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For: Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SYW, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Alfaro-Núñez A, Narula N, Liu L, Burt D, Ellegren H, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MTP, Zhang G. Phylogenomic analyses data of the avian phylogenomics project. Gigascience 2015;4:4. [PMID: 25741440 PMCID: PMC4349222 DOI: 10.1186/s13742-014-0038-1] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 12/16/2014] [Indexed: 11/10/2022]  Open
Number Cited by Other Article(s)
1
Arbore R, Barbosa S, Brejcha J, Ogawa Y, Liu Y, Nicolaï MPJ, Pereira P, Sabatino SJ, Cloutier A, Poon ESK, Marques CI, Andrade P, Debruyn G, Afonso S, Afonso R, Roy SG, Abdu U, Lopes RJ, Mojzeš P, Maršík P, Sin SYW, White MA, Araújo PM, Corbo JC, Carneiro M. A molecular mechanism for bright color variation in parrots. Science 2024;386:eadp7710. [PMID: 39480920 PMCID: PMC7617403 DOI: 10.1126/science.adp7710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 09/05/2024] [Indexed: 11/02/2024]
2
Griffin DK, Kretschmer R, Srikulnath K, Singchat W, O'Connor RE, Romanov MN. Insights into avian molecular cytogenetics-with reptilian comparisons. Mol Cytogenet 2024;17:24. [PMID: 39482771 PMCID: PMC11526677 DOI: 10.1186/s13039-024-00696-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2024] [Accepted: 10/24/2024] [Indexed: 11/03/2024]  Open
3
Blom MP, Peona V, Prost S, Christidis L, Benz BW, Jønsson KA, Suh A, Irestedt M. Hybridization in birds-of-paradise: Widespread ancestral gene flow despite strong sexual selection in a lek-mating system. iScience 2024;27:110300. [PMID: 39055907 PMCID: PMC11269930 DOI: 10.1016/j.isci.2024.110300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 05/08/2024] [Accepted: 06/14/2024] [Indexed: 07/28/2024]  Open
4
Islam R, Rahman A. An alignment-free method for detection of missing regions for phylogenetic analysis. Heliyon 2024;10:e32227. [PMID: 38933968 PMCID: PMC11200290 DOI: 10.1016/j.heliyon.2024.e32227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 05/17/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024]  Open
5
Zheng W, Gojobori J, Suh A, Satta Y. Different Host-Endogenous Retrovirus Relationships between Mammals and Birds Reflected in Genome-Wide Evolutionary Interaction Patterns. Genome Biol Evol 2024;16:evae065. [PMID: 38527852 PMCID: PMC11005779 DOI: 10.1093/gbe/evae065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 02/25/2024] [Accepted: 03/21/2024] [Indexed: 03/27/2024]  Open
6
Reeve AH, Kennedy JD, Pujolar JM, Petersen B, Blom MPK, Alström P, Haryoko T, Ericson PGP, Irestedt M, Nylander JAA, Jønsson KA. The formation of the Indo-Pacific montane avifauna. Nat Commun 2023;14:8215. [PMID: 38081809 PMCID: PMC10713610 DOI: 10.1038/s41467-023-43964-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 11/24/2023] [Indexed: 12/18/2023]  Open
7
Liu B, Warnow T. Weighted ASTRID: fast and accurate species trees from weighted internode distances. Algorithms Mol Biol 2023;18:6. [PMID: 37468904 PMCID: PMC10355063 DOI: 10.1186/s13015-023-00230-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 06/10/2023] [Indexed: 07/21/2023]  Open
8
Ferrer Obiol J, Herranz JM, Paris JR, Whiting JR, Rozas J, Riutort M, González-Solís J. Species delimitation using genomic data to resolve taxonomic uncertainties in a speciation continuum of pelagic seabirds. Mol Phylogenet Evol 2023;179:107671. [PMID: 36442764 DOI: 10.1016/j.ympev.2022.107671] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/28/2022] [Accepted: 11/17/2022] [Indexed: 11/27/2022]
9
