Searching journal content for articles similar to McEvoy et al. 21 (6): 821.

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Research: Comparative genomics of Cryptosporidium parvum reveals the emergence of an outbreak-associated population in Europe and its spread to the United States
- Greta Bellinzona,
- Tiago Nardi,
- Michele Castelli,
- Gherard Batisti Biffignandi,
- Karim Adjou,
- Martha Betson,
- Yannick Blanchard,
- Ioana Bujila,
- Rachel Chalmers,
- Rebecca Davidson,
- Nicoletta D'Avino,
- Tuulia Enbom,
- Jacinto Gomes,
- Gregory Karadjian,
- Christian Klotz,
- Emma Östlund,
- Judith Plutzer,
- Ruska Rimhanen-Finne,
- Guy Robinson,
- Anna Rosa Sannella,
- Jacek Sroka,
- Christen Rune Stensvold,
- Karin Troell,
- Paolo Vatta,
- Barbora Zalewska,
- Claudio Bandi,
- Davide Sassera,
- and Simone M. Cacciò
Genome Res. June 2024 34: 877-887; Published in Advance July 8, 2024, doi:10.1101/gr.278830.123
...isolates from four continents (Africa, Asia, Europe, and North America) and from the two major zoonotic gp60 groups (IIa and IId). Detailed information regarding the data set composition is provided in Supplemental Table S1.Genetic variability among isolatesBy comparing the 140 isolates to the IOWA...
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Research: Population genomics and the evolution of virulence in the fungal pathogen Cryptococcus neoformans
- Christopher A. Desjardins,
- Charles Giamberardino,
- Sean M. Sykes,
- Chen-Hsin Yu,
- Jennifer L. Tenor,
- Yuan Chen,
- Timothy Yang,
- Alexander M. Jones,
- Sheng Sun,
- Miriam R. Haverkamp,
- Joseph Heitman,
- Anastasia P. Litvintseva,
- John R. Perfect,
- and Christina A. Cuomo
Genome Res. July 2017 27: 1207-1219; Published in Advance June 13, 2017, doi:10.1101/gr.218727.116
...that causes approximately 625,000 deaths per year from nervous system infections. Here, we leveraged a unique, genetically diverse population of C. neoformans from sub-Saharan Africa, commonly isolated from mopane trees, to determine how selective pressures in the environment coincidentally adapted C...
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Research: The population genomics of rhesus macaques (Macaca mulatta) based on whole-genome sequences
- Cheng Xue,
- Muthuswamy Raveendran,
- R. Alan Harris,
- Gloria L. Fawcett,
- Xiaoming Liu,
- Simon White,
- Mahmoud Dahdouli,
- David Rio Deiros,
- Jennifer E. Below,
- William Salerno,
- Laura Cox,
- Guoping Fan,
- Betsy Ferguson,
- Julie Horvath,
- Zach Johnson,
- Sree Kanthaswamy,
- H. Michael Kubisch,
- Dahai Liu,
- Michael Platt,
- David G. Smith,
- Binghua Sun,
- Eric J. Vallender,
- Feng Wang,
- Roger W. Wiseman,
- Rui Chen,
- Donna M. Muzny,
- Richard A. Gibbs,
- Fuli Yu,
- and Jeffrey Rogers
Genome Res. December 2016 26: 1651-1662; Published in Advance October 17, 2016, doi:10.1101/gr.204255.116
...and imputation using SNPTools. Following likelihood estimation and imputation, we removed SNVs with homozygous alternative alleles in the reference animal 17573 (n = 16,078 or 0.037%), and removed another 44,174 SNPs that had alternative allele frequency = 0 in theVCF file. This produced a final data set and SNV...
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LETTER: Origin and primary dispersal of the Mycobacterium tuberculosis Beijing genotype: Clues from human phylogeography
- Igor Mokrousov,
- Ho Minh Ly,
- Tatiana Otten,
- Nguyen Ngoc Lan,
- Boris Vyshnevskyi,
- Sven Hoffner,
- and Olga Narvskaya
Genome Res. October 2005 15: 1357-1364; Published in Advance September 16, 2005, doi:10.1101/gr.3840605
...a recent dissemination in this area. To estimate a geographical component of the variation in the Beijing genotype and, ultimately, to partly reconstruct its dispersals, we further compared the four local populations of the Beijing strains (Russia, Vietnam, China, and South Africa). The Bangladesh sample...
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Method: A reduced representation approach to population genetic analyses and applications to human evolution
- Francesca Luca,
- Richard R. Hudson,
- David B. Witonsky,
- and Anna Di Rienzo
Genome Res. July 2011 21: 1087-1098; Published in Advance May 31, 2011, doi:10.1101/gr.119792.110
...a total of 18 human populations, our approach allowed sampling regions that are largely overlapping across individuals and that are representative of the entire . The resequencing data were used to test the serial founder model of human dispersal and to estimate the time of the Out of Africa migration...
