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Leonard WR. Pearl Memorial Lecture. Humans at the extremes: Exploring human adaptation to ecological and social stressors. Am J Hum Biol 2024; 36:e24010. [PMID: 37974340 DOI: 10.1002/ajhb.24010] [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: 08/07/2023] [Revised: 10/22/2023] [Accepted: 10/25/2023] [Indexed: 11/19/2023] Open
Abstract
The field of human biology has long explored how human populations have adapted to extreme environmental circumstances. Yet, it has become increasingly clear that conditions of social stress, poverty, and lifestyle change play equally important roles in shaping human biological variation and health. In this paper, I provide a brief background on the foundational human adaptability research of the International Biological Programme (IBP) from the 1960s, highlighting how its successes and critiques have shaped current research directions in the field. I then discuss and reflect on my own field research that has examined the influence of both environmental and social stresses on human populations living in different ecosystems: the Peruvian Andes, the Siberian arctic, and the Bolivian rainforest. Finally, I consider how the papers in this special issue advance our understanding of human adaptability to extreme conditions and offer directions for future research. Drawing on our field's distinctive evolutionary and biocultural perspectives, human biologists are uniquely positioned to examine how the interplay between social and ecological domains influences the human condition.
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Affiliation(s)
- William R Leonard
- Department of Anthropology & Program in Global Health Studies, Northwestern University, Evanston, Illinois, USA
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Martel RD, Papafragou G, Weigand S, Rolke R, Prawitt D, Birklein F, Treede RD, Magerl W. Interindividual variability in cold-pressor pain sensitivity is not explained by peripheral vascular responding and generalizes to a C-nociceptor-specific pain phenotype. Pain 2024; 165:e1-e14. [PMID: 38284423 DOI: 10.1097/j.pain.0000000000003049] [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: 09/27/2022] [Accepted: 07/07/2023] [Indexed: 01/30/2024]
Abstract
ABSTRACT Pain sensitivity of healthy subjects in the cold-pressor (CP) test was proposed to be dichotomously distributed and to represent a pain sensitivity trait. Still, it has not been systematically explored which factors influence this pain sensitivity readout. The aim of this study was to distinguish potential contributions of local tissue-related factors such as perfusion and thermoregulation or gain settings in nociceptive systems. Cold-pressor-sensitive and CP-insensitive students screened from a medical student laboratory course were recruited for a CP retest with additional cardiovascular and bilateral local vascular monitoring. In addition, comprehensive quantitative sensory testing according to Deutscher Forschungsverbund Neuropathischer Schmerz standards and a sustained pinch test were performed. Cold pressor was reproducible across sessions (Cohen kappa 0.61 ± 0.14, P < 0.005). At 30 seconds in ice water, CP-sensitive subjects exhibited not only more pain (78.6 ± 26.3 vs 29.5 ± 17.5, P < 0.0001) but also significantly stronger increases in mean arterial blood pressure (12.6 ± 9.3 vs 5.6 ± 8.1 mm Hg, P < 0.05) and heart rate (15.0 ± 8.2 vs 7.1 ± 6.2 bpm, P < 0.005), and lower baroreflex sensitivity, but not local or vasoconstrictor reflex-mediated microcirculatory responses. Cold-pressor-sensitive subjects exhibited significantly lower pain thresholds also for cold, heat, and blunt pressure, and enhanced pain summation, but no significant differences in Aδ-nociceptor-mediated punctate mechanical pain. In conclusion, differences in nociceptive signal processing drove systemic cardiovascular responses. Baroreceptor activation suppressed pain and cardiovascular responses more efficiently in CP-insensitive subjects. Cold-pressor sensitivity generalized to a pain trait of C-fiber-mediated nociceptive channels, which was independent of local thermal and vascular changes in the ice-water-exposed hand. Thus, the C-fiber pain trait reflects gain setting of the nociceptive system.
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Affiliation(s)
- Richard D Martel
- Department of Neurophysiology, Mannheim Center for Translational Neurosciences (MCTN), Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany. Martel is now with the Department of Pediatric Surgery, University Medical Center Mannheim, Heidelberg University, Heidelberg, Germany. Papafragou is now with the Vitos Orthopädische Klinik Kassel, Kassel, Germany. Weigand is now with the Department of Internal Medicine I, University of Regensburg, Regensburg, Germany. Rolke is now with the Department of Palliative Care, RWTH Aachen, Aachen, Germany
| | - Georgios Papafragou
- Department of Neurophysiology, Mannheim Center for Translational Neurosciences (MCTN), Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany. Martel is now with the Department of Pediatric Surgery, University Medical Center Mannheim, Heidelberg University, Heidelberg, Germany. Papafragou is now with the Vitos Orthopädische Klinik Kassel, Kassel, Germany. Weigand is now with the Department of Internal Medicine I, University of Regensburg, Regensburg, Germany. Rolke is now with the Department of Palliative Care, RWTH Aachen, Aachen, Germany
| | - Sylvia Weigand
- Department of Neurophysiology, Mannheim Center for Translational Neurosciences (MCTN), Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany. Martel is now with the Department of Pediatric Surgery, University Medical Center Mannheim, Heidelberg University, Heidelberg, Germany. Papafragou is now with the Vitos Orthopädische Klinik Kassel, Kassel, Germany. Weigand is now with the Department of Internal Medicine I, University of Regensburg, Regensburg, Germany. Rolke is now with the Department of Palliative Care, RWTH Aachen, Aachen, Germany
| | | | - Dirk Prawitt
- Pediatric Medicine, Medical Center, Johannes Gutenberg University, Mainz, Germany
| | | | - Rolf-Detlef Treede
- Department of Neurophysiology, Mannheim Center for Translational Neurosciences (MCTN), Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany. Martel is now with the Department of Pediatric Surgery, University Medical Center Mannheim, Heidelberg University, Heidelberg, Germany. Papafragou is now with the Vitos Orthopädische Klinik Kassel, Kassel, Germany. Weigand is now with the Department of Internal Medicine I, University of Regensburg, Regensburg, Germany. Rolke is now with the Department of Palliative Care, RWTH Aachen, Aachen, Germany
| | - Walter Magerl
- Department of Neurophysiology, Mannheim Center for Translational Neurosciences (MCTN), Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany. Martel is now with the Department of Pediatric Surgery, University Medical Center Mannheim, Heidelberg University, Heidelberg, Germany. Papafragou is now with the Vitos Orthopädische Klinik Kassel, Kassel, Germany. Weigand is now with the Department of Internal Medicine I, University of Regensburg, Regensburg, Germany. Rolke is now with the Department of Palliative Care, RWTH Aachen, Aachen, Germany
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Malyarchuk BA, Derenko MV. Genetic history of the Koryaks and Evens of the Magadan region based on Y chromosome polymorphism data. Vavilovskii Zhurnal Genet Selektsii 2024; 28:90-97. [PMID: 38465253 PMCID: PMC10917666 DOI: 10.18699/vjgb-24-11] [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: 09/14/2023] [Revised: 11/29/2023] [Accepted: 11/29/2023] [Indexed: 03/12/2024] Open
Abstract
In order to clarify the history of gene pool formation of the indigenous populations of the Northern Priokhotye (the northern coast of the Sea of Okhotsk), Y-chromosome polymorphisms were studied in the Koryaks and Evens living in the Magadan region. The results of the study showed that the male gene pool of the Koryaks is represented by haplogroups C-B90-B91, N-B202, and Q-B143, which are also widespread in other peoples of Northeastern Siberia, mainly of Paleo-Asiatic origin. High frequency of haplogroup C-B80, typical of other Tungus-Manchurian peoples, is characteristic of the Evens of the Magadan region. The shared components of the gene pools of the Koryaks and Evens are haplogroups R-M17 and I-P37.2 inherited as a result of admixture with Eastern Europeans (mainly Russians). The high frequency of such Y chromosome haplogroups in the Koryaks (16.7 %) and Evens (37.8 %) is indicative of close interethnic contacts during the last centuries, and most probably especially during the Soviet period. The genetic contribution of the European males' Y chromosome significantly prevails over that of maternally inherited mitochondrial DNA. The study of the Y chromosome haplogroup diversity has shown that only relatively young phylogenetic branches have been preserved in the Koryak gene pool. The age of the oldest component of the Koryak gene pool (haplogroup C-B90-B91) is estimated to be about 3.8 thousand years, the age of the younger haplogroups Q-B143 and N-B202 is about 2.8 and 2.4 thousand years, respectively. Haplogroups C-B90-B91 and N-B202 are Siberian in origin, and haplogroup Q-B143 was apparently inherited by the ancestors of the Koryaks and other Paleo-Asiatic peoples from the Paleo-Eskimos as a result of their migrations to Northeast Asia from the Americas. The analysis of microsatellite loci for haplogroup Q-B143 in the Eskimos of Greenland, Canada and Alaska as well as in the indigenous peoples of Northeastern Siberia showed a decrease in genetic diversity from east to west, pointing to the direction of distribution of the Paleo-Eskimo genetic component in the circumpolar region of America and Asia. At the same time, the Evens appeared in the Northern Priokhotye much later (in the XVII century) as a result of the expansion of the Tungusic tribes, which is confirmed by the results of the analysis of haplogroup C-B80 polymorphisms.
