D, Chen, G, Guo, C, Faircloth, BC, Petersen, B, Wang, Z, Zhou, Q, Diekhans, M, Chen, W, Andreu-Sanchez, S, Margaryan, A, Howard, JT, Parent, C, Pacheco, G, Sinding, M-HS, Puetz, L, Cavill, E, Ribeiro, AM, Eckhart, L, Fjeldsa, J, Hosner, PA, Brumfield, RT, Christidis, L, Bertelsen, MF, Sicheritz-Ponten, T, Tietze, DT, Robertson, BC, Song, G, Borgia, G, Claramunt, S, Lovette, IJ, Cowen, SJ, Njoroge, P, Dumbacher, JP, Ryder, OA, Fuchs, J, Bunce, M, Burt, DW, Cracraft, J, Meng, G, Hackett, SJ, Ryan, PG, Jonsson, KA, Jamieson, IG, da Fonseca, RR, Braun, EL, Houde, P, Mirarab, S, Suh, A, Hansson, B, Ponnikas, S, Sigeman, H, Stervander, M, Frandsen, PB, van der Zwan, H, van der Sluis, R, Visser, C, Balakrishnan, CN, Clark, AG, Fitzpatrick, JW, Bowman, R, Chen, N, Cloutier, A, Sackton, TB, Edwards, SV, Foote, DJ, Shakya, SB, Sheldon, FH, Vignal, A, Soares, AER, Shapiro, B, Gonzalez-Solis, J, Ferrer-Obiol, J, Rozas, J, Riutort, M, Tigano, A, Friesen, V, Dalen, L, Urrutia, AO, Szekely, T, Liu, Y, Campana, MG, Corvelo, A, Fleischer, RC, Rutherford, KM, Gemmell, NJ, Dussex, N, Mouritsen, H, Thiele, N, Delmore, K, Liedvogel, M, Franke, A, Hoeppner, MP, Krone, O, Fudickar, AM, Mila, B, Ketterson, ED, Fidler, AE, Friis, G, Parody-Merino, AM, Battley, PF, Cox, MP, Lima, NCB, Prosdocimi, F, Parchman, TL, Schlinger, BA, Loiselle, BA, Blake, JG, Lim, HC, Day, LB, Fuxjager, MJ, Baldwin, MW, Braun, MJ, Wirthlin, M, Dikow, RB, Ryder, TB, Camenisch, G, Keller, LF, DaCosta, JM, Hauber, ME, Louder, MIM, Witt, CC, McGuire, JA, Mudge, J, Megna, LC, Carling, MD, Wang, B, Taylor, SA, Del-Rio, G, Aleixo, A, Vasconcelos, ATR, Mello, CV, Weir, JT, Haussler, D, Li, Q, Yang, H, Wang, J, Lei, F, Rahbek, C, Gilbert, MTP, Graves, GR, Jarvis, ED, Paten, B, and Zhang, G

Abstract

A Correction to this paper has been published: https://doi.org/10.1038/s41586-021-03473-8.

