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For: Spence JP, Song YS. Inference and analysis of population-specific fine-scale recombination maps across 26 diverse human populations. Sci Adv 2019;5:eaaw9206. [PMID: 31681842 PMCID: PMC6810367 DOI: 10.1126/sciadv.aaw9206] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 09/13/2019] [Indexed: 05/28/2023]
Number Cited by Other Article(s)
1
Good BH, Bhatt AS, McDonald MJ. Unraveling the tempo and mode of horizontal gene transfer in bacteria. Trends Microbiol 2025:S0966-842X(25)00100-3. [PMID: 40274494 DOI: 10.1016/j.tim.2025.03.009] [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: 11/23/2024] [Revised: 02/26/2025] [Accepted: 03/20/2025] [Indexed: 04/26/2025]
2
Strütt S, Excoffier L, Peischl S. A generalized structured coalescent for purifying selection without recombination. Genetics 2025;229:iyaf013. [PMID: 39862229 DOI: 10.1093/genetics/iyaf013] [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: 11/07/2024] [Revised: 12/18/2024] [Accepted: 12/30/2024] [Indexed: 01/27/2025]  Open
3
Zhang H, Zhang P, Niu Y, Tao T, Liu G, Dong C, Zheng Z, Zhang Z, Li Y, Niu Z, Liu W, Guo Z, Hu S, Yang Y, Li M, Sun H, Renner SS, Liu J. Genetic basis of camouflage in an alpine plant and its long-term co-evolution with an insect herbivore. Nat Ecol Evol 2025;9:628-638. [PMID: 40065027 DOI: 10.1038/s41559-025-02653-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 01/31/2025] [Indexed: 04/09/2025]
4
Ishigohoka J, Liedvogel M. High-recombining genomic regions affect demography inference based on ancestral recombination graphs. Genetics 2025;229:iyaf004. [PMID: 39790013 PMCID: PMC11912872 DOI: 10.1093/genetics/iyaf004] [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: 02/05/2024] [Accepted: 12/23/2024] [Indexed: 01/12/2025]  Open
5
Barroso GV, Ragsdale AP. A model for background selection in non-equilibrium populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.19.639084. [PMID: 40027808 PMCID: PMC11870586 DOI: 10.1101/2025.02.19.639084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/05/2025]
6
Malinsky M, Talbi M, Zhou C, Maurer N, Sacco S, Shapiro B, Peichel CL, Seehausen O, Salzburger W, Weber JN, Bolnick DI, Green RE, Durbin R. Hi-reComb: constructing recombination maps from bulk gamete Hi-C sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.06.641907. [PMID: 40161681 PMCID: PMC11952307 DOI: 10.1101/2025.03.06.641907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/02/2025]
7
Talbi M, Turner GF, Malinsky M. Rapid evolution of recombination landscapes during the divergence of cichlid ecotypes in Lake Masoko. Evolution 2025;79:364-379. [PMID: 39589917 DOI: 10.1093/evolut/qpae169] [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: 04/30/2024] [Revised: 11/06/2024] [Accepted: 11/25/2024] [Indexed: 11/28/2024]
8
Lalli JL, Bortvin AN, McCoy RC, Werling DM. A T2T-CHM13 recombination map and globally diverse haplotype reference panel improves phasing and imputation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.24.639687. [PMID: 40060455 PMCID: PMC11888259 DOI: 10.1101/2025.02.24.639687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/20/2025]
9
Mowlaei ME, Li C, Jamialahmadi O, Dias R, Chen J, Jamialahmadi B, Rebbeck TR, Carnevale V, Kumar S, Shi X. STICI: Split-Transformer with integrated convolutions for genotype imputation. Nat Commun 2025;16:1218. [PMID: 39890780 PMCID: PMC11785734 DOI: 10.1038/s41467-025-56273-3] [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: 04/23/2024] [Accepted: 01/08/2025] [Indexed: 02/03/2025]  Open
10
van den Belt S, Alachiotis N. Fast and accurate deep learning scans for signatures of natural selection in genomes using FASTER-NN. Commun Biol 2025;8:58. [PMID: 39814854 PMCID: PMC11735897 DOI: 10.1038/s42003-025-07480-7] [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: 07/04/2024] [Accepted: 01/07/2025] [Indexed: 01/18/2025]  Open
