{"id":1119724,"date":"2023-11-30T20:35:12","date_gmt":"2023-12-01T01:35:12","guid":{"rendered":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/uncategorized\/global-genetic-diversity-introgression-and-evolutionary-adaptation-of-indicine-cattle-revealed-by-whole-genome-nature-com\/"},"modified":"2023-11-30T20:35:12","modified_gmt":"2023-12-01T01:35:12","slug":"global-genetic-diversity-introgression-and-evolutionary-adaptation-of-indicine-cattle-revealed-by-whole-genome-nature-com","status":"publish","type":"post","link":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/transhuman-news-blog\/genome\/global-genetic-diversity-introgression-and-evolutionary-adaptation-of-indicine-cattle-revealed-by-whole-genome-nature-com\/","title":{"rendered":"Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome &#8230; &#8211; Nature.com"},"content":{"rendered":"<p><p>        Loftus, R. T., MacHugh, D. E., Bradley, D. G., Sharp, P. M.        & Cunningham, P. Evidence for two independent        domestications of cattle. Proc. Natl Acad. Sci. USA        91, 27572761 (1994).      <\/p>\n<p>        Article ADS CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Verdugo Marta, P. et al. Ancient cattle genomics, origins,        and rapid turnover in the Fertile Crescent. Science        365, 173176 (2019).      <\/p>\n<p>        Article ADS PubMed                Google Scholar      <\/p>\n<p>        Utsunomiya, Y. T. et al. Genomic clues of the evolutionary        history of Bos indicus cattle. Anim. Genet.        50, 557568 (2019).      <\/p>\n<p>        Article CAS PubMed                Google Scholar      <\/p>\n<p>        Thornton, P., Nelson, G., Mayberry, D. & Herrero, M.        Impacts of heat stress on global cattle production during        the 21st century: a modelling study. Lancet Planet.        Health 6, e192e201 (2022).      <\/p>\n<p>        Article        PubMed                Google Scholar      <\/p>\n<p>        Kim, K. et al. The mosaic genome of indigenous African        cattle as a unique genetic resource for African        pastoralism. Nat. Genet. 52, 10991110        (2020).      <\/p>\n<p>        Article        PubMed                Google Scholar      <\/p>\n<p>        Chen, S. et al. Zebu cattle are an exclusive legacy of the        South Asia Neolithic. Mol. Biol. Evol. 27,        16 (2010).      <\/p>\n<p>        Article PubMed                Google Scholar      <\/p>\n<p>        Papachristou, D. et al. Genomic diversity and population        structure of the indigenous Greek and Cypriot cattle        populations. Genet. Sel. Evol. 52, 43 (2020).      <\/p>\n<p>        Article        CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Felius, M. et al. On the history of cattle genetic        resources. Diversity 6, 705750 (2014).      <\/p>\n<p>        Article         Google Scholar      <\/p>\n<p>        Chen, N. et al. Whole-genome resequencing reveals        world-wide ancestry and adaptive introgression events of        domesticated cattle in East Asia. Nat. Commun.        9, 2337 (2018).      <\/p>\n<p>        Article        ADS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Wu, D.-D. et al. Pervasive introgression facilitated        domestication and adaptation in the Bos species complex.        Nat. Ecol. Evol. 2, 11391145 (2018).      <\/p>\n<p>        Article        PubMed                Google Scholar      <\/p>\n<p>        Medugorac, I. et al. Whole-genome analysis of introgressive        hybridization and characterization of the bovine legacy of        Mongolian yaks. Nat. Genet. 49, 470475        (2017).      <\/p>\n<p>        Article CAS PubMed                Google Scholar      <\/p>\n<p>        Sinding, M.-H. S. et al. Kouprey (Bos sauveli) genomes        unveil polytomic origin of wild Asian Bos. iScience        24, 103226 (2021).      <\/p>\n<p>        Article        ADS CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Lenstra, J. A. et al. Meta-analysis of mitochondrial DNA        reveals several population bottlenecks during worldwide        migrations of cattle. Diversity 6, 178187        (2014).      <\/p>\n<p>        Article         Google Scholar      <\/p>\n<p>        Li, Y. et al. Whole-genome sequencing reveals selection        signals among Chinese, Pakistani, and Nepalese goats. J.        Genet. Genomics 50, 362365 (2023).      <\/p>\n<p>        Article        PubMed                Google Scholar      <\/p>\n<p>        Dixit, Y., Hodell, D. A. & Petrie, C. A. Abrupt weakening        of the summer monsoon in northwest India ~4100 yr ago.        Geology 42, 339342 (2014).      <\/p>\n<p>        Article ADS CAS         Google Scholar      <\/p>\n<p>        Ali, N. S., Sartori-Valinotti, J. C. & Bruce, A. J.        Periodic fever, aphthous stomatitis, pharyngitis, and        adenitis (PFAPA) syndrome. Clin. Dermatol.        34, 482486 (2016).      <\/p>\n<p>        Article        PubMed                Google Scholar      <\/p>\n<p>        Duchesne, A. et al. Progressive ataxia of Charolais cattle        highlights a role of KIF1C in sustainable myelination.        PLoS Genet. 14, e1007550 (2018).      <\/p>\n<p>        Article        PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Miyajima, D. et al. Profilin1 regulates sternum development        and endochondral bone formation. J. Biol. Chem.        287, 3354533553 (2012).      <\/p>\n<p>        Article CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Song, K. et al. The transcriptional coactivator CAMTA2        stimulates cardiac growth by opposing class II histone        deacetylases. Cell 125, 453466 (2006).      <\/p>\n<p>        Article        CAS PubMed                Google Scholar      <\/p>\n<p>        Fougerousse, F. et al. The muscle-specific enolase is an        early marker of human myogenesis. J. Muscle Res. Cell        Motil. 22, 535544 (2001).      <\/p>\n<p>        Article CAS PubMed                Google Scholar      <\/p>\n<p>        Kazantseva, A. et al. Human hair growth deficiency is        linked to a genetic defect in the phospholipase gene        LIPH. Science 314, 982985 (2006).      <\/p>\n<p>        Article ADS CAS PubMed                Google Scholar      <\/p>\n<p>        Jirimutu et al. Genome sequences of wild and domestic        bactrian camels. Nat. Commun. 3, 1202 (2012).      <\/p>\n<p>        Article ADS CAS PubMed                Google Scholar      <\/p>\n<p>        Tian, S. et al. Genomic analyses reveal genetic adaptations        to tropical climates in chickens. iScience        23, 101644 (2020).      <\/p>\n<p>        Article        ADS CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Yang, J. et al. Whole-genome sequencing of native sheep        provides insights into rapid adaptations to extreme        environments. Mol. Biol. Evol. 33, 25762592        (2016).      <\/p>\n<p>        Article CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Deng, C., Chen, H., Yang, N., Feng, Y. & Hsueh, A. J. W.        Apela regulates fluid homeostasis by binding to the APJ        receptor to activate Gi. Signal. J. Biol. Chem.        290, 1826118268 (2015).      <\/p>\n<p>        Article CAS PubMed                Google Scholar      <\/p>\n<p>        Jin, H., Fishman, Z. H., Ye, M., Wang, L. & Zuker, C. S.        Top-down control of sweet and bitter taste in the mammalian        brain. Cell 184, 257271.e16 (2021).      <\/p>\n<p>        Article        CAS PubMed                Google Scholar      <\/p>\n<p>        Zhang, K., Lenstra, J. A., Zhang, S., Liu, W. & Liu, J.        Evolution and domestication of the Bovini species. Anim.        Genet. 51, 637657 (2020).      <\/p>\n<p>        Article CAS PubMed                Google Scholar      <\/p>\n<p>        Robinson, T. P. et al. Global Livestock Production        Systems (Food and Agriculture Organization of the        United Nations (FAO) and International Livestock Research        Institute (ILRI), 2011).      <\/p>\n<p>        Li, X., Shen, J. & Ran, Z. Crosstalk between the gut and        the liver via susceptibility loci: novel advances in        inflammatory bowel disease and autoimmune liver disease.        Clin. Immunol. 175, 115123 (2017).      <\/p>\n<p>        Article        CAS PubMed                Google Scholar      <\/p>\n<p>        Dai, W. et al. Whole-exome sequencing identifies MST1R as a        genetic susceptibility gene in nasopharyngeal carcinoma.        Proc. Natl Acad. Sci. USA 113, 33173322        (2016).      <\/p>\n<p>        Article ADS CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Wang, F. et al. Genetic variation in Mon1a affects protein        trafficking and modifies macrophage iron loading in mice.        Nat. Genet. 39, 10251032 (2007).      <\/p>\n<p>        Article CAS PubMed                Google Scholar      <\/p>\n<p>        Tomizawa, Y. et al. Inhibition of lung cancer cell growth        and induction of apoptosis after reexpression of 3p21.3        candidate tumor suppressor gene SEMA3B. Proc. Natl Acad.        Sci. USA 98, 1395413959 (2001).      <\/p>\n<p>        Article ADS CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Raymond, J. R. Jr., Appleton, K. M., Pierce, J. Y. &        Peterson, Y. K. Suppression of GNAI2 message in ovarian        cancer. J. Ovarian Res. 7, 66 (2014).      <\/p>\n<p>        Article PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Potiron, V. A. et al. Semaphorin SEMA3F affects multiple        signaling pathways in lung cancer cells. Cancer Res.        67, 87088715 (2007).      <\/p>\n<p>        Article        CAS PubMed                Google Scholar      <\/p>\n<p>        Bechara, E. G., Sebestyn, E., Bernardis, I., Eyras, E. &        Valcrcel, J. RBM5, 6, and 10 differentially regulate NUMB        alternative splicing to control cancer cell proliferation.        Mol. Cell 52, 720733 (2013).      <\/p>\n<p>        Article        CAS PubMed                Google Scholar      <\/p>\n<p>        Grabek, K. R. et al. Genetic variation drives seasonal        onset of hibernation in the 13-lined ground squirrel.        Commun. Biol. 2, 478 (2019).      <\/p>\n<p>        Article        PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Chen, N. et al. Ancient genomes reveal tropical bovid        species in the Tibetan Plateau contributed to the        prevalence of hunting game until the late Neolithic.        