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For: Thornton KR, Jensen JD. Controlling the false-positive rate in multilocus genome scans for selection. Genetics 2007;175:737-50. [PMID: 17110489 PMCID: PMC1800626 DOI: 10.1534/genetics.106.064642] [Citation(s) in RCA: 138] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2006] [Accepted: 10/18/2006] [Indexed: 11/18/2022]  Open
Number Cited by Other Article(s)
1
Amin MR, Hasan M, DeGiorgio M. Digital Image Processing to Detect Adaptive Evolution. Mol Biol Evol 2024;41:msae242. [PMID: 39565932 PMCID: PMC11631197 DOI: 10.1093/molbev/msae242] [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: 03/20/2024] [Revised: 10/28/2024] [Accepted: 11/13/2024] [Indexed: 11/22/2024]  Open
2
Carvajal-Rodríguez A. iHDSel software: The price equation and the population stability index to detect genomic patterns compatible with selective sweeps. An example with SARS-CoV-2. Biol Methods Protoc 2024;9:bpae089. [PMID: 39679303 PMCID: PMC11646571 DOI: 10.1093/biomethods/bpae089] [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: 09/01/2024] [Revised: 11/19/2024] [Accepted: 11/25/2024] [Indexed: 12/17/2024]  Open
3
Soni V, Terbot JW, Versoza CJ, Pfeifer SP, Jensen JD. A whole-genome scan for evidence of recent positive and balancing selection in aye-ayes (Daubentonia madagascariensis) utilizing a well-fit evolutionary baseline model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.08.622667. [PMID: 39605496 PMCID: PMC11601216 DOI: 10.1101/2024.11.08.622667] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2024]
4
Gouy A, Wang X, Kapopoulou A, Neuenschwander S, Schmid E, Excoffier L, Heckel G. Genomes of Microtus Rodents Highlight the Importance of Olfactory and Immune Systems in Their Fast Radiation. Genome Biol Evol 2024;16:evae233. [PMID: 39445808 PMCID: PMC11579656 DOI: 10.1093/gbe/evae233] [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: 12/10/2023] [Revised: 10/02/2024] [Accepted: 10/07/2024] [Indexed: 10/25/2024]  Open
5
Marsh JI, Johri P. Biases in ARG-Based Inference of Historical Population Size in Populations Experiencing Selection. Mol Biol Evol 2024;41:msae118. [PMID: 38874402 PMCID: PMC11245712 DOI: 10.1093/molbev/msae118] [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: 04/15/2024] [Revised: 06/05/2024] [Accepted: 06/11/2024] [Indexed: 06/15/2024]  Open
6
Soni V, Jensen JD. Temporal challenges in detecting balancing selection from population genomic data. G3 (BETHESDA, MD.) 2024;14:jkae069. [PMID: 38551137 DOI: 10.1093/g3journal/jkae069] [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: 12/21/2023] [Revised: 12/21/2023] [Accepted: 03/19/2024] [Indexed: 04/28/2024]
7
Panigrahi M, Rajawat D, Nayak SS, Ghildiyal K, Sharma A, Jain K, Lei C, Bhushan B, Mishra BP, Dutt T. Landmarks in the history of selective sweeps. Anim Genet 2023;54:667-688. [PMID: 37710403 DOI: 10.1111/age.13355] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/28/2023] [Indexed: 09/16/2023]
8
Soni V, Johri P, Jensen JD. Evaluating power to detect recurrent selective sweeps under increasingly realistic evolutionary null models. Evolution 2023;77:2113-2127. [PMID: 37395482 PMCID: PMC10547124 DOI: 10.1093/evolut/qpad120] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/15/2023] [Accepted: 06/30/2023] [Indexed: 07/04/2023]
9
Mascarenhas R, Meirelles PM, Batalha-Filho H. Urbanization drives adaptive evolution in a Neotropical bird. Curr Zool 2023;69:607-619. [PMID: 37637315 PMCID: PMC10449428 DOI: 10.1093/cz/zoac066] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 08/16/2022] [Indexed: 08/29/2023]  Open
10
Ben-Jemaa S, Adam G, Boussaha M, Bardou P, Klopp C, Mandonnet N, Naves M. Whole genome sequencing reveals signals of adaptive admixture in Creole cattle. Sci Rep 2023;13:12155. [PMID: 37500674 PMCID: PMC10374910 DOI: 10.1038/s41598-023-38774-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 07/14/2023] [Indexed: 07/29/2023]  Open
11
Soni V, Johri P, Jensen JD. Evaluating power to detect recurrent selective sweeps under increasingly realistic evolutionary null models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.15.545166. [PMID: 37398347 PMCID: PMC10312679 DOI: 10.1101/2023.06.15.545166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