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Affiliation(s)
- B A Malyarchuk
- Institute of Biological Problems of the North of the Far-Eastern Branch of the Russian Academy of Sciences, Magadan, Russia
| | - M V Derenko
- Institute of Biological Problems of the North of the Far-Eastern Branch of the Russian Academy of Sciences, Magadan, Russia
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Lin X, Pan J, Hamoudi H, Yu J. THADA inhibits autophagy and increases 5-FU sensitivity in gastric cancer cells via the PI3K/AKT/mTOR signaling pathway. IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2024; 27:195-202. [PMID: 38234670 PMCID: PMC10790288 DOI: 10.22038/ijbms.2023.72055.15668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 09/26/2023] [Indexed: 01/19/2024]
Abstract
Objectives 5-Fluorouracil (5-FU) is currently the main drug used in chemotherapy for gastric cancer (GC). The main clinical problems of 5-FU therapy are insensitivity and acquired resistance to 5-FU. The mechanism of GC cell resistance to 5-FU is currently unknown. Materials and Methods This study employed next-generation sequencing (NGS) to analyze the differentially expressed genes (DEGs) in chemotherapy-sensitive and non-sensitive GC tissues. In addition, a bioinformatics analysis was conducted using the GC dataset of GEO, and further validated and explored through in vitro experiments. Results Thyroid adenoma-associated gene (THADA) was highly expressed in GC tissues from chemotherapy-sensitive patients and was an independent prognostic factor in GC patients receiving postoperative 5-FU adjuvant chemotherapy. Notably, heightened THADA expression in GC cells was associated with the down-regulation of autophagy-related proteins (LC-3, ATG13, ULK1, and TFEB). Furthermore, the PI3K/AKT/mTOR signaling pathway and mTORC1 signaling pathway were remarkably increased in patients with elevated THADA expression. THADA expression was associated with mTOR, the core protein of the mTOR signaling pathway, and related proteins involved in regulating the mTORC1 signaling pathway (mLST8, RHEB, and TSC2). THADA exhibited inhibitory effects on autophagy and augmented the sensitivity of GC cells to 5-FU through the PI3K/AKT/mTOR signaling pathway. Conclusion The findings suggest that THADA may be involved in the regulatory mechanism of GC cell sensitivity to 5-FU. Consequently, the detection of THADA in tumor tissues may bring clinical benefits, specifically for 5-FU-related chemotherapy administered to GC patients with elevated THADA expression.
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Affiliation(s)
- Xianke Lin
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- These authors contributed equally to this work
| | - Jiajia Pan
- Department of Hematology, The First Affiliated Hospital, Zhejiang University College of Medicine, Hangzhou, China
- These authors contributed equally to this work
| | - Hammza Hamoudi
- Zhejiang University College of Medicine, Hangzhou, China
| | - Jiren Yu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Pokharel K, Weldenegodguad M, Dudeck S, Honkatukia M, Lindeberg H, Mazzullo N, Paasivaara A, Peippo J, Soppela P, Stammler F, Kantanen J. Whole-genome sequencing provides novel insights into the evolutionary history and genetic adaptation of reindeer populations in northern Eurasia. Sci Rep 2023; 13:23019. [PMID: 38155192 PMCID: PMC10754820 DOI: 10.1038/s41598-023-50253-7] [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: 09/13/2023] [Accepted: 12/18/2023] [Indexed: 12/30/2023] Open
Abstract
Domestic reindeer (Rangifer tarandus) play a vital role in the culture and livelihoods of indigenous people across northern Eurasia. These animals are well adapted to harsh environmental conditions, such as extreme cold, limited feed availability and long migration distances. Therefore, understanding the genomics of reindeer is crucial for improving their management, conservation and utilisation. In this study, we have generated a new genome assembly for the Fennoscandian domestic reindeer with high contiguity, making it the most complete reference genome for reindeer to date. The new genome assembly was utilised to explore genetic diversity, population structure and selective sweeps in Eurasian Rangifer tarandus populations which was based on the largest population genomic dataset for reindeer, encompassing 58 individuals from diverse populations. Phylogenetic analyses revealed distinct genetic clusters, with the Finnish wild forest reindeer (Rangifer tarandus fennicus) standing out as a unique subspecies. Divergence time estimates suggested a separation of ~ 52 thousand years ago (Kya) between the northern European Rangifer tarandus fennicus and Rangifer tarandus tarandus. Our study identified four main genetic clusters: Fennoscandian, the eastern/northern Russian and Alaskan group, the Finnish forest reindeer, and the Svalbard reindeer. Furthermore, two independent reindeer domestication processes were inferred, suggesting separate origins for the domestic Fennoscandian and eastern/northern Russian reindeer. Notably, shared genes under selection, including retroviral genes, point towards molecular domestication processes that aided adaptation of this species to diverse environments.
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Affiliation(s)
- Kisun Pokharel
- Natural Resources Institute Finland (Luke), Myllytie 1, 31600, Jokioinen, Finland
| | - Melak Weldenegodguad
- Natural Resources Institute Finland (Luke), Myllytie 1, 31600, Jokioinen, Finland
| | - Stephan Dudeck
- Arctic Centre, University of Lapland, 96100, Rovaniemi, Finland
| | | | - Heli Lindeberg
- Natural Resources Institute Finland (Luke), 71750, Maaninka, Finland
| | - Nuccio Mazzullo
- Arctic Centre, University of Lapland, 96100, Rovaniemi, Finland
| | - Antti Paasivaara
- Natural Resources Institute Finland (Luke), Paavo Havaksentie 3, 90570, Oulu, Finland
| | - Jaana Peippo
- Natural Resources Institute Finland (Luke), Myllytie 1, 31600, Jokioinen, Finland
- NordGen-Nordic Genetic Resource Center, 1432, Ås, Norway
| | - Päivi Soppela
- Arctic Centre, University of Lapland, 96100, Rovaniemi, Finland
| | | | - Juha Kantanen
- Natural Resources Institute Finland (Luke), Myllytie 1, 31600, Jokioinen, Finland.
