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1. The Origin and Evolution of Amazonian Species Diversity

Author

Cracraft, J., Ribas, Camila C., d’Horta, F. M., Bates, J., Almeida, R. P., Aleixo, A., Boubli, J. P., Campbell, K. E., Cruz, F. W., Ferreira, M., Fritz, S. C., Grohmann, C. H., Latrubesse, E. M., Lohmann, L. G., Musher, L. J., Nogueira, A., Sawakuchi, A. O., Baker, P., Rull, Valentí, editor, and Carnaval, Ana Carolina, editor

Published
2020
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2. The Origin and Evolution of Amazonian Species Diversity

Author

Cracraft, J., primary, Ribas, Camila C., additional, d’Horta, F. M., additional, Bates, J., additional, Almeida, R. P., additional, Aleixo, A., additional, Boubli, J. P., additional, Campbell, K. E., additional, Cruz, F. W., additional, Ferreira, M., additional, Fritz, S. C., additional, Grohmann, C. H., additional, Latrubesse, E. M., additional, Lohmann, L. G., additional, Musher, L. J., additional, Nogueira, A., additional, Sawakuchi, A. O., additional, and Baker, P., additional

Published
2020
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3. Specimen collection: An essential tool

Author

Rocha, L. A., Aleixo, A., Allen, G., Almeda, F., Baldwin, C. C., Barclay, M. V. L., Bates, J. M., Bauer, A. M., Benzoni, F., Berns, C. M., Berumen, M. L., Blackburn, D. C., Blum, S., Bolaños, F., Bowie, R. C. K., Britz, R., Brown, R. M., Cadena, C. D., Carpenter, K., Ceríaco, L. M., Chakrabarty, P., Chaves, G., Choat, J. H., Clements, K. D., Collette, B. B., Collins, A., Coyne, J., Cracraft, J., Daniel, T., de Carvalho, M. R., de Queiroz, K., Di Dario, F., Drewes, R., Dumbacher, J. P., Engilis, A., Erdmann, M. V., Eschmeyer, W., Feldman, C. R., Fisher, B. L., Fjeldså, J., Fritsch, P. W., Fuchs, J., Getahun, A., Gill, A., Gomon, M., Gosliner, T., Graves, G. R., Griswold, C. E., Guralnick, R., Hartel, K., Helgen, K. M., Ho, H., Iskandar, D. T., Iwamoto, T., Jaafar, Z., James, H. F., Johnson, D., Kavanaugh, D., Knowlton, N., Lacey, E., Larson, H. K., Last, P., Leis, J. M., Lessios, H., Liebherr, J., Lowman, M., Mahler, D. L., Mamonekene, V., Matsuura, K., Mayer, G. C., Mays, H., McCosker, J., McDiarmid, R. W., McGuire, J., Miller, M. J., Mooi, R., Mooi, R. D., Moritz, C., Myers, P., Nachman, M. W., Nussbaum, R. A., Foighil, D. Ó, Parenti, L. R., Parham, J. F., Paul, E., Paulay, G., Pérez-Emán, J., Pérez-Matus, A., Poe, S., Pogonoski, J., Rabosky, D. L., Randall, J. E., Reimer, J. D., Robertson, D. R., Rödel, M.-O., Rodrigues, M. T., Roopnarine, P., Rüber, L., Ryan, M. J., Sheldon, F., Shinohara, G., Short, A., Simison, W. B., Smith-Vaniz, W. F., Springer, V. G., Stiassny, M., Tello, J. G., Thompson, C. W., Trnski, T., Tucker, P., Valqui, T., Vecchione, M., Verheyen, E., Wainwright, P. C., Wheeler, T. A., White, W. T., Will, K., Williams, J. T., Williams, G., Wilson, E. O., Winker, K., Winterbottom, R., and Witt, C. C.