Published
2021

2. Dense sampling of bird diversity increases power of comparative genomics

Author

Feng, S, Stiller, J, Deng, Y, Armstrong, J, Fang, Q, Reeve, AH, Xie, D, Chen, G, Guo, C, Faircloth, BC, Petersen, B, Wang, Z, Zhou, Q, Diekhans, M, Chen, W, Andreu-Sanchez, S, Margaryan, A, Howard, JT, Parent, C, Pacheco, G, Sinding, M-HS, Puetz, L, Cavill, E, Ribeiro, AM, Eckhart, L, Fjeldsa, J, Hosner, PA, Brumfield, RT, Christidis, L, Bertelsen, MF, Sicheritz-Ponten, T, Tietze, DT, Robertson, BC, Song, G, Borgia, G, Claramunt, S, Lovette, IJ, Cowen, SJ, Njoroge, P, Dumbacher, JP, Ryder, OA, Fuchs, J, Bunce, M, Burt, DW, Cracraft, J, Meng, G, Hackett, SJ, Ryan, PG, Jonsson, KA, Jamieson, IG, da Fonseca, RR, Braun, EL, Houde, P, Mirarab, S, Suh, A, Hansson, B, Ponnikas, S, Sigeman, H, Stervander, M, Frandsen, PB, van der Zwan, H, van der Sluis, R, Visser, C, Balakrishnan, CN, Clark, AG, Fitzpatrick, JW, Bowman, R, Chen, N, Cloutier, A, Sackton, TB, Edwards, SV, Foote, DJ, Shakya, SB, Sheldon, FH, Vignal, A, Soares, AER, Shapiro, B, Gonzalez-Solis, J, Ferrer-Obiol, J, Rozas, J, Riutort, M, Tigano, A, Friesen, V, Dalen, L, Urrutia, AO, Szekely, T, Liu, Y, Campana, MG, Corvelo, A, Fleischer, RC, Rutherford, KM, Gemmell, NJ, Dussex, N, Mouritsen, H, Thiele, N, Delmore, K, Liedvogel, M, Franke, A, Hoeppner, MP, Krone, O, Fudickar, AM, Mila, B, Ketterson, ED, Fidler, AE, Friis, G, Parody-Merino, AM, Battley, PF, Cox, MP, Lima, NCB, Prosdocimi, F, Parchman, TL, Schlinger, BA, Loiselle, BA, Blake, JG, Lim, HC, Day, LB, Fuxjager, MJ, Baldwin, MW, Braun, MJ, Wirthlin, M, Dikow, RB, Ryder, TB, Camenisch, G, Keller, LF, DaCosta, JM, Hauber, ME, Louder, MIM, Witt, CC, McGuire, JA, Mudge, J, Megna, LC, Carling, MD, Wang, B, Taylor, SA, Del-Rio, G, Aleixo, A, Vasconcelos, ATR, Mello, CV, Weir, JT, Haussler, D, Li, Q, Yang, H, Wang, J, Lei, F, Rahbek, C, Gilbert, MTP, Graves, GR, Jarvis, ED, Paten, B, Zhang, G, Feng, S, Stiller, J, Deng, Y, Armstrong, J, Fang, Q, Reeve, AH, Xie, D, Chen, G, Guo, C, Faircloth, BC, Petersen, B, Wang, Z, Zhou, Q, Diekhans, M, Chen, W, Andreu-Sanchez, S, Margaryan, A, Howard, JT, Parent, C, Pacheco, G, Sinding, M-HS, Puetz, L, Cavill, E, Ribeiro, AM, Eckhart, L, Fjeldsa, J, Hosner, PA, Brumfield, RT, Christidis, L, Bertelsen, MF, Sicheritz-Ponten, T, Tietze, DT, Robertson, BC, Song, G, Borgia, G, Claramunt, S, Lovette, IJ, Cowen, SJ, Njoroge, P, Dumbacher, JP, Ryder, OA, Fuchs, J, Bunce, M, Burt, DW, Cracraft, J, Meng, G, Hackett, SJ, Ryan, PG, Jonsson, KA, Jamieson, IG, da Fonseca, RR, Braun, EL, Houde, P, Mirarab, S, Suh, A, Hansson, B, Ponnikas, S, Sigeman, H, Stervander, M, Frandsen, PB, van der Zwan, H, van der Sluis, R, Visser, C, Balakrishnan, CN, Clark, AG, Fitzpatrick, JW, Bowman, R, Chen, N, Cloutier, A, Sackton, TB, Edwards, SV, Foote, DJ, Shakya, SB, Sheldon, FH, Vignal, A, Soares, AER, Shapiro, B, Gonzalez-Solis, J, Ferrer-Obiol, J, Rozas, J, Riutort, M, Tigano, A, Friesen, V, Dalen, L, Urrutia, AO, Szekely, T, Liu, Y, Campana, MG, Corvelo, A, Fleischer, RC, Rutherford, KM, Gemmell, NJ, Dussex, N, Mouritsen, H, Thiele, N, Delmore, K, Liedvogel, M, Franke, A, Hoeppner, MP, Krone, O, Fudickar, AM, Mila, B, Ketterson, ED, Fidler, AE, Friis, G, Parody-Merino, AM, Battley, PF, Cox, MP, Lima, NCB, Prosdocimi, F, Parchman, TL, Schlinger, BA, Loiselle, BA, Blake, JG, Lim, HC, Day, LB, Fuxjager, MJ, Baldwin, MW, Braun, MJ, Wirthlin, M, Dikow, RB, Ryder, TB, Camenisch, G, Keller, LF, DaCosta, JM, Hauber, ME, Louder, MIM, Witt, CC, McGuire, JA, Mudge, J, Megna, LC, Carling, MD, Wang, B, Taylor, SA, Del-Rio, G, Aleixo, A, Vasconcelos, ATR, Mello, CV, Weir, JT, Haussler, D, Li, Q, Yang, H, Wang, J, Lei, F, Rahbek, C, Gilbert, MTP, Graves, GR, Jarvis, ED, Paten, B, and Zhang, G

Abstract

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1-4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.

Published
2020

3. Do monarch butterflies use polarized skylight for migratory orientation?

Author

Stalleicken, J, Mukhida, M, Labhart, T, Wehner, R, Frost, B, Mouritsen, H, Stalleicken, J, Mukhida, M, Labhart, T, Wehner, R, Frost, B, and Mouritsen, H

Abstract

To test if migratory monarch butterflies use polarized light patterns as part of their time-compensated sun compass, we recorded their virtual flight paths in a flight simulator while the butterflies were exposed to patches of naturally polarized blue sky, artificial polarizers or a sunny sky. In addition, we tested butterflies with and without the polarized light detectors of their compound eye being occluded. The monarchs' orientation responses suggested that the butterflies did not use the polarized light patterns as a compass cue, nor did they exhibit a specific alignment response towards the axis of polarized light. When given direct view of the sun, migratory monarchs with their polarized light detectors painted out were still able to use their time-compensated compass: non-clockshifted butterflies, with their dorsal rim area occluded, oriented in their typical south-southwesterly migratory direction. Furthermore, they shifted their flight course clockwise by the predicted approximately 90 degrees after being advance clockshifted 6 h. We conclude that in migratory monarch butterflies, polarized light cues are not necessary for a time-compensated celestial compass to work and that the azimuthal position of the sun disc and/or the associated light-intensity and spectral gradients seem to be the migrants' major compass cue.

Published
2005

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