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Ren Y, Chen X, Zheng X, Wang F, Sun R, Wei L, Zhang Y, Liu H, Lin Y, Hong L, Huang X, Chao Z. Diverse WGBS profiles of longissimus dorsi muscle in Hainan black goats and hybrid goats. BMC Genom Data 2023; 24:77. [PMID: 38097986 PMCID: PMC10720224 DOI: 10.1186/s12863-023-01182-x] [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: 02/04/2023] [Accepted: 12/08/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Goat products have played a crucial role in meeting the dietary demands of people since the Neolithic era, giving rise to a multitude of goat breeds globally with varying characteristics and meat qualities. The primary objective of this study is to pinpoint the pivotal genes and their functions responsible for regulating muscle fiber growth in the longissimus dorsi muscle (LDM) through DNA methylation modifications in Hainan black goats and hybrid goats. METHODS Whole-genome bisulfite sequencing (WGBS) was employed to scrutinize the impact of methylation on LDM growth. This was accomplished by comparing methylation differences, gene expression, and their associations with growth-related traits. RESULTS In this study, we identified a total of 3,269 genes from differentially methylated regions (DMR), and detected 189 differentially expressed genes (DEGs) through RNA-seq analysis. Hypo DMR genes were primarily enriched in KEGG terms associated with muscle development, such as MAPK and PI3K-Akt signaling pathways. We selected 11 hub genes from the network that intersected the gene sets within DMR and DEGs, and nine genes exhibited significant correlation with one or more of the three LDM growth traits, namely area, height, and weight of loin eye muscle. Particularly, PRKG1 demonstrated a negative correlation with all three traits. The top five most crucial genes played vital roles in muscle fiber growth: FOXO3 safeguarded the myofiber's immune environment, FOXO6 was involved in myotube development and differentiation, and PRKG1 facilitated vasodilatation to release more glucose. This, in turn, accelerated the transfer of glucose from blood vessels to myofibers, regulated by ADCY5 and AKT2, ultimately ensuring glycogen storage and energy provision in muscle fibers. CONCLUSION This study delved into the diverse methylation modifications affecting critical genes, which collectively contribute to the maintenance of glycogen storage around myofibers, ultimately supporting muscle fiber growth.
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Affiliation(s)
- Yuwei Ren
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, 571100, China
| | - Xing Chen
- Institute of Animal Husbandry and Veterinary, Wuhan Academy of Agricultural Science, Wuhan, 430000, China
| | - Xinli Zheng
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, 571100, China
| | - Feng Wang
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, 571100, China
| | - Ruiping Sun
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, 571100, China
| | - Limin Wei
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, 571100, China
| | - Yan Zhang
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, 571100, China
| | - Hailong Liu
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, 571100, China
| | - Yanning Lin
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, 571100, China
| | - Lingling Hong
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, 571100, China
| | - Xiaoxian Huang
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, 571100, China
| | - Zhe Chao
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, 571100, China.
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Kalyakulina A, Yusipov I, Kondakova E, Bacalini MG, Giuliani C, Sivtseva T, Semenov S, Ksenofontov A, Nikolaeva M, Khusnutdinova E, Zakharova R, Vedunova M, Franceschi C, Ivanchenko M. Epigenetics of the far northern Yakutian population. Clin Epigenetics 2023; 15:189. [PMID: 38053163 PMCID: PMC10699032 DOI: 10.1186/s13148-023-01600-y] [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: 09/22/2023] [Accepted: 11/13/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND Yakuts are one of the indigenous populations of the subarctic and arctic territories of Siberia characterized by a continental subarctic climate with severe winters, with the regular January average temperature in the regional capital city of Yakutsk dipping below - 40 °C. The epigenetic mechanisms of adaptation to such ecologies and environments and, in particular, epigenetic age acceleration in the local population have not been studied before. RESULTS This work reports the first epigenetic study of the Yakutian population using whole-blood DNA methylation data, supplemented with the comparison to the residents of Central Russia. Gene set enrichment analysis revealed, among others, geographic region-specific differentially methylated regions associated with adaptation to climatic conditions (water consumption, digestive system regulation), aging processes (actin filament activity, cell fate), and both of them (channel activity, regulation of steroid and corticosteroid hormone secretion). Further, it is demonstrated that the epigenetic age acceleration of the Yakutian representatives is significantly higher than that of Central Russia counterparts. For both geographic regions, we showed that epigenetically males age faster than females, whereas no significant sex differences were found between the regions. CONCLUSIONS We performed the first study of the epigenetic data of the Yakutia cohort, paying special attention to region-specific features, aging processes, age acceleration, and sex specificity.
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Affiliation(s)
- Alena Kalyakulina
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod, 603022, Russia.
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, 603022, Russia.
| | - Igor Yusipov
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
| | - Elena Kondakova
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
- Institute of Biology and Biomedicine, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
| | | | - Cristina Giuliani
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126, Bologna, Italy
| | - Tatiana Sivtseva
- Research Center of the Medical Institute of the North-Eastern Federal University M.K. Ammosova, Yakutsk, 677013, Russia
| | - Sergey Semenov
- Research Center of the Medical Institute of the North-Eastern Federal University M.K. Ammosova, Yakutsk, 677013, Russia
| | - Artem Ksenofontov
- State Budgetary Institution of the Republic of Sakha (Yakutia) Republican Center for Public Health and Medical Prevention, Yakutsk, 677001, Russia
| | - Maria Nikolaeva
- Research Center of the Medical Institute of the North-Eastern Federal University M.K. Ammosova, Yakutsk, 677013, Russia
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia, 450054
| | - Raisa Zakharova
- Research Center of the Medical Institute of the North-Eastern Federal University M.K. Ammosova, Yakutsk, 677013, Russia
| | - Maria Vedunova
- Institute of Biology and Biomedicine, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
| | - Claudio Franceschi
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
| | - Mikhail Ivanchenko
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
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Huang C, Zhang Y, Liu Y, Liu JX, Hu YM, Tang WW, Wang TD, Huang XB. Prevalence and related factors of abdominal obesity among urban adults aged 35 to 79 years in southwest China. Front Public Health 2023; 11:1117897. [PMID: 38026354 PMCID: PMC10663276 DOI: 10.3389/fpubh.2023.1117897] [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: 12/07/2022] [Accepted: 10/10/2023] [Indexed: 12/01/2023] Open
Abstract
Objectives This study aimed to investigate the prevalence and related factors of abdominal obesity among urban adults aged 35 to 79 years in southwest China. Methods From September 2013 to March 2014, a multi-stage sampling was conducted, and a total of 10,981 people aged 35-79 years living in Chengdu and Chongqing were included. More than 30 investigators were trained in data collection, including questionnaire, anthropometric measurements and blood biomarkers testing. Abdominal obesity was defined as waist circumference ≥ 90 cm for men and ≥ 85 cm for women. Results The prevalence of abdominal obesity was 30.7%, 24.8% in males and 33.9% in females (p < 0.001). The prevalence of abdominal obesity increased with BMI. The prevalence of abdominal obesity was positively correlated with age, sex, marriage, alcohol consumption, hypertension and diabetes, and negatively correlated with high education level, smoking and Physical activity. Conclusion The prevalence of abdominal obesity among adults aged 35-79 in urban communities in southwest China is high, which is close to that of adults in urban communities in China. We should strengthen health education among the population, adopt healthy diet, maintain moderate physical activity and other measures to curb the prevalence of abdominal obesity in urban communities in southwest China.