Proc. Natl Acad. Sci. USA 117, 2815028159        (2020).      <\/p>\n<p>        Article ADS CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Pickrell, J. K. & Pritchard, J. K. Inference of population        splits and mixtures from genome-wide allele frequency data.        PLoS Genet. 8, e1002967 (2012).      <\/p>\n<p>        Article        CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Maples, B. K., Gravel, S., Kenny, E. E. & Bustamante, C. D.        RFMix: a discriminative modeling approach for rapid and        robust local-ancestry inference. Am. J. Hum. Genet.        93, 278288 (2013).      <\/p>\n<p>        Article        CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Malinsky, M., Matschiner, M. & Svardal, H. Dsuite-Fast        D-statistics and related admixture evidence from VCF files.        Mol. Ecol. Resour. 21, 584595 (2021).      <\/p>\n<p>        Article PubMed                Google Scholar      <\/p>\n<p>        Racimo, F., Marnetto, D. & Huerta-Snchez, E. Signatures of        archaic adaptive introgression in present-day human        populations. Mol. Biol. Evol. 34, 296317        (2016).      <\/p>\n<p>        PubMed        Central         Google Scholar      <\/p>\n<p>        Gong, Y. et al. ILDR1 is important for paracellular water        transport and urine concentration mechanism. Proc. Natl        Acad. Sci. USA 114, 52715276 (2017).      <\/p>\n<p>        Article ADS CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Ling, S. et al. Structural mechanism of cooperative        activation of the human calcium-sensing receptor by        Ca2+ ions and L-tryptophan. Cell Res.        31, 383394 (2021).      <\/p>\n<p>        Article        CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Vasilopoulos, Y. et al. Association analysis of the skin        barrier gene cystatin A at the PSORS5 locus in psoriatic        patients: evidence for interaction between PSORS1 and        PSORS5. Eur. J. Hum. Genet. 16, 10021009        (2008).      <\/p>\n<p>        Article CAS PubMed                Google Scholar      <\/p>\n<p>        Kariuki, S. N. & Williams, T. N. Human genetics and malaria        resistance. Hum. Genet. 139, 801811 (2020).      <\/p>\n<p>        Article        PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Gaughan, J. B., Sejian, V., Mader, T. L. & Dunshea, F. R.        Adaptation strategies: ruminants. Anim. Front.        9, 4753 (2019).      <\/p>\n<p>        Article PubMed                Google Scholar      <\/p>\n<p>        Brash, D. E. & Haseltine, W. A. UV-induced mutation        hotspots occur at DNA damage hotspots. Nature        298, 189192 (1982).      <\/p>\n<p>        Article ADS CAS PubMed                Google Scholar      <\/p>\n<p>        Vandewauw, I. et al. A TRP channel trio mediates acute        noxious heat sensing. Nature 555, 662666        (2018).      <\/p>\n<p>        Article ADS CAS PubMed                Google Scholar      <\/p>\n<p>        Lindley, E. P. Contagious bovine pleuropneumonia. In        Diseases of Cattle in the Tropics: Economic and Zoonotic        Relevance (eds Ristic M. & McIntyre W. I. M.)        (Springer, 1981).      <\/p>\n<p>        Van Alfen, N. K. Encyclopedia of Agriculture and Food        Systems (Elsevier, 2014).      <\/p>\n<p>        Brown, C. G. D. Dynamics and impact of tick-borne diseases        of cattle. Trop. Anim. Health Prod. 29, 1S3S        (1997).      <\/p>\n<p>        Article CAS PubMed                Google Scholar      <\/p>\n<p>        Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a        flexible trimmer for Illumina sequence data.        Bioinformatics 30, 21142120 (2014).      <\/p>\n<p><!-- Auto Generated --><\/p>\n<p>Read the original:<br \/>\n<a target=\"_blank\" href=\"https:\/\/www.nature.com\/articles\/s41467-023-43626-z\" title=\"Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome ... - Nature.com\" rel=\"noopener\">Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome ... - Nature.com<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p> Loftus, R. T., MacHugh, D. E., Bradley, D <a href=\"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/transhuman-news-blog\/genome\/global-genetic-diversity-introgression-and-evolutionary-adaptation-of-indicine-cattle-revealed-by-whole-genome-nature-com\/\">Continue reading <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[25],"tags":[],"class_list":["post-1119724","post","type-post","status-publish","format-standard","hentry","category-genome"],"_links":{"self":[{"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/posts\/1119724"}],"collection":[{"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/comments?post=1119724"}],"version-history":[{"count":0,"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/posts\/1119724\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/media?parent=1119724"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/categories?post=1119724"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/tags?post=1119724"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}