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For: Duforet-Frebourg N, Luu K, Laval G, Bazin E, Blum MGB. Detecting Genomic Signatures of Natural Selection with Principal Component Analysis: Application to the 1000 Genomes Data. Mol Biol Evol 2016;33:1082-93. [PMID: 26715629 PMCID: PMC4776707 DOI: 10.1093/molbev/msv334] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]  Open
Number Cited by Other Article(s)
1
Zhao Z, Li S, Han Q, Yang W, Chang C, Li Y, Zhou J, Zeng Q, Zhang A. In situ high-resolution insights into the dynamics of arsenic (As) species and heavy metals across the sediment-water interface in a deep karst reservoir. JOURNAL OF HAZARDOUS MATERIALS 2025;490:137775. [PMID: 40022935 DOI: 10.1016/j.jhazmat.2025.137775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2025] [Revised: 02/17/2025] [Accepted: 02/25/2025] [Indexed: 03/04/2025]
2
Minne AJP, Vranken S, Wheeler D, Wood G, Batley J, Wernberg T, Coleman MA. Strong Environmental and Genome-Wide Population Differentiation Underpins Adaptation and High Genomic Vulnerability in the Dominant Australian Kelp (Ecklonia radiata). Ecol Evol 2025;15:e71158. [PMID: 40365477 PMCID: PMC12068950 DOI: 10.1002/ece3.71158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2024] [Revised: 02/26/2025] [Accepted: 03/07/2025] [Indexed: 05/15/2025]  Open
3
Lippolis A, Gezan SA, Zuidgeest J, Cafaro V, van Dinter BJ, Elzes G, Paulo MJ, Trindade LM. Targeted genotyping (90K-SPET) facilitates genome-wide association studies and the prediction of yield-related traits in faba bean (Vicia faba L.). BMC PLANT BIOLOGY 2025;25:558. [PMID: 40301715 PMCID: PMC12042580 DOI: 10.1186/s12870-025-06546-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Accepted: 04/11/2025] [Indexed: 05/01/2025]
4
Liu Y, Tao H, Jia S, Wang H, Guo L, Hu Z, Zhang W, Liu F. Prognostic value and immune landscapes of disulfidptosis‑related lncRNAs in bladder cancer. Mol Clin Oncol 2025;22:19. [PMID: 39776943 PMCID: PMC11706340 DOI: 10.3892/mco.2024.2814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Accepted: 11/11/2024] [Indexed: 01/11/2025]  Open
5
Mueller SA, Merondun J, Lečić S, Wolf JBW. Epigenetic variation in light of population genetic practice. Nat Commun 2025;16:1028. [PMID: 39863592 PMCID: PMC11762325 DOI: 10.1038/s41467-025-55989-6] [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: 12/20/2023] [Accepted: 01/03/2025] [Indexed: 01/27/2025]  Open
6
Grobler DL, Klein JD, Dicken ML, Mmonwa K, Soekoe M, van Staden M, Hagen SB, Maduna SN, Bester‐van der Merwe AE. Seascape Genomics of the Smooth Hammerhead Shark Sphyrna zygaena Reveals Regional Adaptive Clinal Variation. Ecol Evol 2024;14:e70644. [PMID: 39669504 PMCID: PMC11635309 DOI: 10.1002/ece3.70644] [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: 04/18/2024] [Revised: 11/04/2024] [Accepted: 11/08/2024] [Indexed: 12/14/2024]  Open
7
Congiu M, Cesarani A, Falchi L, Macciotta NPP, Dimauro C. Combined Use of Univariate and Multivariate Approaches to Detect Selection Signatures Associated with Milk or Meat Production in Cattle. Genes (Basel) 2024;15:1516. [PMID: 39766784 PMCID: PMC11675734 DOI: 10.3390/genes15121516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2024] [Revised: 11/19/2024] [Accepted: 11/22/2024] [Indexed: 01/11/2025]  Open
8
Schneider K, Chowdhury M, Tepper M, Khan J, Shortt JA, Gignoux C, Layer R. GenoSiS: A Biobank-Scale Genotype Similarity Search Architecture for Creating Dynamic Patient-Match Cohorts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.02.621671. [PMID: 39554195 PMCID: PMC11565994 DOI: 10.1101/2024.11.02.621671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/19/2024]
9
Chhina AK, Abhari N, Mooers A, Lewthwaite JMM. Linking the spatial and genomic structure of adaptive potential for conservation management: a review. Genome 2024;67:403-423. [PMID: 39083766 DOI: 10.1139/gen-2024-0036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2024]