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Affiliation(s)
- Chuan Huang
- Department of Cardiology, The Second People’s Hospital of Chengdu, Chengdu, Sichuan, China
| | - Ying Zhang
- Department of Neurology, The Second People’s Hospital of Chengdu, Chengdu, Sichuan, China
| | - Ya Liu
- Department of Endocrinology and Metabolism, Second People’s Hospital of Chengdu, Chengdu, Sichuan, China
| | - Jian-Xiong Liu
- Department of Cardiology, The Second People’s Hospital of Chengdu, Chengdu, Sichuan, China
| | - Yong-Mei Hu
- Department of Cardiology, The Second People’s Hospital of Chengdu, Chengdu, Sichuan, China
| | - Wei-Wei Tang
- School of Health Policy and Management, Nanjing Medical University, Nanjing, Jiangsu, China
- Jiangsu Provincial Institute of Health, Nanjing Medical University, Nanjing, Jiangsu, China
- Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Tzung-Dau Wang
- Department of Internal Medicine, Cardiovascular Center and Division of Cardiology, National Taiwan University Hospital, Taipei City, Taiwan, China
| | - Xiao-bo Huang
- Department of Cardiology, The Second People’s Hospital of Chengdu, Chengdu, Sichuan, China
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Derenko M, Denisova G, Litvinov A, Dambueva I, Malyarchuk B. Mitogenomics of the Koryaks and Evens of the northern coast of the Sea of Okhotsk. J Hum Genet 2023; 68:705-712. [PMID: 37316650 DOI: 10.1038/s10038-023-01173-x] [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: 03/24/2023] [Revised: 05/31/2023] [Accepted: 06/07/2023] [Indexed: 06/16/2023]
Abstract
Due to the geographical proximity of the northern coast of the Sea of Okhotsk and Kamchatka Peninsula to the Beringia, the indigenous populations of these territories are of great interest for elucidating the human settlement history of northern Asia and America. Meanwhile, there is a clear shortage of genetic studies of the indigenous populations of the northern coast of the Sea of Okhotsk. Here, in order to examine their fine-scale matrilineal genetic structure, ancestry and relationships with neighboring populations, we analyzed 203 complete mitogenomes (174 of which are new) from population samples of the Koryaks and Evens of the northern coast of the Sea of Okhotsk and the Chukchi of the extreme northeast Asia. The patterns observed underscore the reduced level of genetic diversity found in the Koryak, Even, and Chukchi populations, which, along with the high degree of interpopulation differentiation, may be the result of genetic drift. Our phylogeographic analysis reveals common Paleo-Asiatic ancestry for 51.1% of the Koryaks and 17.8% of the Evens. About third of the mitogenomes found in the Koryaks and Evens might be considered as ethno-specific, as these are virtually absent elsewhere in North, Central and East Asia. Coalescence ages of most of these lineages coincide well with the emergence and development of the Tokarev and Old Koryak archaeological cultures associated with the formation of the Koryaks, as well as with the period of separation and split of the North Tungusic groups migrated northwards from the Lake Baikal or the Amur River area.
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Affiliation(s)
- Miroslava Derenko
- Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya Street, 18, Magadan, 685000, Russia.
| | - Galina Denisova
- Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya Street, 18, Magadan, 685000, Russia
| | - Andrey Litvinov
- Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya Street, 18, Magadan, 685000, Russia
| | - Irina Dambueva
- Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya Street, 18, Magadan, 685000, Russia
| | - Boris Malyarchuk
- Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya Street, 18, Magadan, 685000, Russia
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10
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L Rocha J, Silva P, Santos N, Nakamura M, Afonso S, Qninba A, Boratynski Z, Sudmant PH, Brito JC, Nielsen R, Godinho R. North African fox genomes show signatures of repeated introgression and adaptation to life in deserts. Nat Ecol Evol 2023; 7:1267-1286. [PMID: 37308700 PMCID: PMC10527534 DOI: 10.1038/s41559-023-02094-w] [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: 09/01/2022] [Accepted: 04/26/2023] [Indexed: 06/14/2023]
Abstract
Elucidating the evolutionary process of animal adaptation to deserts is key to understanding adaptive responses to climate change. Here we generated 82 individual whole genomes of four fox species (genus Vulpes) inhabiting the Sahara Desert at different evolutionary times. We show that adaptation of new colonizing species to a hot arid environment has probably been facilitated by introgression and trans-species polymorphisms shared with older desert resident species, including a putatively adaptive 25 Mb genomic region. Scans for signatures of selection implicated genes affecting temperature perception, non-renal water loss and heat production in the recent adaptation of North African red foxes (Vulpes vulpes), after divergence from Eurasian populations approximately 78 thousand years ago. In the extreme desert specialists, Rueppell's fox (V. rueppellii) and fennec (V. zerda), we identified repeated signatures of selection in genes affecting renal water homeostasis supported by gene expression and physiological differences. Our study provides insights into the mechanisms and genetic underpinnings of a natural experiment of repeated adaptation to extreme conditions.
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Affiliation(s)
- Joana L Rocha
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal.
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal.
- Department of Integrative Biology and Department of Statistics, University of California Berkeley, Berkeley, CA, USA.
| | - Pedro Silva
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Nuno Santos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Mónia Nakamura
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Sandra Afonso
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Abdeljebbar Qninba
- Laboratory of Geophysics and Natural Hazards, Geophysics, Natural Patrimony and Green Chemistry Research Center (GEOPAC), Institut Scientifique, Mohammed V University of Rabat, Rabat, Morocco
| | - Zbyszek Boratynski
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Peter H Sudmant
- Department of Integrative Biology and Department of Statistics, University of California Berkeley, Berkeley, CA, USA
- Center for Computational Biology, University of California, Berkeley, CA, USA
| | - José C Brito
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Rasmus Nielsen
- Department of Integrative Biology and Department of Statistics, University of California Berkeley, Berkeley, CA, USA.
- Center for Computational Biology, University of California, Berkeley, CA, USA.
- Globe Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Raquel Godinho
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal.
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal.
- Department of Zoology, University of Johannesburg, Auckland Park, South Africa.
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11
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Malyarchuk BA. The role of Beringia in human adaptation to Arctic conditions based on results of genomic studies of modern and ancient populations. Vavilovskii Zhurnal Genet Selektsii 2023; 27:373-382. [PMID: 37465192 PMCID: PMC10350865 DOI: 10.18699/vjgb-23-45] [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: 08/03/2022] [Revised: 10/15/2022] [Accepted: 10/15/2022] [Indexed: 07/20/2023] Open
Abstract
The results of studies in Quaternary geology, archeology, paleoanthropology and human genetics demonstrate that the ancestors of Native Americans arrived in mid-latitude North America mainly along the Pacific Northwest Coast, but had previously inhabited the Arctic and during the last glacial maximum were in a refugium in Beringia, a land bridge connecting Eurasia and North America. The gene pool of Native Americans is represented by unique haplogroups of mitochondrial DNA and the Y chromosome, the evolutionary age of which ranges from 13 to 22 thousand years. The results of a paleogenomic analysis also show that during the last glacial maximum Beringia was populated by human groups that had arisen as a result of interaction between the most ancient Upper Paleolithic populations of Northern Eurasia and newcomer groups from East Asia. Approximately 20 thousand years ago the Beringian populations began to form, and the duration of their existence in relative isolation is estimated at about 5 thousand years. Thus, the adaptation of the Beringians to the Arctic conditions could have taken several millennia. The adaptation of Amerindian ancestors to high latitudes and cold climates is supported by genomic data showing that adaptive genetic variants in Native Americans are associated with various metabolic pathways: melanin production processes in the skin, hair and eyes, the functioning of the cardiovascular system, energy metabolism and immune response characteristics. Meanwhile, the analysis of the existing hypotheses about the selection of some genetic variants in the Beringian ancestors of the Amerindians in connection with adaptation to the Arctic conditions (for example, in the FADS, ACTN3, EDAR genes) shows the ambiguity of the testing results, which may be due to the loss of some traces of the "Beringian" adaptation in the gene pools of modern Native Americans. The most optimal strategy for further research seems to be the search for adaptive variant.