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Resource: A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes
- Ran Li,
- Mian Gong,
- Xinmiao Zhang,
- Fei Wang,
- Zhenyu Liu,
- Lei Zhang,
- Qimeng Yang,
- Yuan Xu,
- Mengsi Xu,
- Huanhuan Zhang,
- Yunfeng Zhang,
- Xuelei Dai,
- Yuanpeng Gao,
- Zhuangbiao Zhang,
- Wenwen Fang,
- Yuta Yang,
- Weiwei Fu,
- Chunna Cao,
- Peng Yang,
- Zeinab Amiri Ghanatsaman,
- Niloufar Jafarpour Negari,
- Hojjat Asadollahpour Nanaei,
- Xiangpeng Yue,
- Yuxuan Song,
- Xianyong Lan,
- Weidong Deng,
- Xihong Wang,
- Chuanying Pan,
- Ruidong Xiang,
- Eveline M. Ibeagha-Awemu,
- Pat (J.S.) Heslop-Harrison,
- Benjamin D. Rosen,
- Johannes A. Lenstra,
- Shangquan Gan,
- and Yu Jiang
Genome Res. March 2023 33: 463-477; Published in Advance April 3, 2023, doi:10.1101/gr.277372.12
..., Middle East, and Africa, 33 Asiatic mouflons and 8 argali with an average coverage of 18.1× (Fig. 5A, see Methods for the assignment of the breeds and populations). PCA using SVs shows a clear separation of the same clusters as defined by SNPs (Supplemental Fig. S13), suggesting that the SV catalog...
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Resource: A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes
- Ran Li,
- Mian Gong,
- Xinmiao Zhang,
- Fei Wang,
- Zhenyu Liu,
- Lei Zhang,
- Qimeng Yang,
- Yuan Xu,
- Mengsi Xu,
- Huanhuan Zhang,
- Yunfeng Zhang,
- Xuelei Dai,
- Yuanpeng Gao,
- Zhuangbiao Zhang,
- Wenwen Fang,
- Yuta Yang,
- Weiwei Fu,
- Chunna Cao,
- Peng Yang,
- Zeinab Amiri Ghanatsaman,
- Niloufar Jafarpour Negari,
- Hojjat Asadollahpour Nanaei,
- Xiangpeng Yue,
- Yuxuan Song,
- Xianyong Lan,
- Weidong Deng,
- Xihong Wang,
- Chuanying Pan,
- Ruidong Xiang,
- Eveline M. Ibeagha-Awemu,
- Pat (J.S.) Heslop-Harrison,
- Benjamin D. Rosen,
- Johannes A. Lenstra,
- Shangquan Gan,
- and Yu Jiang
Genome Res. March 27, 2023 ; Published in Advance March 27, 2023, doi:10.1101/gr.277372.122
...pan To expand our knowledge of SVs to the population scale, we explored selection signatures of SVs among 45 breeds or populations based on their SV frequency (Supplemental Table S13). The studied breeds/populations included 649 individual domestic sheep from Europe, East Asia, Middle East, and Africa...
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Research: Ancient dog introgression into the Iberian wolf genome may have facilitated adaptation to human-dominated landscapes
- Diana Lobo,
- Hernán E. Morales,
- Cock Van Oosterhout,
- José Vicente López-Bao,
- Pedro Silva,
- Luis Llaneza,
- Carolina Pacheco,
- Diana Castro,
- Germán Hernández-Alonso,
- George Pacheco,
- John Archer,
- M. Thomas P. Gilbert,
- Nuno Ferrand,
- and Raquel Godinho
Genome Res. March 2025 35: 432-445; Published in Advance February 14, 2025, doi:10.1101/gr.279093.124
...Africa Corresponding authors: diana.lobo@cibio.up.pt, rgodinho@cibio.up.ptAbstractUnderstanding how large carnivores respond to increasingly human-dominated landscapes will determine their future adaptive potential. The Iberian wolf (Canis lupus signatus), a gray wolf subspecies endemic to the Iberian...
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Research: Major impacts of widespread structural variation on sorghum
- Zhihai Zhang,
- Joao Paulo Gomes Viana,
- Bosen Zhang,
- Kimberly K.O. Walden,
- Hans Müller Paul,
- Stephen P. Moose,
- Geoffrey P. Morris,
- Chris Daum,
- Kerrie W. Barry,
- Nadia Shakoor,
- and Matthew E. Hudson
Genome Res. February 2024 34: 286-299; Published in Advance March 13, 2024, doi:10.1101/gr.278396.123
...sorghum domestication in northern Africa ∼10,000 yr ago and its subsequent spread to a variety of areas across Africa, India, the Middle East, and east Asia (Lobell et al. 2008; Morris et al. 2013a). Broad distribution of SVs in sorghum and correlation with local adaptation has been reported (Songsomboon...
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Method: A probabilistic method for testing and estimating selection differences between populations
- Yungang He,
- Minxian Wang,
- Xin Huang,
- Ran Li,
- Hongyang Xu,
- Shuhua Xu,
- and Li Jin
Genome Res. December 2015 25: 1903-1909; Published in Advance October 13, 2015, doi:10.1101/gr.192336.115
...: 951–956. Mellars P. 2006. Why did modern human populations disperse from Africa ca. 60,000 years ago? A new model. Proc Natl Acad Sci 103: 9381–9386. Mellars P, Gori KC, Carr M, Soares PA, Richards MB. 2013. Genetic and archaeological perspectives on the initial modern human colonization of southern...

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