Published
2014

4. 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

5. Specimen collection: An essential tool

Author

Sills, Jennifer, Rocha, L. A., Aleixo, A., Allen, G., Almeda, F., Baldwin, C. C., Barclay, M. V.L., Bates, J. M., Bauer, A. M., Benzoni, F., Berns, C. M., Berumen, M. L., Blackburn, D. C., Blum, S., Bolaños, F., Bowie, R. C. K., Britz, R., Brown, R. M., Cadena, C. D., Carpenter, K., Ceríaco, L. M., Chakrabarty, P., Chaves, G., Choat, J. H., Clements, K. D., Collette, B. B., Collins, A., Coyne, J., Cracraft, J., Daniel, T., de Carvalho, M. R., de Queiroz, K., Di Dario, F., Drewes, R., Dumbacher, J. P., Engilis, A., Jr., Erdmann, M. V., Eschmeyer, W., Feldman, C. R., Fisher, B. L., Fjeldså, J., Fritsch, P. W., Fuchs, J., Getahun, A., Gill, A., Gomon, M., Gosliner, T., Graves, G. R., Griswold, C. E., Guralnick, R., Hartel, K., Helgen, K. M., Ho, H., Iskandar, D. T., Iwamoto, T., Jaafar, Z., James, H. F., Johnson, D., Kavanaugh, D., Knowlton, N., Lacey, E., Larson, H. K., Last, P., Leis, J. M., Lessios, H., Liebherr, J., Lowman, M., Mahler, D. L., Mamonekene, V., Matsuura, K., Mayer, G. C., Mays, H., Jr., McCosker, J., McDiarmid, R. W., McGuire, J., Miller, M. J., Mooi, R., Mooi, R. D., Moritz, C., Myers, P., Nachman, M. W., Nussbaum, R. A., Foighil, D. Ó, Parenti, L. R., Parham, J. F., Paul, E., Paulay, G., Pérez-Emán, J., Pérez-Matus, A., Poe, S., Pogonoski, J., Rabosky, D. L., Randall, J. E., Reimer, J. D., Robertson, D. R., Rödel, M.-O., Rodrigues, M. T., Roopnarine, P., Rüber, L., Ryan, M. J., Sheldon, F., Shinohara, G., Short, A., Simison, W. B., Smith-Vaniz, W. F., Springer, V. G., Stiassny, M., Tello, J. G., Thompson, C. W., Trnski, T., Tucker, P., Valqui, T., Vecchione, M., Verheyen, E., Wainwright, P. C., Wheeler, T. A., White, W. T., Will, K., Williams, J. T., Williams, G., Wilson, E. O., Winker, K., Winterbottom, R., and Witt, C. C.

Published
2014

6. 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

7. Chronology of Terra Firme formation in Amazonian lowlands reveals a dynamic Quaternary landscape

Author

Pupim, F.N., primary, Sawakuchi, A.O., additional, Almeida, R.P., additional, Ribas, C.C., additional, Kern, A.K., additional, Hartmann, G.A., additional, Chiessi, C.M., additional, Tamura, L.N., additional, Mineli, T.D., additional, Savian, J.F., additional, Grohmann, C.H., additional, Bertassoli, D.J., additional, Stern, A.G., additional, Cruz, F.W., additional, and Cracraft, J., additional

Published
2019
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9. Specimen collection: An essential tool