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Affiliation(s)
- B A Malyarchuk
- Institute of Biological Problems of the North, Far-East Branch of the Russian Academy of Sciences, Magadan, Russia N.A. Shilo North-East Interdisciplinary Scientific Research Institute, Far-East Branch of the Russian Academy of Sciences, Magadan, Russia
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12
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Li M, Li X, Wu Z, Zhang G, Wang N, Dou M, Liu S, Yang C, Meng G, Sun H, Hvilsom C, Xie G, Li Y, Li ZH, Wang W, Jiang Y, Heller R, Wang Y. Convergent molecular evolution of thermogenesis and circadian rhythm in Arctic ruminants. Proc Biol Sci 2023; 290:20230538. [PMID: 37253422 PMCID: PMC10229229 DOI: 10.1098/rspb.2023.0538] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 05/02/2023] [Indexed: 06/01/2023] Open
Abstract
The muskox and reindeer are the only ruminants that have evolved to survive in harsh Arctic environments. However, the genetic basis of this Arctic adaptation remains largely unclear. Here, we compared a de novo assembled muskox genome with reindeer and other ruminant genomes to identify convergent amino acid substitutions, rapidly evolving genes and positively selected genes among the two Arctic ruminants. We found these candidate genes were mainly involved in brown adipose tissue (BAT) thermogenesis and circadian rhythm. Furthermore, by integrating transcriptomic data from goat adipose tissues (white and brown), we demonstrated that muskox and reindeer may have evolved modulating mitochondrion, lipid metabolism and angiogenesis pathways to enhance BAT thermogenesis. In addition, results from co-immunoprecipitation experiments prove that convergent amino acid substitution of the angiogenesis-related gene hypoxia-inducible factor 2alpha (HIF2A), resulting in weakening of its interaction with prolyl hydroxylase domain-containing protein 2 (PHD2), may increase angiogenesis of BAT. Altogether, our work provides new insights into the molecular mechanisms involved in Arctic adaptation.
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Affiliation(s)
- Manman Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, People's Republic of China
| | - Xinmei Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, People's Republic of China
| | - Zhipei Wu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, People's Republic of China
| | - Guanghui Zhang
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, People's Republic of China
| | - Nini Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, People's Republic of China
| | - Mingle Dou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, People's Republic of China
| | - Shanlin Liu
- Department of Entomology, China Agricultural University, West Yuanmingyuan Road, Beijing 100193, People's Republic of China
| | - Chentao Yang
- BGI Shenzhen, Shenzhen 518083, People's Republic of China
| | - Guanliang Meng
- Centre of Taxonomy and Evolutionary Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Hailu Sun
- BGI Shenzhen, Shenzhen 518083, People's Republic of China
| | | | - Guoxiang Xie
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, People's Republic of China
| | - Yang Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, People's Republic of China
| | - Zhuo hui Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, People's Republic of China
| | - Wei Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, People's Republic of China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, People's Republic of China
| | - Rasmus Heller
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Yu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, People's Republic of China
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, People's Republic of China
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13
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Tobler R, Souilmi Y, Huber CD, Bean N, Turney CSM, Grey ST, Cooper A. The role of genetic selection and climatic factors in the dispersal of anatomically modern humans out of Africa. Proc Natl Acad Sci U S A 2023; 120:e2213061120. [PMID: 37220274 PMCID: PMC10235988 DOI: 10.1073/pnas.2213061120] [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: 07/29/2022] [Accepted: 03/14/2023] [Indexed: 05/25/2023] Open
Abstract
The evolutionarily recent dispersal of anatomically modern humans (AMH) out of Africa (OoA) and across Eurasia provides a unique opportunity to examine the impacts of genetic selection as humans adapted to multiple new environments. Analysis of ancient Eurasian genomic datasets (~1,000 to 45,000 y old) reveals signatures of strong selection, including at least 57 hard sweeps after the initial AMH movement OoA, which have been obscured in modern populations by extensive admixture during the Holocene. The spatiotemporal patterns of these hard sweeps provide a means to reconstruct early AMH population dispersals OoA. We identify a previously unsuspected extended period of genetic adaptation lasting ~30,000 y, potentially in the Arabian Peninsula area, prior to a major Neandertal genetic introgression and subsequent rapid dispersal across Eurasia as far as Australia. Consistent functional targets of selection initiated during this period, which we term the Arabian Standstill, include loci involved in the regulation of fat storage, neural development, skin physiology, and cilia function. Similar adaptive signatures are also evident in introgressed archaic hominin loci and modern Arctic human groups, and we suggest that this signal represents selection for cold adaptation. Surprisingly, many of the candidate selected loci across these groups appear to directly interact and coordinately regulate biological processes, with a number associated with major modern diseases including the ciliopathies, metabolic syndrome, and neurodegenerative disorders. This expands the potential for ancestral human adaptation to directly impact modern diseases, providing a platform for evolutionary medicine.
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Affiliation(s)
- Raymond Tobler
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, SA5005, Australia
| | - Yassine Souilmi
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, SA5005, Australia
- Environment Institute, The University of Adelaide, Adelaide, SA5005, Australia
| | - Christian D. Huber
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, SA5005, Australia
| | - Nigel Bean
- Australian Research Council Centre of Excellence for Mathematical and Statistical Frontiers, The University of Adelaide, Adelaide, SA5005, Australia
- School of Mathematical Sciences, The University of Adelaide, Adelaide, SA5005, Australia
| | - Chris S. M. Turney
- Division of Research, University of Technology Sydney, Ultimo, NSW2007, Australia
| | - Shane T. Grey
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW2052, Australia
- Transplantation Immunology Group, Translation Science Pillar, Garvan Institute of Medical Research, Darlinghurst, NSW2010, Australia
| | - Alan Cooper
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, SA5005, Australia
- Blue Sky Genetics, Ashton, SA5137, Australia
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14
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Zhang Y, Han S, Liu C, Zheng Y, Li H, Gao F, Bian Y, Liu X, Liu H, Hu S, Li Y, Chen ZJ, Zhao S, Zhao H. THADA inhibition in mice protects against type 2 diabetes mellitus by improving pancreatic β-cell function and preserving β-cell mass. Nat Commun 2023; 14:1020. [PMID: 36823211 PMCID: PMC9950491 DOI: 10.1038/s41467-023-36680-0] [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: 11/19/2021] [Accepted: 02/09/2023] [Indexed: 02/25/2023] Open
Abstract
Impaired insulin secretion is a hallmark in type 2 diabetes mellitus (T2DM). THADA has been identified as a candidate gene for T2DM, but its role in glucose homeostasis remains elusive. Here we report that THADA is strongly activated in human and mouse islets of T2DM. Both global and β-cell-specific Thada-knockout mice exhibit improved glycemic control owing to enhanced β-cell function and decreased β-cell apoptosis. THADA reduces endoplasmic reticulum (ER) Ca2+ stores in β-cells by inhibiting Ca2+ re-uptake via SERCA2 and inducing Ca2+ leakage through RyR2. Upon persistent ER stress, THADA interacts with and activates the pro-apoptotic complex comprising DR5, FADD and caspase-8, thus aggravating ER stress-induced apoptosis. Importantly, THADA deficiency protects mice from high-fat high-sucrose diet- and streptozotocin-induced hyperglycemia by restoring insulin secretion and preserving β-cell mass. Moreover, treatment with alnustone inhibits THADA's function, resulting in ameliorated hyperglycemia in obese mice. Collectively, our results support pursuit of THADA as a potential target for developing T2DM therapies.