12
Nandakumar M, Lundberg M, Carlsson F, Råberg L. Balancing selection on the complement system of a wild rodent. BMC Ecol Evol 2023;23:21. [PMID: 37231383 DOI: 10.1186/s12862-023-02122-0] [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: 10/03/2022] [Accepted: 05/10/2023] [Indexed: 05/27/2023]  Open
13
Terbot JW, Johri P, Liphardt SW, Soni V, Pfeifer SP, Cooper BS, Good JM, Jensen JD. Developing an appropriate evolutionary baseline model for the study of SARS-CoV-2 patient samples. PLoS Pathog 2023;19:e1011265. [PMID: 37018331 PMCID: PMC10075409 DOI: 10.1371/journal.ppat.1011265] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023]  Open
14
Jensen JD. Population genetic concerns related to the interpretation of empirical outliers and the neglect of common evolutionary processes. Heredity (Edinb) 2023;130:109-110. [PMID: 36829044 PMCID: PMC9981695 DOI: 10.1038/s41437-022-00575-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 02/26/2023]  Open
15
Burny C, Nolte V, Dolezal M, Schlötterer C. Genome-wide selection signatures reveal widespread synergistic effects of two different stressors in Drosophila melanogaster. Proc Biol Sci 2022;289:20221857. [PMID: 36259211 PMCID: PMC9579754 DOI: 10.1098/rspb.2022.1857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
16
Kumar H, Panigrahi M, Panwar A, Rajawat D, Nayak SS, Saravanan KA, Kaisa K, Parida S, Bhushan B, Dutt T. Machine-Learning Prospects for Detecting Selection Signatures Using Population Genomics Data. J Comput Biol 2022;29:943-960. [PMID: 35639362 DOI: 10.1089/cmb.2021.0447] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]  Open
17
Johri P, Aquadro CF, Beaumont M, Charlesworth B, Excoffier L, Eyre-Walker A, Keightley PD, Lynch M, McVean G, Payseur BA, Pfeifer SP, Stephan W, Jensen JD. Recommendations for improving statistical inference in population genomics. PLoS Biol 2022;20:e3001669. [PMID: 35639797 PMCID: PMC9154105 DOI: 10.1371/journal.pbio.3001669] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]  Open
18
Abrams MB, Brem RB. Temperature-dependent genetics of thermotolerance between yeast species. Front Ecol Evol 2022;10:859904. [PMID: 36911365 PMCID: PMC10004143 DOI: 10.3389/fevo.2022.859904] [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] [Indexed: 11/13/2022]  Open
19
Salloum PM, Santure AW, Lavery SD, de Villemereuil P. Finding the adaptive needles in a population-structured haystack: a case study in a New Zealand mollusc. J Anim Ecol 2022;91:1209-1221. [PMID: 35318661 PMCID: PMC9311215 DOI: 10.1111/1365-2656.13692] [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: 04/04/2021] [Accepted: 03/09/2022] [Indexed: 11/30/2022]
20
Moinet A, Schlichta F, Peischl S, Excoffier L. Strong neutral sweeps occurring during a population contraction. Genetics 2022;220:6529544. [PMID: 35171980 PMCID: PMC8982045 DOI: 10.1093/genetics/iyac021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 01/22/2022] [Indexed: 11/14/2022]  Open
21
Morales-Arce AY, Johri P, Jensen JD. Inferring the distribution of fitness effects in patient-sampled and experimental virus populations: two case studies. Heredity (Edinb) 2022;128:79-87. [PMID: 34987185 PMCID: PMC8728706 DOI: 10.1038/s41437-021-00493-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 12/12/2021] [Accepted: 12/13/2021] [Indexed: 11/19/2022]  Open
22
Johri P, Stephan W, Jensen JD. Soft selective sweeps: Addressing new definitions, evaluating competing models, and interpreting empirical outliers. PLoS Genet 2022;18:e1010022. [PMID: 35202407 PMCID: PMC8870509 DOI: 10.1371/journal.pgen.1010022] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]  Open
23
Johri P, Charlesworth B, Howell EK, Lynch M, Jensen JD. Revisiting the notion of deleterious sweeps. Genetics 2021;219:iyab094. [PMID: 34125884 PMCID: PMC9101445 DOI: 10.1093/genetics/iyab094] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/08/2021] [Indexed: 11/14/2022]  Open
24
Charlesworth B, Jensen JD. Effects of Selection at Linked Sites on Patterns of Genetic Variability. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2021;52:177-197. [PMID: 37089401 PMCID: PMC10120885 DOI: 10.1146/annurev-ecolsys-010621-044528] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