Author

Rocha, L, Aleixo, A, Allen, G, Almeda, F, Baldwin, C, Barclay, M, Bates, J, Bauer, A, Benzoni, F, Berns, C, Berumen, M, Blackburn, D, Blum, S, Bolaños, F, Bowie, R, Britz, R, Brown, R, Cadena, C, Carpenter, K, Ceríaco, L, Chakrabarty, P, Chaves, G, Choat, J, Clements, K, Collette, B, Collins, A, Coyne, J, Cracraft, J, Daniel, T, de Carvalho, M, de Queiroz, K, Di Dario, F, Drewes, R, Dumbacher, J, Engilis Jr., A, Erdmann, M, Eschmeyer, W, Feldman, C, Fisher, B, Fjeldså, J, Fritsch, P, Fuchs, J, Getahun, A, Gill, A, Gomon, M, Gosliner, T, Graves, G, Griswold, C, Guralnick, R, Hartel, K, Helgen, K, Ho, H, Iskandar, D, Iwamoto, T, Jaafar, Z, James, H, Johnson, D, Kavanaugh, D, Knowlton, N, Lacey, E, Larson, H, Last, P, Leis, J, Lessios, H, Liebherr, J, Lowman, M, Mahler, D, Mamonekene, V, Matsuura, K, Mayer, G, Mays Jr., H, Mccosker, J, Mcdiarmid, R, Mcguire, J, Miller, M, Mooi, R, Moritz, C, Myers, P, Nachman, M, Nussbaum, R, Ó Foighil, D, Parenti, L, Parham, J, Paul, E, Paulay, G, Pérez-Emán, J, Pérez-Matus, A, Poe, S, Pogonoski, J, Rabosky, D, Randall, J, Reimer, J, Robertson, D, Rödel, M, Rodrigues, M, Roopnarine, P, Rüber, L, Ryan, M, Sheldon, F, Shinohara, G, Short, A, Simison, W, Smith-Vaniz, W, Springer, V, Stiassny, M, Tello, J, Thompson, C, Trnski, T, Tucker, P, Valqui, T, Vecchione, M, Verheyen, E, Wainwright, P, Wheeler, T, White, W, Will, K, Williams, J, Williams, G, Wilson, E, Winker, K, Winterbottom, R, Witt, C, Rocha, LA, Baldwin, CC, Barclay, MVL, Bates, JM, Bauer, AM, Berns, CM, Berumen, ML, Blackburn, DC, Bowie, RCK, Brown, RM, Cadena, CD, Ceríaco, LM, Choat, JH, Clements, KD, Collette, BB, de Carvalho, MR, Dumbacher, JP, Engilis Jr. , A, Erdmann, MV, Feldman, CR, Fisher, BL, Fritsch, PW, Graves, GR, Griswold, CE, Helgen, KM, Iskandar, DT, James, HF, Larson, HK, Leis, JM, Mahler, DL, Mayer, GC, Mays Jr. , H, McCosker, J, McDiarmid, RW, McGuire, J, Miller, MJ, Mooi, RD, Nachman, MW, Nussbaum, RA, Parenti, LR, Parham, JF, Rabosky, DL, Randall, JE, Reimer, JD, Robertson, DR, Rödel, M-O, Rodrigues, MT, Ryan, MJ, Simison, WB, Smith-Vaniz, WF, Springer, VG, Tello, JG, Thompson, CW, Wainwright, PC, Wheeler, TA, White, WT, Williams, JT, Wilson, EO, Witt, CC