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Affiliation(s)
- Yuqing Zhang
- Center for Reproductive Medicine, Shandong University, 250012, Jinan, Shandong, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, 250012, Jinan, Shandong, China.,Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250012, Jinan, Shandong, China
| | - Shan Han
- Center for Reproductive Medicine, Shandong University, 250012, Jinan, Shandong, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, 250012, Jinan, Shandong, China.,Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250012, Jinan, Shandong, China
| | - Congcong Liu
- Center for Reproductive Medicine, Shandong University, 250012, Jinan, Shandong, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, 250012, Jinan, Shandong, China.,Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250012, Jinan, Shandong, China
| | - Yuanwen Zheng
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250021, Jinan, Shandong, China
| | - Hao Li
- Shandong Provincial Qianfoshan Hospital, Shandong University, 250014, Jinan, Shandong, China
| | - Fei Gao
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Science, 100101, Beijing, China
| | - Yuehong Bian
- Center for Reproductive Medicine, Shandong University, 250012, Jinan, Shandong, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, 250012, Jinan, Shandong, China.,Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250012, Jinan, Shandong, China
| | - Xin Liu
- Center for Reproductive Medicine, Shandong University, 250012, Jinan, Shandong, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, 250012, Jinan, Shandong, China.,Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250012, Jinan, Shandong, China
| | - Hongbin Liu
- Center for Reproductive Medicine, Shandong University, 250012, Jinan, Shandong, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, 250012, Jinan, Shandong, China.,Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250012, Jinan, Shandong, China
| | - Shourui Hu
- Center for Reproductive Medicine, Shandong University, 250012, Jinan, Shandong, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, 250012, Jinan, Shandong, China.,Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250012, Jinan, Shandong, China
| | - Yuxuan Li
- Center for Reproductive Medicine, Shandong University, 250012, Jinan, Shandong, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, 250012, Jinan, Shandong, China.,Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250012, Jinan, Shandong, China
| | - Zi-Jiang Chen
- Center for Reproductive Medicine, Shandong University, 250012, Jinan, Shandong, China. .,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, 250012, Jinan, Shandong, China. .,Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250012, Jinan, Shandong, China. .,Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, 200135, Shanghai, China. .,Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences (No. 2021RU001), Shandong, 250012, Jinan, China.
| | - Shigang Zhao
- Center for Reproductive Medicine, Shandong University, 250012, Jinan, Shandong, China. .,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, 250012, Jinan, Shandong, China. .,Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250012, Jinan, Shandong, China.
| | - Han Zhao
- Center for Reproductive Medicine, Shandong University, 250012, Jinan, Shandong, China. .,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, 250012, Jinan, Shandong, China. .,Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250012, Jinan, Shandong, China.
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15
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Shao D, Yang Y, Shi S, Tong H. Three-Dimensional Organization of Chicken Genome Provides Insights into Genetic Adaptation to Extreme Environments. Genes (Basel) 2022; 13:genes13122317. [PMID: 36553584 PMCID: PMC9778438 DOI: 10.3390/genes13122317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 12/06/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
The high-throughput chromosome conformation capture (Hi-C) technique is widely used to study the functional roles of the three-dimensional (3D) architecture of genomes. However, the knowledge of the 3D genome structure and its dynamics during extreme environmental adaptations remains poor. Here, we characterized 3D genome architectures using the Hi-C technique for chicken liver cells. Upon comparing Lindian chicken (LDC) liver cells with Wenchang chicken (WCC) liver cells, we discovered that environmental adaptation contributed to the switching of A/B compartments, the reorganization of topologically associated domains (TADs), and TAD boundaries in both liver cells. In addition, the analysis of the switching of A/B compartments revealed that the switched compartmental genes (SCGs) were strongly associated with extreme environment adaption-related pathways, including tight junction, notch signaling pathway, vascular smooth muscle contraction, and the RIG-I-like receptor signaling pathway. The findings of this study advanced our understanding of the evolutionary role of chicken 3D genome architecture and its significance in genome activity and transcriptional regulation.
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Affiliation(s)
- Dan Shao
- Laboratory of Poultry Production, College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou 225125, China
| | - Yu Yang
- Laboratory of Poultry Production, College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China
- Correspondence: (Y.Y.); (S.S.)
| | - Shourong Shi
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou 225125, China
- Correspondence: (Y.Y.); (S.S.)
| | - Haibing Tong
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou 225125, China
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16
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Fedorova SA, Khusnutdinova EK. Genetic Structure and Genetic History of the Sakha (Yakuts) Population. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422120031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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17
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Balentine CM, Bolnick DA. Parallel evolution in human populations: A biocultural perspective. Evol Anthropol 2022; 31:302-316. [PMID: 36059181 DOI: 10.1002/evan.21956] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 03/09/2022] [Accepted: 07/30/2022] [Indexed: 12/27/2022]
Abstract
Parallel evolution-where different populations evolve similar traits in response to similar environments-has been a topic of growing interest to biologists and biological anthropologists for decades. Parallel evolution occurs in human populations thanks to myriad biological and cultural mechanisms that permit humans to survive and thrive in diverse environments worldwide. Because humans shape and are shaped by their environments, biocultural approaches that emphasize the interconnections between biology and culture are key to understanding parallel evolution in human populations as well as the nuances of human biological variation and adaptation. In this review, we discuss how biocultural theory has been and can be applied to studies of parallel evolution and adaptation more broadly. We illustrate this through four examples of parallel evolution in humans: malaria resistance, lactase persistence, cold tolerance, and high-altitude adaptation.
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Affiliation(s)
- Christina M Balentine
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA.,Department of Anthropology, University of Connecticut, Storrs, Connecticut, USA
| | - Deborah A Bolnick
- Department of Anthropology, University of Connecticut, Storrs, Connecticut, USA.,Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut, USA
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18
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Zhang Y, Zhang WQ, Tang WW, Zhang WY, Liu JX, Xu RH, Wang TD, Huang XB. The prevalence of obesity-related hypertension among middle-aged and older adults in China. Front Public Health 2022; 10:865870. [PMID: 36504973 PMCID: PMC9731297 DOI: 10.3389/fpubh.2022.865870] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 09/23/2022] [Indexed: 11/25/2022] Open
Abstract
Objective The aim of our study was to assess the prevalence and geographic variation of obesity-related hypertension in China among adults aged 45 years or older. Methods Data were derived from the China Health and Retirement Longitudinal Study (CHARLS) conducted in 2015. Stratified sample households covered 150 counties/districts and 450 villages/urban communities from 28 provinces by using household questionnaires, clinical measurements, and blood-based bioassays. A multivariable non-conditional logistic regression model was used to analyze the risk factors correlated with obesity-related hypertension. Results The prevalence of obesity-related hypertension was 22.7%, ~120 million people, among adults aged 45 years or older in China. For people in the age ranges of 45-54, 55-64, 65-74, and ≥75 years, the prevalence of obesity-related hypertension was 16.7, 24.3, 27, and 26.7%, respectively, and the prevalence of obesity-related hypertension among hypertensive participants was 66.0, 60.9, 54.2, and 47.3%, respectively. Compared with non-obesity-related hypertension, the obesity-related hypertensive patients had a higher prevalence of diabetes mellitus, dyslipidemia, and hyperuricemia (all P < 0.0001). The prevalence of obesity-related hypertension showed a decreasing gradient from north to south and from east to west. Multivariate logistic regression analysis showed that female gender, living in urban areas, diabetes mellitus, dyslipidemia, and hyperuricemia were positively correlated with obesity-related hypertension. Conclusion The prevalence of obesity-related hypertension among adults aged 45 years or older was high in China. Among hypertensive participants, older age was negatively correlated with obesity-related hypertension. Obesity-related hypertensive participants are more prone to aggregation of risk factors of atherosclerotic cardiovascular disease.