10
Hoang N, Sardaripour N, Ramey GD, Schilling K, Liao E, Chen Y, Park JH, Bledsoe X, Landman BA, Gamazon ER, Benton ML, Capra JA, Rubinov M. Integration of estimated regional gene expression with neuroimaging and clinical phenotypes at biobank scale. PLoS Biol 2024;22:e3002782. [PMID: 39269986 PMCID: PMC11424006 DOI: 10.1371/journal.pbio.3002782] [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: 03/22/2024] [Revised: 09/25/2024] [Accepted: 08/01/2024] [Indexed: 09/15/2024]  Open
11
Lasky JR, Takou M, Gamba D, Keitt TH. Estimating scale-specific and localized spatial patterns in allele frequency. Genetics 2024;227:iyae082. [PMID: 38758968 PMCID: PMC11339607 DOI: 10.1093/genetics/iyae082] [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: 09/07/2023] [Revised: 09/07/2023] [Accepted: 04/28/2024] [Indexed: 05/19/2024]  Open
12
Barquera R, Del Castillo-Chávez O, Nägele K, Pérez-Ramallo P, Hernández-Zaragoza DI, Szolek A, Rohrlach AB, Librado P, Childebayeva A, Bianco RA, Penman BS, Acuña-Alonzo V, Lucas M, Lara-Riegos JC, Moo-Mezeta ME, Torres-Romero JC, Roberts P, Kohlbacher O, Warinner C, Krause J. Ancient genomes reveal insights into ritual life at Chichén Itzá. Nature 2024;630:912-919. [PMID: 38867041 PMCID: PMC11208145 DOI: 10.1038/s41586-024-07509-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/02/2024] [Indexed: 06/14/2024]
13
Kess T, Lehnert SJ, Bentzen P, Duffy S, Messmer A, Dempson JB, Newport J, Whidden C, Robertson MJ, Chaput G, Breau C, April J, Gillis C, Kent M, Nugent CM, Bradbury IR. Variable parallelism in the genomic basis of age at maturity across spatial scales in Atlantic Salmon. Ecol Evol 2024;14:e11068. [PMID: 38584771 PMCID: PMC10995719 DOI: 10.1002/ece3.11068] [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: 01/06/2024] [Accepted: 01/31/2024] [Indexed: 04/09/2024]  Open
14
Schiebelhut LM, Guillaume AS, Kuhn A, Schweizer RM, Armstrong EE, Beaumont MA, Byrne M, Cosart T, Hand BK, Howard L, Mussmann SM, Narum SR, Rasteiro R, Rivera-Colón AG, Saarman N, Sethuraman A, Taylor HR, Thomas GWC, Wellenreuther M, Luikart G. Genomics and conservation: Guidance from training to analyses and applications. Mol Ecol Resour 2024;24:e13893. [PMID: 37966259 DOI: 10.1111/1755-0998.13893] [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: 06/10/2022] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/16/2023]
15
Urrutia R, Espejo D, Evens N, Guerra M, Sühn T, Boese A, Hansen C, Fuentealba P, Illanes A, Poblete V. Clustering Methods for Vibro-Acoustic Sensing Features as a Potential Approach to Tissue Characterisation in Robot-Assisted Interventions. SENSORS (BASEL, SWITZERLAND) 2023;23:9297. [PMID: 38067671 PMCID: PMC10708300 DOI: 10.3390/s23239297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/06/2023] [Accepted: 11/11/2023] [Indexed: 12/18/2023]
16
Shu K, Cai C, Chen W, Ding J, Guo Z, Wei Y, Zhang W. Prognostic value and immune landscapes of immunogenic cell death-associated lncRNAs in lung adenocarcinoma. Sci Rep 2023;13:19151. [PMID: 37932413 PMCID: PMC10628222 DOI: 10.1038/s41598-023-46669-w] [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: 06/16/2023] [Accepted: 11/03/2023] [Indexed: 11/08/2023]  Open
17
Chambers EA, Bishop AP, Wang IJ. Individual-based landscape genomics for conservation: An analysis pipeline. Mol Ecol Resour 2023. [PMID: 37883295 DOI: 10.1111/1755-0998.13884] [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: 03/27/2023] [Revised: 08/18/2023] [Accepted: 10/03/2023] [Indexed: 10/28/2023]
18