, Rocha, L, Aleixo, A, Allen, G, Almeda, F, Baldwin, C, Barclay, M, Bates, J, Bauer, A, Benzoni, F, Berns, C, Berumen, M, Blackburn, D, Blum, S, Bolaños, F, Bowie, R, Britz, R, Brown, R, Cadena, C, Carpenter, K, Ceríaco, L, Chakrabarty, P, Chaves, G, Choat, J, Clements, K, Collette, B, Collins, A, Coyne, J, Cracraft, J, Daniel, T, de Carvalho, M, de Queiroz, K, Di Dario, F, Drewes, R, Dumbacher, J, Engilis Jr., A, Erdmann, M, Eschmeyer, W, Feldman, C, Fisher, B, Fjeldså, J, Fritsch, P, Fuchs, J, Getahun, A, Gill, A, Gomon, M, Gosliner, T, Graves, G, Griswold, C, Guralnick, R, Hartel, K, Helgen, K, Ho, H, Iskandar, D, Iwamoto, T, Jaafar, Z, James, H, Johnson, D, Kavanaugh, D, Knowlton, N, Lacey, E, Larson, H, Last, P, Leis, J, Lessios, H, Liebherr, J, Lowman, M, Mahler, D, Mamonekene, V, Matsuura, K, Mayer, G, Mays Jr., H, Mccosker, J, Mcdiarmid, R, Mcguire, J, Miller, M, Mooi, R, Moritz, C, Myers, P, Nachman, M, Nussbaum, R, Ó Foighil, D, Parenti, L, Parham, J, Paul, E, Paulay, G, Pérez-Emán, J, Pérez-Matus, A, Poe, S, Pogonoski, J, Rabosky, D, Randall, J, Reimer, J, Robertson, D, Rödel, M, Rodrigues, M, Roopnarine, P, Rüber, L, Ryan, M, Sheldon, F, Shinohara, G, Short, A, Simison, W, Smith-Vaniz, W, Springer, V, Stiassny, M, Tello, J, Thompson, C, Trnski, T, Tucker, P, Valqui, T, Vecchione, M, Verheyen, E, Wainwright, P, Wheeler, T, White, W, Will, K, Williams, J, Williams, G, Wilson, E, Winker, K, Winterbottom, R, Witt, C, Rocha, LA, Baldwin, CC, Barclay, MVL, Bates, JM, Bauer, AM, Berns, CM, Berumen, ML, Blackburn, DC, Bowie, RCK, Brown, RM, Cadena, CD, Ceríaco, LM, Choat, JH, Clements, KD, Collette, BB, de Carvalho, MR, Dumbacher, JP, Engilis Jr. , A, Erdmann, MV, Feldman, CR, Fisher, BL, Fritsch, PW, Graves, GR, Griswold, CE, Helgen, KM, Iskandar, DT, James, HF, Larson, HK, Leis, JM, Mahler, DL, Mayer, GC, Mays Jr. , H, McCosker, J, McDiarmid, RW, McGuire, J, Miller, MJ, Mooi, RD, Nachman, MW, Nussbaum, RA, Parenti, LR, Parham, JF, Rabosky, DL, Randall, JE, Reimer, JD, Robertson, DR, Rödel, M-O, Rodrigues, MT, Ryan, MJ, Simison, WB, Smith-Vaniz, WF, Springer, VG, Tello, JG, Thompson, CW, Wainwright, PC, Wheeler, TA, White, WT, Williams, JT, Wilson, EO, and Witt, CC

