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A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing
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“The similarity of neuronal scaling rules between songbirds and parrots is not too surprising, considering their close phylogenetic relationship (48–51).”
From Birds have primate-like numbers of neurons in the forebrain (2016) · cites this paper as [51]
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Taxon sampling and the accuracy of phylogenetic analyses
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Longrich, N. R., Martill, D. M., & Andres, B. (2018) · PLoS Biology · doi:10.1371/journal.pbio.2001663 · Cited by 113
The skull roof tracks the brain during the evolution and development of reptiles including birds
Fabbri, M., Mongiardino Koch, N., Pritchard, A. C., Hanson, M., Hoffman, E., Bever, G. S., Balanoff, A. M., Morris, Z. S., Field, D. J., Camacho, J., et al. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0288-2 · Cited by 112
Self-citationHaddad, S., Shin, S., Lemmon, A. R., Lemmon, E. M., Švácha, P., Farrell, B. D., Ślipiński, A., Windsor, D. M., & McKenna, D. D. (2017) · Systematic Entomology · doi:10.1111/syen.12257 · Cited by 115
Self-citationThe Lombard Effect: From Acoustics to Neural Mechanisms
Luo, J., Hage, S. R., & Moss, C. F. (2018) · Trends in Neurosciences · doi:10.1016/j.tins.2018.07.011 · Cited by 115
Fragmentary Gene Sequences Negatively Impact Gene Tree and Species Tree Reconstruction
Sayyari, E., Whitfield, J. B., & Mirarab, S. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx261 · Cited by 112
Birds of a feather? Parrot and corvid cognition compared
Lambert, M. L., Jacobs, I. F., Osvath, M., & von Bayern, A. M. P. (2018) · Behaviour · doi:10.1163/1568539x-00003527 · Cited by 111
Worthy, T. H., Degrange, F. J., Handley, W. D., & Lee, M. S. Y. (2017) · Royal Society Open Science · doi:10.1098/rsos.170975 · Cited by 105
“([3]: analyses with Vegavis included).”
The evolution of mechanisms involved in vertebrate endothermy
Legendre, L. J., & Davesne, D. (2020) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2019.0136 · Cited by 111
Resolving the psyllid tree of life: phylogenomic analyses of the superfamily Psylloidea (Hemiptera)
Percy, D. M., Crampton‐Platt, A., Sveinsson, S., Lemmon, A. R., Lemmon, E. M., Ouvrard, D., & Burckhardt, D. (2018) · Systematic Entomology · doi:10.1111/syen.12302 · Cited by 108
Self-citationGermline-restricted chromosome (GRC) is widespread among songbirds
Torgasheva, A. A., Malinovskaya, L. P., Zadesenets, K. S., Karamysheva, T. V., Kizilova, E. A., Akberdina, E. A., Pristyazhnyuk, I. E., Shnaider, E. P., Volodkina, V., Saifitdinova, A. F., et al. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1817373116 · Cited by 102
Machado, R. J. P., Gillung, J. P., Winterton, S. L., Garzón‐Orduña, I. J., Lemmon, A. R., Lemmon, E. M., & Oswald, J. D. (2018) · Systematic Entomology · doi:10.1111/syen.12334 · Cited by 105
Self-citationThe Past Sure is Tense: On Interpreting Phylogenetic Divergence Time Estimates
Brown, J. W., & Smith, S. A. (2017) · Systematic Biology · doi:10.1093/sysbio/syx074 · Cited by 103
“2014), where (re)analyses have repeatedly led to incongruous inferred evolutionary timeframes (e.g., Ericson et al. 2006 vs. Brown et al. 2007; Jarvis et al. 2014 vs. Mitchell et al. 2015; Prum et al. 2015).”