11
Topaloudis A, Cumer T, Lavanchy E, Ducrest AL, Simon C, Machado AP, Paposhvili N, Roulin A, Goudet J. The recombination landscape of the barn owl, from families to populations. Genetics 2025;229:1-50. [PMID: 39545468 PMCID: PMC11708917 DOI: 10.1093/genetics/iyae190] [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: 07/26/2024] [Accepted: 11/01/2024] [Indexed: 11/17/2024]  Open
12
Soni V, Versoza CJ, Terbot JW, Jensen JD, Pfeifer SP. Inferring fine-scale mutation and recombination rate maps in aye-ayes ( Daubentonia madagascariensis ). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.28.630620. [PMID: 39763842 PMCID: PMC11703150 DOI: 10.1101/2024.12.28.630620] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2025]
13
Schield DR, Carter JK, Scordato ESC, Levin II, Wilkins MR, Mueller SA, Gompert Z, Nosil P, Wolf JBW, Safran RJ. Sexual selection promotes reproductive isolation in barn swallows. Science 2024;386:eadj8766. [PMID: 39666856 DOI: 10.1126/science.adj8766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 06/25/2024] [Accepted: 10/11/2024] [Indexed: 12/14/2024]
14
Ishigohoka J, Bascón-Cardozo K, Bours A, Fuß J, Rhie A, Mountcastle J, Haase B, Chow W, Collins J, Howe K, Uliano-Silva M, Fedrigo O, Jarvis ED, Pérez-Tris J, Illera JC, Liedvogel M. Distinct patterns of genetic variation at low-recombining genomic regions represent haplotype structure. Evolution 2024;78:1916-1935. [PMID: 39208288 DOI: 10.1093/evolut/qpae117] [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: 05/06/2024] [Revised: 07/26/2024] [Accepted: 09/24/2024] [Indexed: 09/04/2024]
15
Amorim CEG, Di C, Lin M, Marsden C, Del Carpio CA, Mah JC, Robinson J, Kim BY, Mooney JA, Cornejo OE, Lohmueller KE. Evolutionary consequences of domestication on the selective effects of new amino acid changing mutations in canids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.13.623529. [PMID: 39605619 PMCID: PMC11601280 DOI: 10.1101/2024.11.13.623529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2024]
16
Lyulina AS, Liu Z, Good BH. Linkage equilibrium between rare mutations. Genetics 2024;228:iyae145. [PMID: 39222343 PMCID: PMC11538400 DOI: 10.1093/genetics/iyae145] [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: 04/05/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024]  Open
17
Zhang J, Lyu H, Chen J, Cao X, Du R, Ma L, Wang N, Zhu Z, Rao J, Wang J, Zhong K, Lyu Y, Wang Y, Lin T, Zhou Y, Zhou Y, Zhu G, Fei Z, Klee H, Huang S. Releasing a sugar brake generates sweeter tomato without yield penalty. Nature 2024;635:647-656. [PMID: 39537922 PMCID: PMC11578880 DOI: 10.1038/s41586-024-08186-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 10/09/2024] [Indexed: 11/16/2024]
18
Escuer P, Guirao-Rico S, Arnedo MA, Sánchez-Gracia A, Rozas J. Population Genomics of Adaptive Radiations: Exceptionally High Levels of Genetic Diversity and Recombination in an Endemic Spider From the Canary Islands. Mol Ecol 2024;33:e17547. [PMID: 39400446 DOI: 10.1111/mec.17547] [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: 04/17/2024] [Revised: 08/26/2024] [Accepted: 09/24/2024] [Indexed: 10/15/2024]
19
van den Belt S, Zhao H, Alachiotis N. Scalable CNN-based classification of selective sweeps using derived allele frequencies. Bioinformatics 2024;40:ii29-ii36. [PMID: 39230693 PMCID: PMC11373383 DOI: 10.1093/bioinformatics/btae385] [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] [Indexed: 09/05/2024]  Open
20
Takayama J, Makino S, Funayama T, Ueki M, Narita A, Murakami K, Orui M, Ishikuro M, Obara T, Kuriyama S, Yamamoto M, Tamiya G. A fine-scale genetic map of the Japanese population. Clin Genet 2024;106:284-292. [PMID: 38719617 DOI: 10.1111/cge.14536] [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: 10/03/2023] [Revised: 04/13/2024] [Accepted: 04/15/2024] [Indexed: 08/13/2024]