Published
2014

10. Whole-genome analyses resolve early branches in the tree of life of modern birds

Author

Jarvis, E., Mirarab, S., Aberer, A., Li, B., Houde, P., Li, C., Ho, S., Faircloth, B., Nabholz, B., Howard, J., Suh, A., Weber, C., da Fonseca, R., Li, J., Zhang, F., Li, H., Zhou, L., Narala, N., Liu, L., Ganapathy, G., boussau, B., Bayzid, M.S., Zavidovych, V., Subramanian, S., Gabaldon, T., Capella-Gutierrez, S., Huerta-Cepas, J., Rekepalli, B., Munch, K., Schierup, M., Lindow, B., Warren, W., Ray, D., Green, R., Bruford, M., Zhan, X., Dixon, A., Li, S., Li, N., Huang, Y., Derryberry, E., Bertelsen, M., Sheldon, F., Brumfield, R., Mello, C., Lovell, P., Wirthlin, M., Schneider, M., Prosdocimi, F., Samaniego, J.A., Velazquez, A., Alfaro-Nunez, A., Campos, P., Petersen, B., Sicheritz-Ponten, T., Pas, A., Bailey, T., Scofield, P., Bunce, Michael, Lambert, D., Zhou, Q., Perelman, P., Driskell, A., Shapiro, B., Xiong, Z., Zeng, Y., Liu, S., Li, Z., Liu, B., Wu, K., Xiao, J., Xiong, Y., Zheng, Q., Zhang, Y., Yang, H., Wang, J., Smeds, L., Rheindt, F., Braun, M., Fjeldsa, J., Oelando, L., Barker, K., Jonsson, K., Johnson, W., Koepfli, K., O'Brien, S., Haussler, D., Ryder, O., Rahbek, C., Willerslev, E., Graves, G., Glenn, T., McCormack, J., Burt, D., Ellegren, H., Alstrom, P., Edwards, S., Stamatakis, A., Mindell, D., Cracraft, J., Braun, E., Warnow, T., Wang, Jun, Gilbert, Thomas, Zhang, G., Jarvis, E., Mirarab, S., Aberer, A., Li, B., Houde, P., Li, C., Ho, S., Faircloth, B., Nabholz, B., Howard, J., Suh, A., Weber, C., da Fonseca, R., Li, J., Zhang, F., Li, H., Zhou, L., Narala, N., Liu, L., Ganapathy, G., boussau, B., Bayzid, M.S., Zavidovych, V., Subramanian, S., Gabaldon, T., Capella-Gutierrez, S., Huerta-Cepas, J., Rekepalli, B., Munch, K., Schierup, M., Lindow, B., Warren, W., Ray, D., Green, R., Bruford, M., Zhan, X., Dixon, A., Li, S., Li, N., Huang, Y., Derryberry, E., Bertelsen, M., Sheldon, F., Brumfield, R., Mello, C., Lovell, P., Wirthlin, M., Schneider, M., Prosdocimi, F., Samaniego, J.A., Velazquez, A., Alfaro-Nunez, A., Campos, P., Petersen, B., Sicheritz-Ponten, T., Pas, A., Bailey, T., Scofield, P., Bunce, Michael, Lambert, D., Zhou, Q., Perelman, P., Driskell, A., Shapiro, B., Xiong, Z., Zeng, Y., Liu, S., Li, Z., Liu, B., Wu, K., Xiao, J., Xiong, Y., Zheng, Q., Zhang, Y., Yang, H., Wang, J., Smeds, L., Rheindt, F., Braun, M., Fjeldsa, J., Oelando, L., Barker, K., Jonsson, K., Johnson, W., Koepfli, K., O'Brien, S., Haussler, D., Ryder, O., Rahbek, C., Willerslev, E., Graves, G., Glenn, T., McCormack, J., Burt, D., Ellegren, H., Alstrom, P., Edwards, S., Stamatakis, A., Mindell, D., Cracraft, J., Braun, E., Warnow, T., Wang, Jun, Gilbert, Thomas, and Zhang, G.

Abstract

To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.

Published
2014

11. Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species

Author

Haussler, D., O'Brien, S. J., Ryder, O. A., Barker, F. K., Clamp, M., Crawford, A. J., Hanner, R., Hanotte, O., Johnson, W. E., McGuire, J. A., Miller, W., Murphy, R. W., Murphy, W. J., Sheldon, F. H., Sinervo, B., Venkatesh, B., Wiley, E. O., Allendorf, F. W., Amato, G., Baker, C. S., Bauer, A., Beja-Pereira, A., Bermingham, E., Bernardi, G., Bonvicino, C. R., Brenner, S., Burke, T., Cracraft, J., Diekhans, M., Edwards, S., Ericson, P. G. P., Estes, J., Fjelsda, J., Flesness, N., Gamble, T., Gaubert, Philippe, Graphodatsky, A. S., Graves, J. A. M., Green, E. D., Green, R. E., Hackett, S., Hebert, P., Helgen, K. M., Joseph, L., Kessing, B., Kingsley, D. M., Lewin, H. A., Luikart, G., Martelli, P., Moreira, M. A. M., Nguyen, N., Orti, G., Pike, B. L., Rawson, D. M., Schuster, S. C., Seuanez, H. N., Shaffer, H. B., Springer, M. S., Stuart, J. M., Sumner, J., Teeling, E., Vrijenhoek, R. C., Ward, R. D., Warren, W. C., Wayne, R., Williams, T. M., Wolfe, N. D., Zhang, Y. P., Graph-Odatsky, A., Felsenfeld, A., and Turner, S.