BackgroundPhylogeny and classification of Odonata using targeted genomics
Bybee, S., Kalkman, V. J., Erickson, R. J., Frandsen, P. B., Breinholt, J. W., Suvorov, A., Dijkstra, K. B., Cordero‐Rivera, A., Skevington, J. H., Abbott, J. C., et al. (2021) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2021.107115 · Cited by 111
Self-citationSchroeter, E. R., DeHart, C. J., Cleland, T. P., Zheng, W., Thomas, P. M., Kelleher, N. L., Bern, M., & Schweitzer, M. H. (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6b00873 · Cited by 94
Resolving Rapid Radiations within Angiosperm Families Using Anchored Phylogenomics
Léveillé‐Bourret, É., Starr, J. R., Ford, B. A., Lemmon, E. M., & Lemmon, A. R. (2017) · Systematic Biology · doi:10.1093/sysbio/syx050 · Cited by 98
“Orthology, Filtering and Alignment Orthology was determined for genes with multiple copies following Prum et al. (2015).”
InfluentialSelf-citationHigher-Level Phylogeny and Reclassification of Lampyridae (Coleoptera: Elateroidea)
Martin, G. J., Stanger‐Hall, K. F., Branham, M. A., da Silveira, L. F. L., Lower, S. E., Hall, D. W., Li, X., Lemmon, A. R., Lemmon, E. M., & Bybee, S. (2019) · Insect Systematics and Diversity · doi:10.1093/isd/ixz024 · Cited by 106
Self-citationSuh, A., Witt, C. C., Menger, J. D. S., Sadanandan, K. R., Podsiadłowski, L., Gerth, M., Weigert, A., McGuire, J. A., Mudge, J., Edwards, S. V., et al. (2016) · Nature Communications · doi:10.1038/ncomms11396 · Cited by 94
Climatic shifts drove major contractions in avian latitudinal distributions throughout the Cenozoic
Saupe, E. E., Farnsworth, A., Lunt, D. J., Sagoo, N., Pham, K. V., & Field, D. J. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1903866116 · Cited by 100
Self-citationThe Multispecies Coalescent Model Outperforms Concatenation Across Diverse Phylogenomic Data Sets
Jiang, X., Edwards, S. V., & Liu, L. (2020) · Systematic Biology · doi:10.1093/sysbio/syaa008 · Cited by 103
Sex determination and gonadal sex differentiation in the chicken model
Hirst, C. E., Major, A. T., & Smith, C. A. (2018) · The International Journal of Developmental Biology · doi:10.1387/ijdb.170319cs · Cited by 97
Life History Traits, Protein Evolution, and the Nearly Neutral Theory in Amniotes
Figuet, E., Nabholz, B., Bonneau, M., Mas‐Carrió, E., Nadachowska‐Brzyska, K., Ellegren, H., & Galtier, N. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw033 · Cited by 95
“We evaluated the robustness of our phylogenetic analyses to the choice of topology by employing the alternative trees from Prum et al. (2015) for birds and from Meredith et al. (2011) for mammals, and by switching the controversial (Iguana, (Basiliscus, Anolis)) node in nonavian sauropsids (Wiens…”
MethodSun, Z., Pan, T., Hu, C., Sun, L., Ding, H., Wang, H., Zhang, C., Jin, H., Chang, Q., Kan, X., et al. (2017) · PLoS ONE · doi:10.1371/journal.pone.0184529 · Cited by 95
Karyotype Evolution in Birds: From Conventional Staining to Chromosome Painting
Kretschmer, R., Ferguson-Smith, M., & de Oliveira, E. H. C. (2018) · Genes · doi:10.3390/genes9040181 · Cited by 97
“Conversely, birds of prey, currently including Falconiformes and Accipitriformes, have a variety of rearranged karyotypes with species with diploid numbers close to 80, such as in Cathartidae, but also species with fewer chromosomes, or with only a few pairs of microchromosomes, as in some hawks and eagles, and low di…”
BackgroundResultInfluentialAnalyzing Contentious Relationships and Outlier Genes in Phylogenomics
Walker, J. F., Brown, J. W., & Smith, S. A. (2018) · Systematic Biology · doi:10.1093/sysbio/syy043 · Cited by 93