Wang N, Braun EL, Liang B, Cracraft J, Smith SA. Categorical edge-based analyses of phylogenomic data reveal conflicting signals for difficult relationships in the avian tree. Mol Phylogenet Evol 2022;174:107550. [PMID: 35691570 DOI: 10.1016/j.ympev.2022.107550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 05/13/2022] [Accepted: 06/02/2022] [Indexed: 11/28/2022]
10
Ng CS, Lai CK, Ke HM, Lee HH, Chen CF, Tang PC, Cheng HC, Lu MJ, Li WH, Tsai IJ. Genome Assembly and Evolutionary Analysis of the Mandarin Duck Aix galericulata Reveal Strong Genome Conservation among Ducks. Genome Biol Evol 2022;14:evac083. [PMID: 35640266 PMCID: PMC9189614 DOI: 10.1093/gbe/evac083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2022] [Indexed: 11/13/2022]  Open
11
Rahman MA, Tutul AA, Abdullah SM, Bayzid MS. CHAPAO: Likelihood and hierarchical reference-based representation of biomolecular sequences and applications to compressing multiple sequence alignments. PLoS One 2022;17:e0265360. [PMID: 35436292 PMCID: PMC9015123 DOI: 10.1371/journal.pone.0265360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 02/28/2022] [Indexed: 11/18/2022]  Open
12
Hansen CCR, Westfall KM, Pálsson S. Evaluation of four methods to identify the homozygotic sex chromosome in small populations. BMC Genomics 2022;23:160. [PMID: 35209843 PMCID: PMC8867824 DOI: 10.1186/s12864-022-08393-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 02/15/2022] [Indexed: 11/10/2022]  Open
13
Sin SYW, Cloutier A, Nevitt G, Edwards SV. Olfactory receptor subgenome and expression in a highly olfactory procellariiform seabird. Genetics 2021;220:6458329. [PMID: 34888634 DOI: 10.1093/genetics/iyab210] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 10/04/2021] [Indexed: 11/13/2022]  Open
14
Ferrer Obiol J, James HF, Chesser RT, Bretagnolle V, González-Solís J, Rozas J, Riutort M, Welch AJ. Integrating Sequence Capture and Restriction Site-Associated DNA Sequencing to Resolve Recent Radiations of Pelagic Seabirds. Syst Biol 2021;70:976-996. [PMID: 33512506 PMCID: PMC8357341 DOI: 10.1093/sysbio/syaa101] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 11/13/2020] [Accepted: 12/15/2020] [Indexed: 01/01/2023]  Open
15
Vanamamalai VK, Garg P, Kolluri G, Gandham RK, Jali I, Sharma S. Transcriptomic analysis to infer key molecular players involved during host response to NDV challenge in Gallus gallus (Leghorn & Fayoumi). Sci Rep 2021;11:8486. [PMID: 33875770 PMCID: PMC8055681 DOI: 10.1038/s41598-021-88029-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 03/22/2021] [Indexed: 11/09/2022]  Open
16
Minh BQ, Hahn MW, Lanfear R. New Methods to Calculate Concordance Factors for Phylogenomic Datasets. Mol Biol Evol 2021;37:2727-2733. [PMID: 32365179 PMCID: PMC7475031 DOI: 10.1093/molbev/msaa106] [Citation(s) in RCA: 313] [Impact Index Per Article: 78.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]  Open
17
Recuerda M, Vizueta J, Cuevas-Caballé C, Blanco G, Rozas J, Milá B. Chromosome-Level Genome Assembly of the Common Chaffinch (Aves: Fringilla coelebs): A Valuable Resource for Evolutionary Biology. Genome Biol Evol 2021;13:evab034. [PMID: 33616654 PMCID: PMC8046334 DOI: 10.1093/gbe/evab034] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/16/2021] [Indexed: 12/26/2022]  Open
18
Minh BQ, Dang CC, Vinh LS, Lanfear R. QMaker: Fast and accurate method to estimate empirical models of protein evolution. Syst Biol 2021;70:1046-1060. [PMID: 33616668 PMCID: PMC8357343 DOI: 10.1093/sysbio/syab010] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 12/25/2020] [Accepted: 02/10/2021] [Indexed: 11/29/2022]  Open
19