21
Ohadi M, Arabfard M, Khamse S, Alizadeh S, Vafadar S, Bayat H, Tajeddin N, Maddi AMA, Delbari A, Khorram Khorshid HR. Novel crossover and recombination hotspots massively spread across primate genomes. Biol Direct 2024;19:70. [PMID: 39169390 PMCID: PMC11340189 DOI: 10.1186/s13062-024-00508-8] [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: 05/09/2024] [Accepted: 07/29/2024] [Indexed: 08/23/2024]  Open
22
Li L, Comi TJ, Bierman RF, Akey JM. Recurrent gene flow between Neanderthals and modern humans over the past 200,000 years. Science 2024;385:eadi1768. [PMID: 38991054 DOI: 10.1126/science.adi1768] [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: 07/05/2023] [Accepted: 05/14/2024] [Indexed: 07/13/2024]
23
Dutheil JY. On the estimation of genome-average recombination rates. Genetics 2024;227:iyae051. [PMID: 38565705 PMCID: PMC11232287 DOI: 10.1093/genetics/iyae051] [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: 01/22/2024] [Revised: 03/13/2024] [Accepted: 03/20/2024] [Indexed: 04/04/2024]  Open
24
Joseph J, Prentout D, Laverré A, Tricou T, Duret L. High prevalence of PRDM9-independent recombination hotspots in placental mammals. Proc Natl Acad Sci U S A 2024;121:e2401973121. [PMID: 38809707 PMCID: PMC11161765 DOI: 10.1073/pnas.2401973121] [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: 02/08/2024] [Accepted: 04/26/2024] [Indexed: 05/31/2024]  Open
25
Chen Z, Zhou M, Sun Y, Tang X, Zhang Z, Huang L. Exploration of Genome-Wide Recombination Rate Variation Patterns at Different Scales in Pigs. Animals (Basel) 2024;14:1345. [PMID: 38731349 PMCID: PMC11083071 DOI: 10.3390/ani14091345] [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: 04/05/2024] [Revised: 04/27/2024] [Accepted: 04/28/2024] [Indexed: 05/13/2024]  Open
26
Liu X, Koyama S, Tomizuka K, Takata S, Ishikawa Y, Ito S, Kosugi S, Suzuki K, Hikino K, Koido M, Koike Y, Horikoshi M, Gakuhari T, Ikegawa S, Matsuda K, Momozawa Y, Ito K, Kamatani Y, Terao C. Decoding triancestral origins, archaic introgression, and natural selection in the Japanese population by whole-genome sequencing. SCIENCE ADVANCES 2024;10:eadi8419. [PMID: 38630824 PMCID: PMC11023554 DOI: 10.1126/sciadv.adi8419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 03/07/2024] [Indexed: 04/19/2024]
27
Lyulina AS, Liu Z, Good BH. Linkage equilibrium between rare mutations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.28.587282. [PMID: 38617331 PMCID: PMC11014483 DOI: 10.1101/2024.03.28.587282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
28
Aw AJ, Spence JP, Song YS. A SIMPLE AND FLEXIBLE TEST OF SAMPLE EXCHANGEABILITY WITH APPLICATIONS TO STATISTICAL GENOMICS. Ann Appl Stat 2024;18:858-881. [PMID: 38784669 PMCID: PMC11115382 DOI: 10.1214/23-aoas1817] [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: 05/25/2024]
29
Jiang Z, Zang W, Ericson PGP, Song G, Wu S, Feng S, Drovetski SV, Liu G, Zhang D, Saitoh T, Alström P, Edwards SV, Lei F, Qu Y. Gene flow and an anomaly zone complicate phylogenomic inference in a rapidly radiated avian family (Prunellidae). BMC Biol 2024;22:49. [PMID: 38413944 PMCID: PMC10900574 DOI: 10.1186/s12915-024-01848-7] [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: 11/11/2023] [Accepted: 02/15/2024] [Indexed: 02/29/2024]  Open
30
Hoge C, de Manuel M, Mahgoub M, Okami N, Fuller Z, Banerjee S, Baker Z, McNulty M, Andolfatto P, Macfarlan TS, Schumer M, Tzika AC, Przeworski M. Patterns of recombination in snakes reveal a tug-of-war between PRDM9 and promoter-like features. Science 2024;383:eadj7026. [PMID: 38386752 DOI: 10.1126/science.adj7026] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 01/04/2024] [Indexed: 02/24/2024]