25
Johri P, Riall K, Becher H, Excoffier L, Charlesworth B, Jensen JD. The Impact of Purifying and Background Selection on the Inference of Population History: Problems and Prospects. Mol Biol Evol 2021;38:2986-3003. [PMID: 33591322 PMCID: PMC8233493 DOI: 10.1093/molbev/msab050] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]  Open
26
Johri P, Riall K, Becher H, Excoffier L, Charlesworth B, Jensen JD. The impact of purifying and background selection on the inference of population history: problems and prospects. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33501439 PMCID: PMC7836109 DOI: 10.1101/2020.04.28.066365] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
27
Population Genomics on the Fly: Recent Advances in Drosophila. Methods Mol Biol 2021;2090:357-396. [PMID: 31975175 DOI: 10.1007/978-1-0716-0199-0_15] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
28
Morales-Arce AY, Sabin SJ, Stone AC, Jensen JD. The population genomics of within-host Mycobacterium tuberculosis. Heredity (Edinb) 2020;126:1-9. [PMID: 33060846 DOI: 10.1038/s41437-020-00377-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/02/2020] [Accepted: 10/03/2020] [Indexed: 11/09/2022]  Open
29
Harris RB, Jensen JD. Considering Genomic Scans for Selection as Coalescent Model Choice. Genome Biol Evol 2020;12:871-877. [PMID: 32396636 PMCID: PMC7313662 DOI: 10.1093/gbe/evaa093] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2020] [Indexed: 12/17/2022]  Open
30
Johri P, Charlesworth B, Jensen JD. Toward an Evolutionarily Appropriate Null Model: Jointly Inferring Demography and Purifying Selection. Genetics 2020;215:173-192. [PMID: 32152045 PMCID: PMC7198275 DOI: 10.1534/genetics.119.303002] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/05/2020] [Indexed: 01/27/2023]  Open
31
Ebrahimi A, Lawson SS, McKenna JR, Jacobs DF. Morpho-Physiological and Genomic Evaluation of Juglans Species Reveals Regional Maladaptation to Cold Stress. FRONTIERS IN PLANT SCIENCE 2020;11:229. [PMID: 32210997 PMCID: PMC7077431 DOI: 10.3389/fpls.2020.00229] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 02/14/2020] [Indexed: 05/02/2023]
32
Scossa F, Fernie AR. The evolution of metabolism: How to test evolutionary hypotheses at the genomic level. Comput Struct Biotechnol J 2020;18:482-500. [PMID: 32180906 PMCID: PMC7063335 DOI: 10.1016/j.csbj.2020.02.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 01/21/2023]  Open
33
Apata M, Pfeifer SP. Recent population genomic insights into the genetic basis of arsenic tolerance in humans: the difficulties of identifying positively selected loci in strongly bottlenecked populations. Heredity (Edinb) 2020;124:253-262. [PMID: 31776483 PMCID: PMC6972707 DOI: 10.1038/s41437-019-0285-0] [Citation(s) in RCA: 4] [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: 06/06/2019] [Revised: 10/22/2019] [Accepted: 11/13/2019] [Indexed: 02/06/2023]  Open
34
Koropoulis A, Alachiotis N, Pavlidis P. Detecting Positive Selection in Populations Using Genetic Data. Methods Mol Biol 2020;2090:87-123. [PMID: 31975165 DOI: 10.1007/978-1-0716-0199-0_5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
35
Cullingham CI, Peery RM, Fortier CE, Mahon EL, Cooke JEK, Coltman DW. Linking genotype to phenotype to identify genetic variation relating to host susceptibility in the mountain pine beetle system. Evol Appl 2020;13:48-61. [PMID: 31892943 PMCID: PMC6935584 DOI: 10.1111/eva.12773] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 01/09/2019] [Accepted: 01/13/2019] [Indexed: 12/24/2022]  Open
36
Thornton KR. Polygenic Adaptation to an Environmental Shift: Temporal Dynamics of Variation Under Gaussian Stabilizing Selection and Additive Effects on a Single Trait. Genetics 2019;213:1513-1530. [PMID: 31653678 PMCID: PMC6893385 DOI: 10.1534/genetics.119.302662] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 10/21/2019] [Indexed: 11/26/2022]  Open
37
Kapopoulou A, Pfeifer SP, Jensen JD, Laurent S. The Demographic History of African Drosophila melanogaster. Genome Biol Evol 2019;10:2338-2342. [PMID: 30169784 PMCID: PMC6363051 DOI: 10.1093/gbe/evy185] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2018] [Indexed: 11/14/2022]  Open