De Mendoza RS, Gómez RO, Tambussi CP. The lacrimal/ectethmoid region of waterfowl (Aves, Anseriformes): Phylogenetic signal and major evolutionary patterns. J Morphol 2020;281:1486-1500. [PMID: 32936967 DOI: 10.1002/jmor.21265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 08/02/2020] [Accepted: 09/02/2020] [Indexed: 11/08/2022]
20
Wang S, Chang WL, Zhang Q, Ma M, Yang F, Zhuo D, Hans HIC, Yang R, Wu P, Habib M, Juan WT, Chuong CM. Variations of Mesozoic feathers: Insights from the morphogenesis of extant feather rachises. Evolution 2020;74:2121-2133. [PMID: 32614075 DOI: 10.1111/evo.14051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 06/21/2020] [Accepted: 06/27/2020] [Indexed: 12/14/2022]
21
Degrandi TM, Barcellos SA, Costa AL, Garnero ADV, Hass I, Gunski RJ. Introducing the Bird Chromosome Database: An Overview of Cytogenetic Studies in Birds. Cytogenet Genome Res 2020;160:199-205. [PMID: 32369809 DOI: 10.1159/000507768] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 03/26/2020] [Indexed: 11/19/2022]  Open
22
Deep-Time Demographic Inference Suggests Ecological Release as Driver of Neoavian Adaptive Radiation. DIVERSITY-BASEL 2020. [DOI: 10.3390/d12040164] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
23
Lee H, Kim J, Weber JA, Chung O, Cho YS, Jho S, Jun J, Kim HM, Lim J, Choi JP, Jeon S, Blazyte A, Edwards JS, Paek WK, Bhak J. Whole Genome Analysis of the Red-Crowned Crane Provides Insight into Avian Longevity. Mol Cells 2020;43:86-95. [PMID: 31940721 PMCID: PMC6999708 DOI: 10.14348/molcells.2019.0190] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/31/2019] [Accepted: 12/18/2019] [Indexed: 11/29/2022]  Open
24
Dhar R, Seethy A, Pethusamy K, Singh S, Rohil V, Purkayastha K, Mukherjee I, Goswami S, Singh R, Raj A, Srivastava T, Acharya S, Rajashekhar B, Karmakar S. De novo assembly of the Indian blue peacock (Pavo cristatus) genome using Oxford Nanopore technology and Illumina sequencing. Gigascience 2019;8:5488106. [PMID: 31077316 PMCID: PMC6511069 DOI: 10.1093/gigascience/giz038] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 09/30/2018] [Accepted: 03/18/2019] [Indexed: 01/23/2023]  Open
25
Cloutier A, Sackton TB, Grayson P, Clamp M, Baker AJ, Edwards SV. Whole-Genome Analyses Resolve the Phylogeny of Flightless Birds (Palaeognathae) in the Presence of an Empirical Anomaly Zone. Syst Biol 2019;68:937-955. [PMID: 31135914 PMCID: PMC6857515 DOI: 10.1093/sysbio/syz019] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 03/06/2019] [Accepted: 04/09/2019] [Indexed: 01/17/2023]  Open
26
Braun EL. An evolutionary model motivated by physicochemical properties of amino acids reveals variation among proteins. Bioinformatics 2019;34:i350-i356. [PMID: 29950007 PMCID: PMC6022633 DOI: 10.1093/bioinformatics/bty261] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
27
A Multireference-Based Whole Genome Assembly for the Obligate Ant-Following Antbird, Rhegmatorhina melanosticta (Thamnophilidae). DIVERSITY-BASEL 2019. [DOI: 10.3390/d11090144] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
28
Phylogenetic Signal of Indels and the Neoavian Radiation. DIVERSITY-BASEL 2019. [DOI: 10.3390/d11070108] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
29
Weber CC, Whelan S. Physicochemical Amino Acid Properties Better Describe Substitution Rates in Large Populations. Mol Biol Evol 2019;36:679-690. [PMID: 30668757 DOI: 10.1093/molbev/msz003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
30