Chen W, Shu K, Cai C, Ding J, Zhang X, Zhang W, Wang K. Prognostic value and immune landscapes of immunogenic cell death-related lncRNAs in hepatocellular carcinoma. Biosci Rep 2023;43:BSR20230634. [PMID: 37584192 PMCID: PMC10500227 DOI: 10.1042/bsr20230634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 05/31/2023] [Accepted: 08/15/2023] [Indexed: 08/17/2023]  Open
19
González-Peñas J, de Hoyos L, Díaz-Caneja CM, Andreu-Bernabeu Á, Stella C, Gurriarán X, Fañanás L, Bobes J, González-Pinto A, Crespo-Facorro B, Martorell L, Vilella E, Muntané G, Molto MD, Gonzalez-Piqueras JC, Parellada M, Arango C, Costas J. Recent natural selection conferred protection against schizophrenia by non-antagonistic pleiotropy. Sci Rep 2023;13:15500. [PMID: 37726359 PMCID: PMC10509162 DOI: 10.1038/s41598-023-42578-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 09/12/2023] [Indexed: 09/21/2023]  Open
20
Karjanto N. Investigating difficulties and enhancing understanding in linear algebra: Leveraging SageMath and ChatGPT for (orthogonal) diagonalization and singular value decomposition. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023;20:16551-16595. [PMID: 37920024 DOI: 10.3934/mbe.2023738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
21
Valette T, Leitwein M, Lascaux JM, Desmarais E, Berrebi P, Guinand B. Redundancy analysis, genome-wide association studies and the pigmentation of brown trout (Salmo trutta L.). JOURNAL OF FISH BIOLOGY 2023;102:96-118. [PMID: 36218076 DOI: 10.1111/jfb.15243] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
22
Feng S, Wan W, Li Y, Wang D, Ren G, Ma T, Ru D. Transcriptome-based analyses of adaptive divergence between two closely related spruce species on the Qinghai-Tibet plateau and adjacent regions. Mol Ecol 2023;32:476-491. [PMID: 36320185 DOI: 10.1111/mec.16758] [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: 04/11/2022] [Revised: 10/07/2022] [Accepted: 10/17/2022] [Indexed: 11/17/2022]
23
Gauff RPM, Lejeusne C, Greff S, Loisel S, Bohner O, Davoult D. Impact of in Situ Simulated Climate Change on Communities and Non-Indigenous Species: Two Climates, Two Responses. J Chem Ecol 2022;48:761-771. [PMID: 36100819 DOI: 10.1007/s10886-022-01380-4] [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: 04/19/2022] [Revised: 07/21/2022] [Accepted: 08/05/2022] [Indexed: 11/24/2022]
24
Qin X, Chiang CWK, Gaggiotti OE. Deciphering signatures of natural selection via deep learning. Brief Bioinform 2022;23:6686736. [PMID: 36056746 PMCID: PMC9487700 DOI: 10.1093/bib/bbac354] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/11/2022] [Accepted: 07/28/2022] [Indexed: 11/12/2022]  Open
25
Elhaik E. Principal Component Analyses (PCA)-based findings in population genetic studies are highly biased and must be reevaluated. Sci Rep 2022;12:14683. [PMID: 36038559 PMCID: PMC9424212 DOI: 10.1038/s41598-022-14395-4] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 06/06/2022] [Indexed: 12/29/2022]  Open
26
Tournebize R, Borner L, Manel S, Meynard CN, Vigouroux Y, Crouzillat D, Fournier C, Kassam M, Descombes P, Tranchant-Dubreuil C, Parrinello H, Kiwuka C, Sumirat U, Legnate H, Kambale JL, Sonké B, Mahinga JC, Musoli P, Janssens SB, Stoffelen P, de Kochko A, Poncet V. Ecological and genomic vulnerability to climate change across native populations of Robusta coffee (Coffea canephora). GLOBAL CHANGE BIOLOGY 2022;28:4124-4142. [PMID: 35527235 DOI: 10.1111/gcb.16191] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 02/11/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
27
Zhou W, Zhang W. A novel pyroptosis-related lncRNA prognostic signature associated with the immune microenvironment in lung squamous cell carcinoma. BMC Cancer 2022;22:694. [PMID: 35739504 PMCID: PMC9229145 DOI: 10.1186/s12885-022-09790-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/16/2022] [Indexed: 11/18/2022]  Open
28