38
The population genetics of crypsis in vertebrates: recent insights from mice, hares, and lizards. Heredity (Edinb) 2019;124:1-14. [PMID: 31399719 PMCID: PMC6906368 DOI: 10.1038/s41437-019-0257-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 07/16/2019] [Accepted: 07/25/2019] [Indexed: 12/22/2022]  Open
39
Kjeldsen SR, Raadsma HW, Leigh KA, Tobey JR, Phalen D, Krockenberger A, Ellis WA, Hynes E, Higgins DP, Zenger KR. Genomic comparisons reveal biogeographic and anthropogenic impacts in the koala (Phascolarctos cinereus): a dietary-specialist species distributed across heterogeneous environments. Heredity (Edinb) 2019;122:525-544. [PMID: 30209291 PMCID: PMC6461856 DOI: 10.1038/s41437-018-0144-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 06/07/2018] [Accepted: 08/01/2018] [Indexed: 02/05/2023]  Open
40
Jensen JD, Payseur BA, Stephan W, Aquadro CF, Lynch M, Charlesworth D, Charlesworth B. The importance of the Neutral Theory in 1968 and 50 years on: A response to Kern and Hahn 2018. Evolution 2019;73:111-114. [PMID: 30460993 PMCID: PMC6496948 DOI: 10.1111/evo.13650] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 11/09/2018] [Indexed: 01/31/2023]
41
Bay RA, Harrigan RJ, Buermann W, Underwood VL, Gibbs HL, Smith TB, Ruegg K. Response to Comment on "Genomic signals of selection predict climate-driven population declines in a migratory bird". Science 2018;361:361/6401/eaat7279. [PMID: 30072513 DOI: 10.1126/science.aat7956] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/05/2018] [Indexed: 11/02/2022]
42
Wang MS, Otecko NO, Wang S, Wu DD, Yang MM, Xu YL, Murphy RW, Peng MS, Zhang YP. An Evolutionary Genomic Perspective on the Breeding of Dwarf Chickens. Mol Biol Evol 2018;34:3081-3088. [PMID: 28961939 DOI: 10.1093/molbev/msx227] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]  Open
43
Weigand H, Leese F. Detecting signatures of positive selection in non-model species using genomic data. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly007] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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LaBonte NR, Zhao P, Woeste K. Signatures of Selection in the Genomes of Chinese Chestnut (Castanea mollissima Blume): The Roots of Nut Tree Domestication. FRONTIERS IN PLANT SCIENCE 2018;9:810. [PMID: 29988533 PMCID: PMC6026767 DOI: 10.3389/fpls.2018.00810] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/25/2018] [Indexed: 05/18/2023]
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Population Genomics of Colonization and Invasion. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_22] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Coalescent Processes with Skewed Offspring Distributions and Nonequilibrium Demography. Genetics 2017;208:323-338. [PMID: 29127263 DOI: 10.1534/genetics.117.300499] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 10/30/2017] [Indexed: 11/18/2022]  Open
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Pfeifer SP. The Demographic and Adaptive History of the African Green Monkey. Mol Biol Evol 2017;34:1055-1065. [PMID: 28199709 DOI: 10.1093/molbev/msx056] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]  Open
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Refining the Use of Linkage Disequilibrium as a Robust Signature of Selective Sweeps. Genetics 2017;203:1807-25. [PMID: 27516617 DOI: 10.1534/genetics.115.185900] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 04/05/2016] [Indexed: 12/12/2022]  Open
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Pavlidis P, Alachiotis N. A survey of methods and tools to detect recent and strong positive selection. ACTA ACUST UNITED AC 2017;24:7. [PMID: 28405579 PMCID: PMC5385031 DOI: 10.1186/s40709-017-0064-0] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 03/29/2017] [Indexed: 01/25/2023]
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Freedman AH, Lohmueller KE, Wayne RK. Evolutionary History, Selective Sweeps, and Deleterious Variation in the Dog. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2016. [DOI: 10.1146/annurev-ecolsys-121415-032155] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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