Subjects
vertebrate biology, ancestral state reconstruction, molecular evolution, species conservation, comparative genomics, G10K
Abstract

The human genome project has been recently complemented by whole-genome assessment sequence of 32 mammals and 24 nonmammalian vertebrate species suitable for comparative genomic analyses. Here we anticipate a precipitous drop in costs and increase in sequencing efficiency, with concomitant development of improved annotation technology and, therefore, propose to create a collection of tissue and DNA specimens for 10 000 vertebrate species specifically designated for whole-genome sequencing in the very near future. For this purpose, we, the Genome 10K Community of Scientists (G10KCOS), will assemble and allocate a biospecimen collection of some 16 203 representative vertebrate species spanning evolutionary diversity across living mammals, birds, nonavian reptiles, amphibians, and fishes (ca. 60 000 living species). In this proposal, we present precise counts for these 16 203 individual species with specimens presently tagged and stipulated for DNA sequencing by the G10KCOS. DNA sequencing has ushered in a new era of investigation in the biological sciences, allowing us to embark for the first time on a truly comprehensive study of vertebrate evolution, the results of which will touch nearly every aspect of vertebrate biological enquiry.

Published
2009

14. Are crustaceans monophyletic?

Author

Schram, F.R., Konemann, S., Cracraft, J., Donaghue, M.J., and Systematische en Geografische Dierkunde (inactive) (IBED, FNWI)

Published
2004

16. Being good at science, biopolitics, and mentorship: how to become a marvalee wake and move mountains

Author

Cracraft, J.

Subjects
Zoology and wildlife conservation
Abstract

Philosophers and historians of science have pondered the causal dynamics of scientific progress but much of that assessment relies on one's idea of scientific progress. That can be measured in many ways, qualitatively by how new ideas change the way we pose scientific questions or solve them, quantitatively by the degree to which new ideas or methods are incorporated into others' works, by the numbers of disciples one has and how they replicate and extend one's ideas, attitudes, and vision, among other ways. Progress is also made by building the scientific endeavor, from research institutions, funding agencies, formal and informal teaching programs, local, national, and international organizations and collaborations. All of these efforts create a foundation for the growth of science. Some of us are good at one or two aspects of this but not others, and that is just fine. It all feeds into making science not only intellectually vibrant and makes the world a better place as well. Few scientists can do it all, however, or have the energy to even try. Marvalee Wake is one of those persons who does it all. The lessons she can teach are grounded in who she is and what she accomplishes. Her impact on the scientific lives of organismal biologists has been profound, well beyond her own research work. Her influence on those honored to work with her has been no less significant. Each of us, as students of science and biology, can look to her for inspiration and a way to move mountains.

Published
2003

17. Letters

Author

Cracraft, J. E., Tompkins, Stuart R., Mosely, Philip E., and Bădina, Ovidiu

Published
1967

20. A Berlin for Historians.

Author

Cracraft, J.

Subjects
*MODERN philosophers, *LIBERALISM, *PLURALISM
Abstract

On his death in 1997 Isaiah Berlin was widely hailed as a leading philosopher of political liberalism. This article takes the position that Berlin’s philosophical views, particularly those on freedom and cultural pluralism, can also be construed as a valuable guide for historians working in the present, “postmodernist” climate of debate. It further argues that Berlin’s character and career, the subjects already of considerable critical inquiry, lend added authority to these views. The focus is on three lengthy essays on history written by Berlin in the 1950s, one of which was first published in the first issue of this journal. The article concludes, following Berlin, that it is the responsibility of historians, as historians, to recognize the often incommensurate plurality of ultimate values to which their fellow human beings historically have subscribed and to judge, as judge they sometimes must, with that recognition fully in mind. If the result of these as well as the other choices that they make is a plurality of histories, of contending subjects, approaches, methods, and outcomes, that is only to be expected, indeed welcomed. It is freedom in practice, and infinitely preferable as such to any known alternative. [ABSTRACT FROM AUTHOR]

Published
2002
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22. Recovering phylogenetic signal from DNA sequences: relationships within the corvine assemblage (class aves) as inferred from complete sequences of the mitochondrial DNA cytochrome-b gene.