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Affiliation(s)
- Yang Zhang
- Department of Cardiology, Chengdu Second People's Hospital, Chengdu, China
| | - Wen-Qiang Zhang
- Department of Epidemiology and Health Statistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Wei-Wei Tang
- School of Health Policy and Management, Nanjing Medical University, Nanjing, China,Institute of Healthy Jiangsu Development, Nanjing Medical University, Nanjing, China
| | - Wen-Yong Zhang
- Department of Cardiology, Chengdu Second People's Hospital, Chengdu, China
| | - Jian-Xiong Liu
- Department of Cardiology, Chengdu Second People's Hospital, Chengdu, China
| | - Rong-Hua Xu
- Stroke Center, Chengdu Second People's Hospital, Chengdu, China
| | - Tzung-Dau Wang
- Division of Cardiology, Department of Internal Medicine, National Taiwan University Hospital, Taipei City, Taiwan,*Correspondence: Tzung-Dau Wang
| | - Xiao-Bo Huang
- Department of Cardiology, Chengdu Second People's Hospital, Chengdu, China,Xiao-Bo Huang
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19
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Aboul-Naga AM, Alsamman AM, El Allali A, Elshafie MH, Abdelal ES, Abdelkhalek TM, Abdelsabour TH, Mohamed LG, Hamwieh A. Genome-wide analysis identified candidate variants and genes associated with heat stress adaptation in Egyptian sheep breeds. Front Genet 2022; 13:898522. [PMID: 36263427 PMCID: PMC9574253 DOI: 10.3389/fgene.2022.898522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 09/05/2022] [Indexed: 11/24/2022] Open
Abstract
Heat stress caused by climatic changes is one of the most significant stresses on livestock in hot and dry areas. It has particularly adverse effects on the ability of the breed to maintain homeothermy. Developing countries are advised to protect and prepare their animal resources in the face of potential threats such as climate change. The current study was conducted in Egypt’s three hot and dry agro-ecological zones. Three local sheep breeds (Saidi, Wahati, and Barki) were studied with a total of 206 ewes. The animals were exercised under natural heat stress. The heat tolerance index of the animals was calculated to identify animals with high and low heat tolerance based on their response to meteorological and physiological parameters. Genomic variation in these breeds was assessed using 64,756 single nucleotide polymorphic markers (SNPs). From the perspective of comparative adaptability to harsh conditions, our objective was to investigate the genomic structure that might control the adaptability of local sheep breeds to environmental stress under hot and dry conditions. In addition, indices of population structure and diversity of local breeds were examined. Measures of genetic diversity showed a significant influence of breed and location on populations. The standardized index of association (rbarD) ranged from 0.0012 (Dakhla) to 0.026 (Assuit), while for the breed, they ranged from 0.004 (Wahati) to 0.0103 (Saidi). The index of association analysis (Ia) ranged from 1.42 (Dakhla) to 35.88 (Assuit) by location and from 6.58 (Wahati) to 15.36 (Saidi) by breed. The most significant SNPs associated with heat tolerance were found in the MYO5A, PRKG1, GSTCD, and RTN1 genes (p ≤ 0.0001). MYO5A produces a protein widely distributed in the melanin-producing neural crest of the skin. Genetic association between genetic and phenotypic variations showed that OAR1_18300122.1, located in ST3GAL3, had the greatest positive effect on heat tolerance. Genome-wide association analysis identified SNPs associated with heat tolerance in the PLCB1, STEAP3, KSR2, UNC13C, PEBP4, and GPAT2 genes.
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Affiliation(s)
- Adel M. Aboul-Naga
- Animal Production Research Institute, Agriculture Research Center (ARC), Cairo, Egypt
- *Correspondence: Adel M. Aboul-Naga, ; Alsamman M. Alsamman,
| | - Alsamman M. Alsamman
- Agricultural Genetic Engineering Research Institute, Giza, Egypt
- *Correspondence: Adel M. Aboul-Naga, ; Alsamman M. Alsamman,
| | - Achraf El Allali
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Mohmed H. Elshafie
- Animal Production Research Institute, Agriculture Research Center (ARC), Cairo, Egypt
| | - Ehab S. Abdelal
- Animal Production Research Institute, Agriculture Research Center (ARC), Cairo, Egypt
| | - Tarek M. Abdelkhalek
- Animal Production Research Institute, Agriculture Research Center (ARC), Cairo, Egypt
| | - Taha H. Abdelsabour
- Animal Production Research Institute, Agriculture Research Center (ARC), Cairo, Egypt
| | - Layaly G. Mohamed
- Animal Production Research Institute, Agriculture Research Center (ARC), Cairo, Egypt
| | - Aladdin Hamwieh
- International Center For Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
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20
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Kolesnikov NA, Kharkov VN, Zarubin AA, Voevoda MI, Gubina MA, Shtygasheva OV, Maksimova NR, Sukhomyasova AL, Stepanov VA. Signals of Directed Selection in the Indigenous Populations of Siberia. RUSS J GENET+ 2022. [DOI: 10.1134/s102279542204007x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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21
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Funk H, DiVita DJ, Sizemore HE, Wehrle K, Miller CLW, Fraley ME, Mullins AK, Guy AR, Phizicky EM, Guy MP. Identification of a Trm732 Motif Required for 2'- O-methylation of the tRNA Anticodon Loop by Trm7. ACS OMEGA 2022; 7:13667-13675. [PMID: 35559166 PMCID: PMC9088939 DOI: 10.1021/acsomega.1c07231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/31/2022] [Indexed: 06/15/2023]
Abstract
Posttranscriptional tRNA modifications are essential for proper gene expression, and defects in the enzymes that perform tRNA modifications are associated with numerous human disorders. Throughout eukaryotes, 2'-O-methylation of residues 32 and 34 of the anticodon loop of tRNA is important for proper translation, and in humans, a lack of these modifications results in non-syndromic X-linked intellectual disability. In yeast, the methyltransferase Trm7 forms a complex with Trm732 to 2'-O-methylate tRNA residue 32 and with Trm734 to 2'-O-methylate tRNA residue 34. Trm732 and Trm734 are required for the methylation activity of Trm7, but the role of these auxiliary proteins is not clear. Additionally, Trm732 and Trm734 homologs are implicated in biological processes not directly related to translation, suggesting that these proteins may have additional cellular functions. To identify critical amino acids in Trm732, we generated variants and tested their ability to function in yeast cells. We identified a conserved RRSAGLP motif in the conserved DUF2428 domain of Trm732 that is required for tRNA modification activity by both yeast Trm732 and its human homolog, THADA. The identification of Trm732 variants that lack tRNA modification activity will help to determine if other biological functions ascribed to Trm732 and THADA are directly due to tRNA modification or to secondary effects due to other functions of these proteins.