Amandine C, Ebert D, Stukenbrock E, Rodríguez de la Vega RC, Tiffin P, Croll D, Tellier A. Unraveling coevolutionary dynamics using ecological genomics. Trends Genet 2022;38:1003-1012. [PMID: 35715278 DOI: 10.1016/j.tig.2022.05.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 05/08/2022] [Accepted: 05/10/2022] [Indexed: 11/27/2022]
29
Peña R, Schleuning M, Miñarro M. M, García D. Variable relationships between trait diversity and avian ecological functions in agroecosystems. Funct Ecol 2022. [DOI: 10.1111/1365-2435.14102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
30
Wang X, Zhang H, Ye J, Gao M, Jiang Q, Zhao T, Wang S, Mao W, Wang K, Wang Q, Chen X, Hou X, Han D. Genome Instability-Associated Long Non-Coding RNAs Reveal Biomarkers for Glioma Immunotherapy and Prognosis. Front Genet 2022;13:850888. [PMID: 35571034 PMCID: PMC9094631 DOI: 10.3389/fgene.2022.850888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022]  Open
31
Peter BM. A geometric relationship of F 2 , F 3 and F 4 -statistics with principal component analysis. Philos Trans R Soc Lond B Biol Sci 2022;377:20200413. [PMID: 35430884 PMCID: PMC9014194 DOI: 10.1098/rstb.2020.0413] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]  Open
32
Hellwig T, Abbo S, Ophir R. Phylogeny and disparate selection signatures suggest two genetically independent domestication events in pea (Pisum L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022;110:419-439. [PMID: 35061306 PMCID: PMC9303476 DOI: 10.1111/tpj.15678] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 01/15/2022] [Indexed: 05/25/2023]
33
Saitou M, Masuda N, Gokcumen O. Similarity-Based Analysis of Allele Frequency Distribution among Multiple Populations Identifies Adaptive Genomic Structural Variants. Mol Biol Evol 2022;39:msab313. [PMID: 34718708 PMCID: PMC8896759 DOI: 10.1093/molbev/msab313] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]  Open
34
Pélissié B, Chen YH, Cohen ZP, Crossley MS, Hawthorne DJ, Izzo V, Schoville SD. Genome resequencing reveals rapid, repeated evolution in the Colorado potato beetle. Mol Biol Evol 2022;39:6511499. [PMID: 35044459 PMCID: PMC8826761 DOI: 10.1093/molbev/msac016] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
35
Cheng JY, Stern AJ, Racimo F, Nielsen R. Detecting Selection in Multiple Populations by Modeling Ancestral Admixture Components. Mol Biol Evol 2022;39:msab294. [PMID: 34626111 PMCID: PMC8763095 DOI: 10.1093/molbev/msab294] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]  Open
36
Padakanti S, Tiong KL, Chen YB, Yeang CH. Genotypes of informative loci from 1000 Genomes data allude evolution and mixing of human populations. Sci Rep 2021;11:17741. [PMID: 34493766 PMCID: PMC8423758 DOI: 10.1038/s41598-021-97129-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 08/13/2021] [Indexed: 11/11/2022]  Open
37
A spectral theory for Wright's inbreeding coefficients and related quantities. PLoS Genet 2021;17:e1009665. [PMID: 34280184 PMCID: PMC8320931 DOI: 10.1371/journal.pgen.1009665] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 07/29/2021] [Accepted: 06/13/2021] [Indexed: 12/20/2022]  Open
38
Bourgeois YXC, Warren BH. An overview of current population genomics methods for the analysis of whole-genome resequencing data in eukaryotes. Mol Ecol 2021;30:6036-6071. [PMID: 34009688 DOI: 10.1111/mec.15989] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 04/26/2021] [Accepted: 05/11/2021] [Indexed: 01/01/2023]
39
The genomes of ancient date palms germinated from 2,000 y old seeds. Proc Natl Acad Sci U S A 2021;118:2025337118. [PMID: 33941705 PMCID: PMC8126781 DOI: 10.1073/pnas.2025337118] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]  Open
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Juma EO, Allan BF, Kim CH, Stone C, Dunlap C, Muturi EJ. The larval environment strongly influences the bacterial communities of Aedes triseriatus and Aedes japonicus (Diptera: Culicidae). Sci Rep 2021;11:7910. [PMID: 33846445 PMCID: PMC8042029 DOI: 10.1038/s41598-021-87017-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 03/22/2021] [Indexed: 02/01/2023]  Open