Author

Helm-Bychowski, K and Cracraft, J

Abstract

Phylogenetic analysis of cytochrome-b sequences and cranial osteological characters for nine genera of corvine passerine birds supports the hypothesis that the two major groups of birds of paradise, the manucodines and paradisaeinines, constitute a monophyletic group and that their postulated sister group is the Corvidae (crows, jays, and allies). The data are also consistent with the hypothesis that the bowerbirds are not closely related to the birds of paradise but instead lie near the base of the corvine assemblage. The corvine radiation exemplifies a case of multiple star phylogenies embedded within a major clade, with the branching pattern characterized by very short internodal divergence times. Such histories are difficult to resolve no matter what type of data is employed, because little change accumulates between branching events. With respect to sequence data, reconstructed tree topologies are sensitive to the choice of outgroup and to the method of analysis (e.g., transversion vs. global parsimony). In such cases, assessing the "reliability" of a best-fit or most-parsimonious tree inferred from any particular data set becomes problematic. Statistical tests of tree topologies that depend on random sampling of characters will generally be inconclusive in that all cladistic components will tend to be poorly supported because relatively few character-state changes will be recorded between branching events. It is suggested, on the other hand, that congruence in cladistic signal across different data sets may be a potentially more useful method for evaluating the reliability of the signal of any one data set. Resolution of star phylogenies will probably be possible only if DNA sequence and morphological characters are combined in a single analysis.

Published
1993
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23. The growth patterns of three hindlimb muscles in the chicken

Author

Helmi, C and Cracraft, J

Subjects
Muscles, Body Weight, Age Factors, Animals, Regression Analysis, Muscle Development, Chickens, Research Article, Hindlimb
Abstract

This study was designed to investigate the growth patterns of three hindlimb muscles of the chicken relative to the functional-biomechanical demands of increasing body size. The biceps femoris, a bipennate non-postural muscle, grew relatively faster in terms of wet and dry weight than did the parallel-fibred adductor superficialis or the unipennate adductor profundus, both postural muscles. All three muscles exhibited positive allometry (relative to body weight) in muscle length but only biceps femoris and adductor profundus showed positive allometry in cross sectional area adductor superficialis having isometric growth in this parameter. In biceps femoris and adductor superficialis the lengths of the longest and shortest fasciculi grew at equal rates, whereas in adductor profundus the shortest fasciculi grew faster than the longest. We conclude that muscle weight alone is an insufficient indicator of changing function in growing muscle. Hence, growth studies should include other functionally relevant parameters such as cross sectional area, which is proportional to the force-producing capabilities of the muscle, or fibre (fasciculus) length, which is indicative of the absolute amount of stretching or shortening that is possible and of the contraction velocity.

Published
1977

48. Reviews.

Author

Cracraft, J.

Subjects
ARCHITECTURE & Planning of Classical Moscow: A Cultural History, The (Book)
Abstract

Reviews the book `The Architecture and Planning of Classical Moscow: A Cultural History,` by Albert J. Schmidt.