Pennaraptoran Theropod Dinosaurs Past Progress and New Frontiers
Pittman, M., & Xu, X. (2020) · Bulletin of the American Museum of Natural History · doi:10.1206/0003-0090.440.1.1 · Cited by 95
Vijay, N., Weissensteiner, M. H., Burri, R., Kawakami, T., Ellegren, H., & Wolf, J. B. W. (2017) · Molecular Ecology · doi:10.1111/mec.14195 · Cited by 92
Larson, D. W., Brown, C. M., & Evans, D. C. (2016) · Current Biology · doi:10.1016/j.cub.2016.03.039 · Cited by 94
Ibáñez‐Álamo, J. D., Morelli, F., Benedetti, Y., Rubio, E., Jokimäki, J., Pérez‐Contreras, T., Sprau, P., Suhonen, J., Tryjanowski, P., Kaisanlahti‐Jokimäki, M., et al. (2019) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2019.135477 · Cited by 97
Heinicke, M. P., Lemmon, A. R., Lemmon, E. M., McGrath, K. E., & Hedges, S. B. (2017) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2017.09.021 · Cited by 87
Self-citationEcosystem services provided by Neotropical birds
Michel, N. L., Whelan, C. J., & Verutes, G. M. (2020) · Ornithological Applications · doi:10.1093/condor/duaa022 · Cited by 103
Commentary: Defining Raptors and Birds of Prey
McClure, C. J. W., Schulwitz, S. E., Anderson, D. L., Robinson, B. W., Mojica, E. K., Therrien, J., Oleyar, M. D., & Johnson, J. A. (2019) · Journal of Raptor Research · doi:10.3356/0892-1016-53.4.419 · Cited by 99
BaitFisher: A Software Package for Multispecies Target DNA Enrichment Probe Design
Mayer, C., Sann, M., Donath, A., Meixner, M., Podsiadłowski, L., Peters, R. S., Petersen, M., Meusemann, K., Liere, K., Wägele, J., et al. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw056 · Cited by 86
Body mass‐corrected molecular rate for bird mitochondrial DNA
Nabholz, B., Lanfear, R., & Fuchs, J. (2016) · Molecular Ecology · doi:10.1111/mec.13780 · Cited by 85
“5 Myr was used in all analyses except calibration set 1 (see Table 1) (Longrich et al. 2011; Prum et al. 2015) .”
InfluentialBuckley, M., Warwood, S., van Dongen, B., Kitchener, A. C., & Manning, P. L. (2017) · Proceedings of the Royal Society B: Biological Sciences · doi:10.1098/rspb.2017.0544 · Cited by 61
“being earliest diverging from the extant bird lineage [23], this became no longer possible.”
BackgroundChen, M., Liang, D., & Zhang, P. (2017) · Genome Biology and Evolution · doi:10.1093/gbe/evx147 · Cited by 88
Dool, S. E., Puechmaille, S. J., Foley, N. M., Allegrini, B., Bastian, A., Mutumi, G. L., Maluleke, T. G., Odendaal, L. J., Teeling, E. C., & Jacobs, D. S. (2016) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2016.01.003 · Cited by 92
Uncovering the genomic signature of ancient introgression between white oak lineages (Quercus)
Crowl, A. A., Manos, P. S., McVay, J. D., Lemmon, A. R., Lemmon, E. M., & Hipp, A. L. (2019) · New Phytologist · doi:10.1111/nph.15842 · Cited by 86
Self-citationReconstructing the geographic and climatic origins of long‐distance bird migrations
Dufour, P., Descamps, S., Chantepie, S., Renaud, J., Guéguen, M., Schiffers, K. H., Thuiller, W., & Lavergne, S. (2019) · Journal of Biogeography · doi:10.1111/jbi.13700 · Cited by 92
The conservation genetics juggling act: integrating genetics and ecology, science and policy
Haig, S. M., Miller, M. P., Bellinger, M. R., Draheim, H. M., Mercer, D. M., & Mullins, T. D. (2015) · Evolutionary Applications · doi:10.1111/eva.12337 · Cited by 91
“The exponential increase in information yielded and our new ability to address questions of local adaptation and evolutionary potential, among many others, is phenomenal (Harrison et al. 2014; Prum et al. 2015).”