31
Ariad D, Madjunkova S, Madjunkov M, Chen S, Abramov R, Librach C, McCoy RC. Aberrant landscapes of maternal meiotic crossovers contribute to aneuploidies in human embryos. Genome Res 2024;34:70-84. [PMID: 38071472 PMCID: PMC10903951 DOI: 10.1101/gr.278168.123] [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: 06/12/2023] [Accepted: 11/21/2023] [Indexed: 12/19/2023]
32
Bascón-Cardozo K, Bours A, Manthey G, Durieux G, Dutheil JY, Pruisscher P, Odenthal-Hesse L, Liedvogel M. Fine-Scale Map Reveals Highly Variable Recombination Rates Associated with Genomic Features in the Eurasian Blackcap. Genome Biol Evol 2024;16:evad233. [PMID: 38198800 PMCID: PMC10781513 DOI: 10.1093/gbe/evad233] [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] [Accepted: 12/12/2023] [Indexed: 01/12/2024]  Open
33
Versoza CJ, Weiss S, Johal R, La Rosa B, Jensen JD, Pfeifer SP. Novel Insights into the Landscape of Crossover and Noncrossover Events in Rhesus Macaques (Macaca mulatta). Genome Biol Evol 2024;16:evad223. [PMID: 38051960 PMCID: PMC10773715 DOI: 10.1093/gbe/evad223] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/04/2023] [Accepted: 11/28/2023] [Indexed: 12/07/2023]  Open
34
Dinh BL, Tang E, Taparra K, Nakatsuka N, Chen F, Chiang CWK. Recombination map tailored to Native Hawaiians may improve robustness of genomic scans for positive selection. Hum Genet 2024;143:85-99. [PMID: 38157018 PMCID: PMC10794367 DOI: 10.1007/s00439-023-02625-2] [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: 09/02/2023] [Accepted: 11/25/2023] [Indexed: 01/03/2024]
35
Ariad D, Madjunkova S, Madjunkov M, Chen S, Abramov R, Librach C, McCoy RC. Aberrant landscapes of maternal meiotic crossovers contribute to aneuploidies in human embryos. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.07.543910. [PMID: 37333422 PMCID: PMC10274764 DOI: 10.1101/2023.06.07.543910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
36
Spence JP, Zeng T, Mostafavi H, Pritchard JK. Scaling the discrete-time Wright-Fisher model to biobank-scale datasets. Genetics 2023;225:iyad168. [PMID: 37724741 PMCID: PMC10627256 DOI: 10.1093/genetics/iyad168] [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: 06/01/2023] [Revised: 06/01/2023] [Accepted: 09/08/2023] [Indexed: 09/21/2023]  Open
37
Baker Z, Przeworski M, Sella G. Down the Penrose stairs, or how selection for fewer recombination hotspots maintains their existence. eLife 2023;12:e83769. [PMID: 37830496 PMCID: PMC10703446 DOI: 10.7554/elife.83769] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/12/2023] [Indexed: 10/14/2023]  Open
38
Pivirotto AM, Platt A, Patel R, Kumar S, Hey J. Analyses of allele age and fitness impact reveal human beneficial alleles to be older than neutral controls. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.09.561569. [PMID: 37873438 PMCID: PMC10592680 DOI: 10.1101/2023.10.09.561569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
39
Liu X, Matsunami M, Horikoshi M, Ito S, Ishikawa Y, Suzuki K, Momozawa Y, Niida S, Kimura R, Ozaki K, Maeda S, Imamura M, Terao C. Natural Selection Signatures in the Hondo and Ryukyu Japanese Subpopulations. Mol Biol Evol 2023;40:msad231. [PMID: 37903429 PMCID: PMC10615566 DOI: 10.1093/molbev/msad231] [Citation(s) in RCA: 4] [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] [Received: 03/27/2023] [Revised: 09/20/2023] [Accepted: 10/06/2023] [Indexed: 11/01/2023]  Open
40
Nait Saada J, Tsangalidou Z, Stricker M, Palamara PF. Inference of Coalescence Times and Variant Ages Using Convolutional Neural Networks. Mol Biol Evol 2023;40:msad211. [PMID: 37738175 PMCID: PMC10581698 DOI: 10.1093/molbev/msad211] [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: 03/06/2023] [Revised: 09/11/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023]  Open