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Qi GA, Zheng YT, Lin F, Huang X, Duan LW, You Y, Liu H, Wang Y, Xu HM, Chen GB. EigenGWAS: An online visualizing and interactive application for detecting genomic signatures of natural selection. Mol Ecol Resour 2021;21:1732-1744. [PMID: 33665976 DOI: 10.1111/1755-0998.13370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 01/17/2021] [Accepted: 02/25/2021] [Indexed: 11/30/2022]
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Gain C, François O. LEA 3: Factor models in population genetics and ecological genomics with R. Mol Ecol Resour 2021;21:2738-2748. [PMID: 33638893 DOI: 10.1111/1755-0998.13366] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 01/21/2021] [Accepted: 02/23/2021] [Indexed: 12/12/2022]
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Cotoras DD, Suenaga M, Mikheyev AS. Intraspecific niche partition without speciation: individual level web polymorphism within a single island spider population. Proc Biol Sci 2021;288:20203138. [PMID: 33593195 PMCID: PMC7934906 DOI: 10.1098/rspb.2020.3138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]  Open
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Exploring Population Structure with Admixture Models and Principal Component Analysis. Methods Mol Biol 2021;2090:67-86. [PMID: 31975164 DOI: 10.1007/978-1-0716-0199-0_4] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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Adaptive introgression from maize has facilitated the establishment of teosinte as a noxious weed in Europe. Proc Natl Acad Sci U S A 2020;117:25618-25627. [PMID: 32989136 DOI: 10.1073/pnas.2006633117] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]  Open
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Skim-Sequencing Based Genotyping Reveals Genetic Divergence of the Wild and Domesticated Population of Black Tiger Shrimp (Penaeus monodon) in the Indo-Pacific Region. BIOLOGY 2020;9:biology9090277. [PMID: 32906759 PMCID: PMC7564732 DOI: 10.3390/biology9090277] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/25/2020] [Accepted: 09/02/2020] [Indexed: 11/16/2022]
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Van Cleemput E, Van Meerbeek K, Helsen K, Honnay O, Somers B. Remotely sensed plant traits can provide insights into ecosystem impacts of plant invasions: a case study covering two functionally different invaders. Biol Invasions 2020. [DOI: 10.1007/s10530-020-02338-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Pfeifer B, Alachiotis N, Pavlidis P, Schimek MG. Genome scans for selection and introgression based on k-nearest neighbour techniques. Mol Ecol Resour 2020;20:1597-1609. [PMID: 32639602 PMCID: PMC7689739 DOI: 10.1111/1755-0998.13221] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 06/22/2020] [Accepted: 06/29/2020] [Indexed: 12/27/2022]
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Ahmad HI, Ahmad MJ, Jabbir F, Ahmar S, Ahmad N, Elokil AA, Chen J. The Domestication Makeup: Evolution, Survival, and Challenges. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00103] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]  Open
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Nistor GI, Dillman RO. Cytokine network analysis of immune responses before and after autologous dendritic cell and tumor cell vaccine immunotherapies in a randomized trial. J Transl Med 2020;18:176. [PMID: 32316978 PMCID: PMC7171762 DOI: 10.1186/s12967-020-02328-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 04/02/2020] [Indexed: 02/08/2023]  Open
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