BackgroundMargres, M. J., Wray, K. P., Hassinger, A. T. B., Ward, M. J., McGivern, J. J., Lemmon, E. M., Lemmon, A. R., & Rokyta, D. R. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx231 · Cited by 91
“Divergent reference assembly was used to map reads to the probe regions and extend the assembly into the flanking regions; Calamaria pavimentata was chosen as the reference for the anchored assembly (Prum et al. 2015; Ruane et al. 2015) and B.”
MethodInfluentialSelf-citationNear, T. J., MacGuigan, D. J., Parker, E., Struthers, C. D., JONES, C. D., & Dornburg, A. (2018) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2018.09.001 · Cited by 84
Self-citationMinimum variance rooting of phylogenetic trees and implications for species tree reconstruction
Mai, U., Sayyari, E., & Mirarab, S. (2017) · PLoS ONE · doi:10.1371/journal.pone.0182238 · Cited by 87
Introducing the Bird Chromosome Database: An Overview of Cytogenetic Studies in Birds
Degrandi, T. M., Barcellos, S. A., Costa, A. L., Garnero, A. D. V., Hass, I., & Gunski, R. J. (2020) · Cytogenetic and Genome Research · doi:10.1159/000507768 · Cited by 94
Mitchell, N. J., Lewis, P. O., Lemmon, E. M., Lemmon, A. R., & Holsinger, K. E. (2017) · American Journal of Botany · doi:10.3732/ajb.1600227 · Cited by 86
Self-citationA global analysis of selection at the avian MHC
Minias, P., Pikus, E., Whittingham, L. A., & Dunn, P. O. (2018) · Evolution · doi:10.1111/evo.13490 · Cited by 85
“Tree topology and divergence times were based on Claramunt and Cracraft (2015) and Prum et al. (2015).”
BackgroundMethodNavalón, G., Marugán‐Lobón, J., Bright, J. A., Cooney, C. R., & Rayfield, E. J. (2020) · Nature Ecology & Evolution · doi:10.1038/s41559-019-1092-y · Cited by 86
Branstetter, M. G., Childers, A. K., Cox-Foster, D., Hopper, K. R., Kapheim, K. M., Toth, A. L., & Worley, K. C. (2017) · Current Opinion in Insect Science · doi:10.1016/j.cois.2017.11.008 · Cited by 85
On the importance of homology in the age of phylogenomics
Springer, M. S., & Gatesy, J. (2017) · Systematics and Biodiversity · doi:10.1080/14772000.2017.1401016 · Cited by 83
Gatesy, J., Meredith, R. W., Janečka, J. E., Simmons, M. P., Murphy, W. J., & Springer, M. S. (2016) · Cladistics · doi:10.1111/cla.12170 · Cited by 81
“This computationally demanding process makes rigorous MP-EST analyses intractable for large systematic datasets with many taxa (e.g. Wickett et al., 2014; Prum et al., 2015).”
Allio, R., Scornavacca, C., Nabholz, B., Clamens, A., Sperling, F. A. H., & Condamine, F. L. (2019) · Systematic Biology · doi:10.1093/sysbio/syz030 · Cited by 86
History is written by the victors: The effect of the push of the past on the fossil record
Budd, G. E., & Mann, R. P. (2018) · Evolution · doi:10.1111/evo.13593 · Cited by 85
Rapid diversification of alpine bamboos associated with the uplift of the Hengduan Mountains
Ye, X., Ma, P., Yang, G., Guo, C., Zhang, Y., Chen, Y., Guo, Z., & Li, D.-Z. (2019) · Journal of Biogeography · doi:10.1111/jbi.13723 · Cited by 81
Ksepka, D. T., Stidham, T. A., & Williamson, T. E. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1700188114 · Cited by 93
“In the present study, a “naïve” reconstruction using the molecular scaffold tree with only extant taxa and no branch length data supports a single origin of semizygodactyly in the most recent common ancestor of Coraciimorphae + Strigiformes, along with two independent origins of full zygodactyly in Piciformes and Psit…”
BackgroundMethodInfluentialSwanson, D. L., McKechnie, A. E., & Vézina, F. (2017) · Journal of Comparative Physiology B · doi:10.1007/s00360-017-1096-3 · Cited by 80
Asynchronous evolution of interdependent nest characters across the avian phylogeny
Fang, Y., Tuanmu, M., & Hung, C. (2018) · Nature Communications · doi:10.1038/s41467-018-04265-x · Cited by 80
de Moya, R. S., Yoshizawa, K., Walden, K. K. O., Sweet, A. D., Dietrich, C. H., & Johnson Kevin, P. (2020) · Systematic Biology · doi:10.1093/sysbio/syaa075 · Cited by 79
“…access to new data types originating from 46 different genomic regions (e.g. ultra-conserved elements (UCE) and single-copy protein-coding 47 orthologs) (Jarvis et al. 2014; Prum et al. 2015) or from post transcriptional processes (i.e. 48 transcriptomes) (Misof et al. 2014; Johnson et al. 2018a).”