41
Heraghty SD, Jackson JM, Lozier JD. Whole genome analyses reveal weak signatures of population structure and environmentally associated local adaptation in an important North American pollinator, the bumble bee Bombus vosnesenskii. Mol Ecol 2023;32:5479-5497. [PMID: 37702957 DOI: 10.1111/mec.17125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 08/21/2023] [Accepted: 08/24/2023] [Indexed: 09/14/2023]
42
Li Z, Liu X, Wang C, Li Z, Jiang B, Zhang R, Tong L, Qu Y, He S, Chen H, Mao Y, Li Q, Pook T, Wu Y, Zan Y, Zhang H, Li L, Wen K, Chen Y. The pig pangenome provides insights into the roles of coding structural variations in genetic diversity and adaptation. Genome Res 2023;33:1833-1847. [PMID: 37914227 PMCID: PMC10691484 DOI: 10.1101/gr.277638.122] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 09/12/2023] [Indexed: 11/03/2023]
43
Bours A, Pruisscher P, Bascón-Cardozo K, Odenthal-Hesse L, Liedvogel M. The blackcap (Sylvia atricapilla) genome reveals a recent accumulation of LTR retrotransposons. Sci Rep 2023;13:16471. [PMID: 37777595 PMCID: PMC10542752 DOI: 10.1038/s41598-023-43090-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 09/19/2023] [Indexed: 10/02/2023]  Open
44
Dinh BL, Tang E, Taparra K, Nakatsuka N, Chen F, Chiang CWK. Recombination map tailored to Native Hawaiians improves robustness of genomic scans for positive selection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.12.548735. [PMID: 37503129 PMCID: PMC10370006 DOI: 10.1101/2023.07.12.548735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
45
He H, Yang H, Foo R, Chan W, Zhu F, Liu Y, Zhou X, Ma L, Wang LF, Zhai W. Population genomic analysis reveals distinct demographics and recent adaptation in the black flying fox (Pteropus alecto). J Genet Genomics 2023;50:554-562. [PMID: 37182682 DOI: 10.1016/j.jgg.2023.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 05/03/2023] [Accepted: 05/03/2023] [Indexed: 05/16/2023]
46
Hoge C, de Manuel M, Mahgoub M, Okami N, Fuller Z, Banerjee S, Baker Z, McNulty M, Andolfatto P, Macfarlan TS, Schumer M, Tzika AC, Przeworski M. Patterns of recombination in snakes reveal a tug of war between PRDM9 and promoter-like features. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.11.548536. [PMID: 37502971 PMCID: PMC10369914 DOI: 10.1101/2023.07.11.548536] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
47
Naseri A, Yue W, Zhang S, Zhi D. Fast inference of genetic recombination rates in biobank scale data. Genome Res 2023;33:1015-1022. [PMID: 37349109 PMCID: PMC10538484 DOI: 10.1101/gr.277676.123] [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: 01/06/2023] [Accepted: 06/09/2023] [Indexed: 06/24/2023]
48
Wang N, Cao S, Liu Z, Xiao H, Hu J, Xu X, Chen P, Ma Z, Ye J, Chai L, Guo W, Larkin RM, Xu Q, Morrell PL, Zhou Y, Deng X. Genomic conservation of crop wild relatives: A case study of citrus. PLoS Genet 2023;19:e1010811. [PMID: 37339133 DOI: 10.1371/journal.pgen.1010811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 06/01/2023] [Indexed: 06/22/2023]  Open
49
Colbran LL, Ramos-Almodovar FC, Mathieson I. A gene-level test for directional selection on gene expression. Genetics 2023;224:iyad060. [PMID: 37036411 PMCID: PMC10213495 DOI: 10.1093/genetics/iyad060] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 01/11/2023] [Accepted: 03/31/2023] [Indexed: 04/11/2023]  Open
50
Spence JP, Zeng T, Mostafavi H, Pritchard JK. Scaling the Discrete-time Wright Fisher model to biobank-scale datasets. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.19.541517. [PMID: 37293115 PMCID: PMC10245735 DOI: 10.1101/2023.05.19.541517] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
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