Published
1990

50. Images are not and should not ever be type specimens: a rebuttal to GarraffoniFreitas

Author

Rogers, D. Christopher, Ahyong, Shane T., Boyko, Christopher B., D'Acoz, Cedric D'Udekem, Asakura, Akira, An, Joanmei, Bain, Bonnie A., Bartels, Paul, Beladjal, Lynda, Brusca, Richard C., Cairns, Stephen D., Castro, Peter, Chaboo, Caroline, Chan, Tin-Yam, Cracraft, Joel, Crandall, Keith, Cumberlidge, Neil, Davie, Peter J. F., Dworschak, Peter C., Engel, Michael S., Fagundo, Raquel A., Felder, Darryl L., Forro, Laszlo, Fransen, Charles H. J. M., Gelder, Stuart R., Gerken, Sarah, Glasby, Chris, Govedich, Fredric R., Guinot, Daniele, Hann, Brenda J., Heard, Richard W., Hoberg, Eric P., Hyzny, Matus, Norena Janssen, Carolina, Jacobus, Luke, Kimsey, Lynn S., Korovchinsky, Nikolai M., Kotov, Alexey A., Lee, Jonathan, Lemaitre, Rafael, Macpherson, Enrique, Maeda-Martinez, Alejandro M., Manconi, Renata, Mantelatto, Fernando L., Marrone, Federico, Martens, Koen, Meland, Kenneth, Merrin, Kelly L., Mooi, Rich, Nelson, Diane, Olesen, Jorgen, Overstreet, Robin M., Perissinotto, Renzo, Prendini, Lorenzo, Rabet, Nicolas, Rahayu, Dwi L., Ratcliffe, Brett C., Read, Geoffrey, Sanoamuang, La-orsri, Schmidt-Rhaesa, Andreas, Schnabel, Kareen, Segers, Hendrik, Shields, Jeffrey D., Sinev, Artem, Taiti, Stefano, Timms, Brian, Tudge, Christopher, Van Damme, Kay, van der Meij, Sancia, Van Syoc, Robert, Vinarski, Maxim V., Wallace, Robert, Wells, Samuel, Wilkens, Richard, Wilson, Edward O., Williams, Bronwyn W., Williams, Jason D., Wilson, George D. F. (Buz), Yoshida, Ryuta, Rogers, D., Ahyong, S., Boyko, C., D'Acoz, C., Asakura, A., An, J., Bain, B., Bartels, P., Beladjal, L., Brusca, R., Cairns, S., Castro, P., Chaboo, C., Chan, T., Cracraft, J., Crandall, K., Cumberlidge, N., Davie, P., Dworschak, P., Engel, M., Fagundo, R., Felder, D., Forro, L., Fransen, C., Gelder, S., Gerken, S., Glasby, C., Govedich, F., Guinot, D., Hann, B., Heard, R., Hoberg, E., Hyzny, M., Janssen, C., Jacobus, L., Kimsey, L., Korovchinsky, N., Kotov, A., Lee, J., Lemaitre, R., Macpherson, E., Maeda Martinez, A., Manconi, R., Mantelatto, F., Marrone, F., Martens, K., Meland, K., Merrin, K., Mooi, R., Nelson, D., Olesen, J., Overstreet, R., Perissinotto, R., Prendini, L., Rabet, N., Rahayu, D., Ratcliffe, B., Read, G., Sanoamuang, L., Schmidt Rhaesa, A., Segers, H., Shields, J., Sinev, A., Taiti, S., Timms, B., Tudge, C., Van Damme, K., van der Meij, S., Van Syoc, R., Vinarski, M., Wallace, R., Wells, S., Wilkens, R., Wilson, E., Williams, B., Williams, J., Wilson, G., and Yoshida, R.

Subjects
0106 biological sciences, Programming language, Rebuttal, education, Type specimens, 010607 zoology, Settore BIO/05 - Zoologia, Biology, computer.software_genre, 010603 evolutionary biology, 01 natural sciences, Type (biology), Order (business), Code (cryptography), Images, Photography, Animals, Animal Science and Zoology, computer, Biological sciences, Zoology, Ecology, Evolution, Behavior and Systematics
Abstract

Note. This original form of this rebuttal was submitted to Science on 3 March 2017 (limited to 300 words as per Science editorial policy) but rejected on 13 March 2017. Herein, we elaborate on our original Science submission in order to more fully address the issue without the length limitations. This rebuttal is followed by the list of the signatories who supported our original submission.

Published
2017
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