BackgroundAnchored Phylogenomics of Angiosperms I: Assessing the Robustness of Phylogenetic EstimatesPreprint
Buddenhagen, C. E., Lemmon, A. R., Lemmon, E. M., Bruhl, J. J., Cappa, J. J., Clement, W. L., Donoghue, M. J., Edwards, E. J., Hipp, A. L., Kortyna, M., et al. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/086298 · Cited by 84
“For each of these species, we identified homologous regions following Prum et al. (2015), using Arabidopsis and Oryza as references (>55% similarity to one of the references was required).”
BackgroundMethodInfluentialSelf-citationInterrogating Genomic-Scale Data to Resolve Recalcitrant Nodes in the Spider Tree of Life
Kulkarni, S., Kallal, R. J., Wood, H. M., Dimitrov, D., Giribet, G., & Hormiga, G. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa251 · Cited by 80
“This conundrum has impacted phylogenetic studies of many groups of organisms, including birds (Jarvis et al. 2014; Prum et al. 2015; Walker et al. 2018; Cloutier et al. 2019), placental mammals (Morgan et al. 2013; Romiguier et al. 2013), extant angiosperms (Zanis et al. 2002; Wickett et al. 2014;…”
BackgroundMasters, J. C., Génin, F., Zhang, Y., Pellen, R., Huck, T., Mazza, P., Rabineau, M., Doucouré, M., & Aslanian, D. (2020) · Journal of Biogeography · doi:10.1111/jbi.14032 · Cited by 84
Whole genome sequencing data and de novo draft assemblies for 66 teleost species
Malmstrøm, M., Matschiner, M., Tørresen, O. K., Jakobsen, K. S., & Jentoft, S. (2017) · Scientific Data · doi:10.1038/sdata.2016.132 · Cited by 75
Fifty-eighth supplement to the American Ornithological Society'sCheck-list of North American Birds
Chesser, R. T., Burns, K. J., Cicero, C., Dunn, J. L., Kratter, A. W., Lovette, I. J., Rasmussen, P. C., Remsen, J. V., Rising, J. D., Stotz, D. F., et al. (2017) · The Auk · doi:10.1642/auk-17-72.1 · Cited by 78
Johnson, A. J., McKenna, D. D., Jordal, B. H., Cognato, A. I., Smith, S. M., Lemmon, A. R., Lemmon, E. M., & Hulcr, J. (2018) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2018.05.028 · Cited by 78
Self-citationWing bone geometry reveals active flight in Archaeopteryx
Voeten, D. F. A. E., Cubo, J., de Margerie, E., Röper, M., Beyrand, V., Bureš, S., Tafforeau, P., & Sanchez, S. (2018) · Nature Communications · doi:10.1038/s41467-018-03296-8 · Cited by 77
Discovery and Characterization of Novel RNA Viruses in Aquatic North American Wild Birds
Canuti, M., Kroyer, A. N. K., Ojkić, D., Whitney, H. G., Robertson, G. J., & Lang, A. S. (2019) · Viruses · doi:10.3390/v11090768 · Cited by 78
The dynamics of stem and crown groups
Budd, G. E., & Mann, R. P. (2020) · Science Advances · doi:10.1126/sciadv.aaz1626 · Cited by 80
Phylogenomics from Whole Genome Sequences Using aTRAM
Allen, J. M., Boyd, B. M., Nguyen, N., Vachaspati, P., Warnow, T. J., Huang, D. I., Grady, P. G. S., Bell, K. C., Cronk, Q., Mugisha, L., et al. (2016) · Systematic Biology · doi:10.1093/sysbio/syw105 · Cited by 80
“These approaches have proved useful in collecting data for difficult phylogenetic problems, particularly in organisms with larger genomes (Misof et al. 2014; Prum et al. 2015).”