Statistical binning leads to profound model violation due to gene tree error incurred by trying to avoid gene tree error. Mol Phylogenet Evol 2019;134:164-171. [DOI: 10.1016/j.ympev.2019.02.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 11/30/2018] [Accepted: 02/14/2019] [Indexed: 11/19/2022]
31
Sarmashghi S, Bohmann K, P. Gilbert MT, Bafna V, Mirarab S. Skmer: assembly-free and alignment-free sample identification using genome skims. Genome Biol 2019;20:34. [PMID: 30760303 PMCID: PMC6374904 DOI: 10.1186/s13059-019-1632-4] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 01/16/2019] [Indexed: 01/10/2023]  Open
32
Tambussi CP, Degrange FJ, De Mendoza RS, Sferco E, Santillana S. A stem anseriform from the early Palaeocene of Antarctica provides new key evidence in the early evolution of waterfowl. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zly085] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
33
Hieronymus TL, Waugh DA, Clarke JA. A new zygodactylid species indicates the persistence of stem passerines into the early Oligocene in North America. BMC Evol Biol 2019;19:3. [PMID: 30611195 PMCID: PMC6321701 DOI: 10.1186/s12862-018-1319-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 12/04/2018] [Indexed: 11/10/2022]  Open
34
Formenti G, Chiara M, Poveda L, Francoijs KJ, Bonisoli-Alquati A, Canova L, Gianfranceschi L, Horner DS, Saino N. SMRT long reads and Direct Label and Stain optical maps allow the generation of a high-quality genome assembly for the European barn swallow (Hirundo rustica rustica). Gigascience 2019;8:5202456. [PMID: 30496513 PMCID: PMC6324554 DOI: 10.1093/gigascience/giy142] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 10/06/2018] [Accepted: 11/14/2018] [Indexed: 11/12/2022]  Open
35
Adams RH, Castoe TA. Supergene validation: A model-based protocol for assessing the accuracy of non-model-based supergene methods. MethodsX 2019;6:2181-2188. [PMID: 31667118 PMCID: PMC6812401 DOI: 10.1016/j.mex.2019.09.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 09/19/2019] [Indexed: 11/16/2022]  Open
36
Workman RE, Myrka AM, Wong GW, Tseng E, Welch KC, Timp W. Single-molecule, full-length transcript sequencing provides insight into the extreme metabolism of the ruby-throated hummingbird Archilochus colubris. Gigascience 2018;7:1-12. [PMID: 29618047 PMCID: PMC5869288 DOI: 10.1093/gigascience/giy009] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 02/07/2018] [Indexed: 01/09/2023]  Open
37
Gilbert PS, Wu J, Simon MW, Sinsheimer JS, Alfaro ME. Filtering nucleotide sites by phylogenetic signal to noise ratio increases confidence in the Neoaves phylogeny generated from ultraconserved elements. Mol Phylogenet Evol 2018;126:116-128. [PMID: 29626666 PMCID: PMC6217972 DOI: 10.1016/j.ympev.2018.03.033] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 03/20/2018] [Accepted: 03/29/2018] [Indexed: 02/06/2023]
38
So many genes, so little time: A practical approach to divergence-time estimation in the genomic era. PLoS One 2018;13:e0197433. [PMID: 29772020 PMCID: PMC5957400 DOI: 10.1371/journal.pone.0197433] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 05/02/2018] [Indexed: 11/24/2022]  Open
39
Schiavo G, Strillacci MG, Ribani A, Bovo S, Roman-Ponce SI, Cerolini S, Bertolini F, Bagnato A, Fontanesi L. Few mitochondrial DNA sequences are inserted into the turkey (Meleagris gallopavo) nuclear genome: evolutionary analyses and informativity in the domestic lineage. Anim Genet 2018. [PMID: 29521475 DOI: 10.1111/age.12648] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
40
Edwards SV, Cloutier A, Baker AJ. Conserved Nonexonic Elements: A Novel Class of Marker for Phylogenomics. Syst Biol 2017;66:1028-1044. [PMID: 28637293 PMCID: PMC5790140 DOI: 10.1093/sysbio/syx058] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 06/03/2017] [Accepted: 06/06/2017] [Indexed: 01/12/2023]  Open