BackgroundCatanach, T. A., Halley, M. R., & Pirro, S. (2025) · Biological Journal of the Linnean Society · doi:10.1093/biolinnean/blae028 · Cited by 76
Richards, E. J., Brown, J. M., Barley, A. J., Chong, R. A., & Thomson, R. C. (2018) · Systematic Biology · doi:10.1093/sysbio/syy013 · Cited by 79
“We obtained all available (as of 31 July 2014) complete tetrapod mitochondrial genome sequences from GenBank, which we organized into six data sets comprising the major lineages within the clade: Crocodilians (n= 20), Turtles (n=53), Squamates (n=120), Amphibians (n=157), Birds (n=253), and Mammals (n=575).”
MethodInfluentialThe singing question: re‐conceptualizing birdsong
Rose, E. M., Prior, N. H., & Ball, G. F. (2021) · Biological reviews/Biological reviews of the Cambridge Philosophical Society · doi:10.1111/brv.12800 · Cited by 82
“However, recent phylogenies show that parrots are in fact a sister group to the songbirds, so phylogeny is not a reason to restrict the term ‘song’ to oscines (Prum et al., 2015; Feng et al., 2020).”
BackgroundDumont, M., Tafforeau, P., Bertin, T., Bhullar, B.-A. S., Field, D. J., Schulp, A. S., Strilisky, B., Thivichon‐Prince, B., Viriot, L., & Louchart, A. (2016) · BMC Evolutionary Biology · doi:10.1186/s12862-016-0753-6 · Cited by 76
“and exhibit tremendous disparity in their feeding ecologies and diets [1, 2].”
BackgroundSelf-citationWu, Y., Hadly, E. A., Teng, W., Hao, Y., Liang, W., Liu, Y., & Wang, H. (2016) · Scientific Reports · doi:10.1038/srep33578 · Cited by 80
Grealy, A. C., Phillips, M. J., Miller, G. H., Gilbert, M. T. P., Rouillard, J. M., Lambert, D. M., Bunce, M., & Haile, J. (2017) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2017.01.005 · Cited by 77
Johnson, M. G., Pokorny, L., Dodsworth, S., Botigué, L. R., Cowan, R. S., Devault, A. M., Eiserhardt, W. L., Epitawalage, N., Forest, F., Kim, J. T., et al. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/361618 · Cited by 77
Cardillo, M., Weston, P. H., Reynolds, Z. K. M., Olde, P. M., Mast, A., Lemmon, E. M., Lemmon, A. R., & Bromham, L. D. (2017) · Evolution · doi:10.1111/evo.13276 · Cited by 79
Self-citationPyron, R. A., Hsieh, F. W., Lemmon, A. R., Lemmon, E. M., & Hendry, C. R. (2016) · Zoological Journal of the Linnean Society · doi:10.1111/zoj.12392 · Cited by 74
“Reads passing the Casava quality filter were processed following Prum et al. (2015).”
MethodSelf-citationHirst, C. E., Major, A. T., Ayers, K. L., Brown, R. J., Mariette, M. M., Sackton, T. B., & Smith, C. A. (2017) · Endocrinology · doi:10.1210/en.2017-00316 · Cited by 75
“in the emu and zebra finch, representing the two other major clades of birds (Paleognathae and Neoaves, respectively) (64).”
BackgroundWild hummingbirds discriminate nonspectral colors
Stoddard, M. C., Eyster, H. N., Hogan, B. G., Morris, D. H., Soucy, E. R., & Inouye, D. W. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1919377117 · Cited by 77
“Hummingbirds and swifts form a diurnal subclade nested in the historically nocturnal Strisores, a group that includes nightjars, nighthawks, and relatives (64).”
BackgroundLeslie, A. B., Beaulieu, J. M., & Mathews, S. (2017) · New Phytologist · doi:10.1111/nph.14456 · Cited by 74
“…which to investigate evolution of seed size because they are the most species-rich (c. 615 extant species), have the widest geographic distribution, are ecologically diverse (see Farjon, 2010; Farjon & Filer, 2013) and have a well-resolved phylogeny (Rai et al., 2008; Leslie et al., 2012).”
BackgroundAndersen, M. J., McCullough, J. M., Mauck, W. M., Smith, B. T., & Moyle, R. G. (2017) · Journal of Biogeography · doi:10.1111/jbi.13139 · Cited by 73
“tions from fossil-calibrated avian timetrees (Claramunt & Cracraft, 2015; Prum et al., 2015).”
BackgroundMethodInfluentialBright, J. A., Marugán‐Lobón, J., Rayfield, E. J., & Cobb, S. N. (2019) · BMC Evolutionary Biology · doi:10.1186/s12862-019-1432-1 · Cited by 82
Genetic and Molecular Basis of Feather Diversity in Birds
Ng, C. S., & Li, W. (2018) · Genome Biology and Evolution · doi:10.1093/gbe/evy180 · Cited by 73
Data Types and the Phylogeny of Neoaves
Braun, E. L., & Kimball, R. T. (2021) · Birds · doi:10.3390/birds2010001 · Cited by 73
Soares, A. E. R., Novak, B. J., Haile, J., Heupink, T. H., Fjeldså, J., Gilbert, M. T. P., Poinar, H. N., Church, G. M., & Shapiro, B. (2016) · BMC Evolutionary Biology · doi:10.1186/s12862-016-0800-3 · Cited by 75
“Pereira et al. [5], who used a more taxonomically comprehensive phylogeny of both mitochondrial and nuclear DNA to infer that the dodo and solitaire diverged from the Caloenas lineage 33.5–50 Mya and from each other 15–30 Mya.”
BackgroundMethodInfluentialKlopfstein, S., Langille, B. L., Spasojevic, T., Broad, G. R., Cooper, S. J., Austin, A. D., & Niehuis, O. (2018) · Systematic Entomology · doi:10.1111/syen.12333 · Cited by 69
“The importance of these questions is underlined by the increasing number of phylogenomic studies that arrive at contradictory conclusions, despite including hundreds to thousands of genes (e.g. McCormack et al., 2013a; Sharma et al., 2014; Prum et al., 2015; Streicher et al., 2016).”
BackgroundMethodMaple phylogeny and biogeography inferred from phylogenomic data
Li, J., Stukel, M., Bussies, P. L., Skinner, K., Lemmon, A. R., Lemmon, E. M., Brown, K. S., Bekmetjev, A., & Swenson, N. G. (2019) · Journal of Systematics and Evolution · doi:10.1111/jse.12535 · Cited by 72
Self-citationPollock, H. S., Brawn, J. D., & Cheviron, Z. A. (2020) · Functional Ecology · doi:10.1111/1365-2435.13693 · Cited by 76
Evolutionary Integration and Modularity in the Archosaur Cranium
Felice, R. N., Watanabe, A., Cuff, A. R., Noirault, E., Pol, D., Witmer, L. M., Norell, M. A., O’Connor, P. M., & Goswami, A. (2019) · Integrative and Comparative Biology · doi:10.1093/icb/icz052 · Cited by 72
Fast and Accurate Estimates of Divergence Times from Big Data
Mello, B., Tao, Q., Tamura, K., & Kumar, S. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw247 · Cited by 63
“(A) Bayesian and RelTime timescales for the Birds B dataset (Prum et al. 2015).”