41
Dyomin A, Volodkina V, Koshel E, Galkina S, Saifitdinova A, Gaginskaya E. Evolution of ribosomal internal transcribed spacers in Deuterostomia. Mol Phylogenet Evol 2017;116:87-96. [PMID: 28860009 DOI: 10.1016/j.ympev.2017.08.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 08/11/2017] [Accepted: 08/25/2017] [Indexed: 11/30/2022]
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Indrischek H, Prohaska SJ, Gurevich VV, Gurevich EV, Stadler PF. Uncovering missing pieces: duplication and deletion history of arrestins in deuterostomes. BMC Evol Biol 2017;17:163. [PMID: 28683816 PMCID: PMC5501109 DOI: 10.1186/s12862-017-1001-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 06/19/2017] [Indexed: 12/13/2022]  Open
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Raven N, Lisovski S, Klaassen M, Lo N, Madsen T, Ho SYW, Ujvari B. Purifying selection and concerted evolution of RNA-sensing toll-like receptors in migratory waders. INFECTION GENETICS AND EVOLUTION 2017;53:135-145. [PMID: 28528860 DOI: 10.1016/j.meegid.2017.05.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Revised: 05/15/2017] [Accepted: 05/17/2017] [Indexed: 01/05/2023]
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Sarver BA, Keeble S, Cosart T, Tucker PK, Dean MD, Good JM. Phylogenomic Insights into Mouse Evolution Using a Pseudoreference Approach. Genome Biol Evol 2017;9:726-739. [PMID: 28338821 PMCID: PMC5381554 DOI: 10.1093/gbe/evx034] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2017] [Indexed: 12/15/2022]  Open
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Suh A. The phylogenomic forest of bird trees contains a hard polytomy at the root of Neoaves. ZOOL SCR 2016. [DOI: 10.1111/zsc.12213] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Mason AS, Fulton JE, Hocking PM, Burt DW. A new look at the LTR retrotransposon content of the chicken genome. BMC Genomics 2016;17:688. [PMID: 27577548 PMCID: PMC5006616 DOI: 10.1186/s12864-016-3043-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 08/24/2016] [Indexed: 11/23/2022]  Open
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Edmunds SC, Li P, Hunter CI, Xiao SZ, Davidson RL, Nogoy N, Goodman L. Experiences in integrated data and research object publishing using GigaDB. INTERNATIONAL JOURNAL ON DIGITAL LIBRARIES 2016. [DOI: 10.1007/s00799-016-0174-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Suh A, Witt CC, Menger J, Sadanandan KR, Podsiadlowski L, Gerth M, Weigert A, McGuire JA, Mudge J, Edwards SV, Rheindt FE. Ancient horizontal transfers of retrotransposons between birds and ancestors of human pathogenic nematodes. Nat Commun 2016;7:11396. [PMID: 27097561 PMCID: PMC4844689 DOI: 10.1038/ncomms11396] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 03/21/2016] [Indexed: 02/08/2023]  Open
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Kobert K, Salichos L, Rokas A, Stamatakis A. Computing the Internode Certainty and Related Measures from Partial Gene Trees. Mol Biol Evol 2016;33:1606-17. [PMID: 26915959 PMCID: PMC4868120 DOI: 10.1093/molbev/msw040] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]  Open
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Borowiec ML. AMAS: a fast tool for alignment manipulation and computing of summary statistics. PeerJ 2016;4:e1660. [PMID: 26835189 DOI: 10.7287/peerj.preprints.1355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 01/13/2016] [Indexed: 05/26/2023]  Open
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