BackgroundMethodTucker, D. B., Colli, G. R., Giugliano, L. G., Hedges, S. B., Hendry, C. R., Lemmon, E. M., Lemmon, A. R., Sites, J. W., & Pyron, R. A. (2016) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2016.07.002 · Cited by 68
Self-citationTargeted Sampling and Target Capture: Assessing Phylogeographic Concordance with Genome-wide Data
Barrow, L. N., Lemmon, A. R., & Lemmon, E. M. (2018) · Systematic Biology · doi:10.1093/sysbio/syy021 · Cited by 64
Self-citationInterspecific comparison of the fecal microbiota structure in three Arctic migratory bird species
Cho, H., & Lee, W. Y. (2020) · Ecology and Evolution · doi:10.1002/ece3.6299 · Cited by 66
Record breaking achievements by spiders and the scientists who study them
Mammola, S., Michalik, P., Hebets, E. A., & Isaia, M. (2017) · PeerJ · doi:10.7717/peerj.3972 · Cited by 66
“70 Myr ago (Prum et al., 2015)], spiders have inhabited our planet for at least 300 million years.”
BackgroundWater lilies as emerging models for Darwin’s abominable mystery
Chen, F., Liu, X., Yu, C., Chen, Y., Tang, H., & Zhang, L. (2017) · Horticulture Research · doi:10.1038/hortres.2017.51 · Cited by 70
Canoville, A., Schweitzer, M. H., & Zanno, L. E. (2019) · BMC Evolutionary Biology · doi:10.1186/s12862-019-1402-7 · Cited by 67
Early origin of sweet perception in the songbird radiation
Toda, Y., Ko, M., Liang, Q., Miller, E. T., Rico‐Guevara, A., Nakagita, T., Sakakibara, A., Uemura, K., Sackton, T. B., Hayakawa, T., et al. (2021) · Science · doi:10.1126/science.abf6505 · Cited by 60
Deep evolutionary diversification of semicircular canals in archosaurs
Bronzati, M., Benson, R., Evers, S., Ezcurra, M. D., Cabreira, S. F., Choiniere, J. N., Dollman, K., Paulina‐Carabajal, A., Radermacher, V. J., da Silva, L. R., et al. (2021) · Current Biology · doi:10.1016/j.cub.2021.03.086 · Cited by 64
Phylogenomic conflict coincides with rapid morphological innovation
Parins‐Fukuchi, C., Stull, G. W., & Smith, S. A. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2023058118 · Cited by 66
Genome-wide diversity in the California condor tracks its prehistoric abundance and decline
Robinson, J. A., Bowie, R. C. K., Dudchenko, O., Aiden, E. L., Hendrickson, S. L., Steiner, C., Ryder, O. A., Mindell, D. P., & Wall, J. D. (2021) · Current Biology · doi:10.1016/j.cub.2021.04.035 · Cited by 70
On the universality of target‐enrichment baits for phylogenomic research
Bossert, S., & Danforth, B. N. (2018) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.12988 · Cited by 64
“…is the use of 120 bp long nucleotide baits for in-solution hybridizations with highly conserved DNA fragments (e.g. Fragoso- Martínez et al., 2017; Lemmon et al., 2012; Prum et al., 2015 for AE- based studies, and Branstetter, Danforth, et al., 2017; Starrett et al., 2016 for the UCE approach).”
BackgroundBlaimer, B. B., Ward, P. S., Schultz, T. R., Fisher, B. L., & Brady, S. G. (2018) · Insect Systematics and Diversity · doi:10.1093/isd/ixy013 · Cited by 64
Metadata
- Authors
- Prum, R. O., Berv, J. S., Dornburg, A., Field, D. J., Townsend, J. P., Lemmon, E. M., & Lemmon, A. R.
- Affiliations
- Yale University (US)
- ORCID
- Venue
- Nature
- Published
- 2016-06
- Volume
- 534
- Issue
- 7607
- Pages
- S7-S8
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W4231969088
- Cited by
- 928
- References
- 7
- Citations by year
- 2026: 1 · 2025: 4 · 2024: 6 · 2023: 13 · 2022: 10 · 2021: 152 · 2020: 170 · 2019: 159 · 2018: 147 · 2017: 164 · 2016: 94
- FWCI
- 156.34
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- Topics
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Paleontology and Evolutionary Biology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- avian phylogeny, Neoaves, anchored hybrid enrichment, nuclear loci, avian evolution, hoatzin, waterbirds, landbirds, divergence time estimation, dinosaur systematics
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