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Affiliation(s)
- Holly
M. Funk
- Department
of Chemistry & Biochemistry, Northern
Kentucky University, Highland
Heights, Kentucky 41076, United States
| | - Daisy J. DiVita
- Department
of Chemistry & Biochemistry, Northern
Kentucky University, Highland
Heights, Kentucky 41076, United States
| | - Hannah E. Sizemore
- Department
of Chemistry & Biochemistry, Northern
Kentucky University, Highland
Heights, Kentucky 41076, United States
| | - Kendal Wehrle
- Department
of Chemistry & Biochemistry, Northern
Kentucky University, Highland
Heights, Kentucky 41076, United States
| | - Catherine L. W. Miller
- Department
of Biochemistry and Biophysics, University
of Rochester School of Medicine, Rochester, New York 14642, United States
| | - Morgan E. Fraley
- Department
of Chemistry & Biochemistry, Northern
Kentucky University, Highland
Heights, Kentucky 41076, United States
| | - Alex K. Mullins
- Department
of Chemistry & Biochemistry, Northern
Kentucky University, Highland
Heights, Kentucky 41076, United States
| | - Adrian R. Guy
- Department
of Chemistry & Biochemistry, Northern
Kentucky University, Highland
Heights, Kentucky 41076, United States
| | - Eric M. Phizicky
- Department
of Biochemistry and Biophysics, University
of Rochester School of Medicine, Rochester, New York 14642, United States
| | - Michael P. Guy
- Department
of Chemistry & Biochemistry, Northern
Kentucky University, Highland
Heights, Kentucky 41076, United States
- Department
of Biochemistry and Biophysics, University
of Rochester School of Medicine, Rochester, New York 14642, United States
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22
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Cavedon M, vonHoldt B, Hebblewhite M, Hegel T, Heppenheimer E, Hervieux D, Mariani S, Schwantje H, Steenweg R, Watters M, Musiani M. Selection of both habitat and genes in specialized and endangered caribou. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2022; 36. [PMID: 35146809 DOI: 10.1111/cobi.13900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 01/26/2022] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
Genetic mechanisms determining habitat selection and specialization of individuals within species have been hypothesized, but not tested at the appropriate individual level in nature. In this work, we analyzed habitat selection for 139 GPS-collared caribou belonging to three declining ecotypes sampled throughout Northwestern Canada. We used Resource Selection Functions (RSFs) comparing resources at used and available locations. We found that the three caribou ecotypes differed in their use of habitat suggesting specialization. On expected grounds, we also found differences in habitat selection between summer and winter, but also, originally, among the individuals within an ecotype. We next obtained Single Nucleotide Polymorphisms (SNPs) for the same caribou individuals, we detected those associated to habitat selection, and then identified genes linked to these SNPs. These genes had functions related in other organisms to habitat and dietary specializations, and climatic adaptations. We therefore suggest that individual variation in habitat selection was based on genotypic variation in the SNPs of individual caribou, indicating that genetic forces underlie habitat and diet selection in the species. We also suggest that the associations between habitat and genes that we detected may lead to lack of resilience in the species, thus contributing to caribou endangerment. Our work emphasizes that similar mechanisms may exist for other specialized, endangered species. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Maria Cavedon
- Faculty of Environmental Design, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Bridgett vonHoldt
- Department of Ecology & Evolutionary Biology, Princeton University, 106A Guyot Hall, Princeton, NJ, 08544-2016, USA
| | - Mark Hebblewhite
- Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, College of Forestry and Conservation, University of Montana, Montana, MT, 59812, USA
| | - Troy Hegel
- Yukon Department of Environment, Whitehorse, Yukon, Y1A 2C6, Canada
- Fish and Wildlife Stewardship Branch, Alberta Environment and Parks, 4999 98 Ave., Edmonton, AB, T6B 2×3, Canada
| | - Elizabeth Heppenheimer
- Department of Ecology & Evolutionary Biology, Princeton University, 106A Guyot Hall, Princeton, NJ, 08544-2016, USA
| | - Dave Hervieux
- Fish and Wildlife Stewardship Branch, Alberta Environment and Parks, Grande Prairie, AB, T8V 6J4, Canada
| | - Stefano Mariani
- School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, UK
| | - Helen Schwantje
- Wildlife and Habitat Branch, Ministry of Forests, Lands, Natural Resource Operations and Rural Development, Government of British Columbia, 2080 Labieux Road, Nanaimo, BC, V9T 6J 9, Canada
| | - Robin Steenweg
- Pacific Region, Canadian Wildlife Service, Environment and Climate Change Canada, 5421 Robertson Road, Delta, BC, V4K 3N2, Canada
| | - Megan Watters
- Land and Resource Specialist, 300 - 10003 110th Avenue Fort, St. John, BC, V1J 6M7, Canada
| | - Marco Musiani
- Dept. of Biological Sciences, Faculty of Science and Veterinary Medicine (Joint Appointment), University of Calgary, Calgary, AB, T2N 1N4, Canada
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23
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Malyarchuk BA, Derenko MV, Denisova GA. Adaptive Changes in Fatty Acid Desaturation Genes in Indigenous Populations of Northeast Siberia. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421120103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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24
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Yudin NS, Yurchenko AA, Larkin DM. [Signatures of selection and candidate genes for adaptation to extreme environmental factors in the genomes of Turano-Mongolian cattle breeds]. Vavilovskii Zhurnal Genet Selektsii 2021; 25:190-201. [PMID: 34901717 PMCID: PMC8627871 DOI: 10.18699/vj21.023] [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: 09/20/2020] [Revised: 10/18/2020] [Accepted: 10/20/2020] [Indexed: 11/19/2022] Open
Abstract
Changes in the environment force populations of organisms to adapt to new conditions, either through phenotypic plasticity or through genetic or epigenetic changes. Signatures of selection, such as specific changes in the frequency of alleles and haplotypes, as well as the reduction or increase in genetic diversity, help to identify changes in the cattle genome in response to natural and artificial selection, as well as loci and genetic variants directly affecting adaptive and economically important traits. Advances in genetics and biotechnology enable a rapid transfer of unique genetic variants that have originated in local cattle breeds in the process of adaptation to local environments into the genomes of cosmopolitan high-performance breeds, in order to preserve their outstanding performance in new environments. It is also possible to use genomic selection approach to increase the frequency of already present adaptive alleles in cosmopolitan breeds. The review examines recent work on the origin and evolution of Turano-Mongolian cattle breeds, adaptation of Turano-Mongolian cattle to extreme environments, and summarizes available information on potential candidate genes for climate adaptation of Turano-Mongolian breeds, including cold resistance genes, immune response genes, and high-altitude adaptation genes. The authors conclude that the current literature data do not provide preference to one of the two possible scenarios of Turano-Mongolian breed origins: as a result of the domestication of a wild aurochs at East Asia or as a result of the migration of taurine proto-population from the Middle East. Turano-Mongolian breeds show a high degree of adaptation to extreme climatic conditions (cold, heat, lack of oxygen in the highlands) and parasites (mosquitoes, ticks, bacterial and viral infections). As a result of high-density genotyping and sequencing of genomes and transcriptomes, prospective candidate genes and genetic variants involved in adaptation to environmental factors have recently been identified.
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Affiliation(s)
- N S Yudin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A A Yurchenko
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - D M Larkin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia The Royal Veterinary College, University of London, London, United Kingdom
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25
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Mitogenomics of modern Mongolic-speaking populations. Mol Genet Genomics 2021; 297:47-62. [PMID: 34757478 DOI: 10.1007/s00438-021-01830-w] [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: 03/11/2021] [Accepted: 10/27/2021] [Indexed: 10/19/2022]
Abstract
Here, we present a comprehensive data set of 489 complete mitogenomes (211 of which are new) from four Mongolic-speaking populations (Mongols, Barghuts, Khamnigans, and Buryats) to investigate their matrilineal genetic structure, ancestry and relationship with other ethnic groups. We show that along with very high levels of genetic diversity and lack of genetic differentiation, Mongolic-speaking populations exhibit strong genetic resemblance to East Asian populations of Chinese, Japanese, and Uyghurs. Phylogeographic analysis of complete mitogenomes reveals the presence of different components in the gene pools of modern Mongolic-speaking populations-the main East Eurasian component is represented by mtDNA lineages of East Asian, Siberian and autochthonous (the Baikal region/Mongolian) ancestry, whereas the less pronounced West Eurasian component can be ascribed to Europe and West Asia/Caucasus. We also observed that up to one third of the mtDNA subhaplogroups identified in Mongolic-speaking populations can be considered as Mongolic-specific with the coalescence age of most of them not exceeding 1.7 kya. This coincides well with the population size growth which started around 1.1 kya and is detectable only in the Bayesian Skyline Plot constructed based on Mongolic-specific mitogenomes. Our data suggest that the genetic structure established during the Mongol empire is still retained in present-day Mongolic-speaking populations.
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26
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Yasukochi Y, Shin S, Wakabayashi H, Maeda T. Upregulation of cathepsin L gene under mild cold conditions in young Japanese male adults. J Physiol Anthropol 2021; 40:16. [PMID: 34686211 PMCID: PMC8533667 DOI: 10.1186/s40101-021-00267-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 10/09/2021] [Indexed: 12/03/2022] Open
Abstract
Background Physiological thermoregulatory systems in humans have been a key factor for adaptation to local environments after their exodus from Africa, particularly, to cold environments outside Africa. Recent studies using high-throughput sequencing have identified various genes responsible for cold adaptation. However, the molecular mechanisms underlying initial thermoregulation in response to acute cold exposure remain unclear. Therefore, we investigated transcriptional profiles of six young Japanese male adults exposed to acute cold stress. Methods In a climatic chamber, the air temperature was maintained at 28°C for 65 min and was then gradually decreased to 19°C for 70 min. Saliva samples were obtained from the subjects at 28°C before and after 19°C cold exposure and were used for RNA sequencing. Results In the cold exposure experiment, expression levels of 14 genes were significantly changed [false discovery rate (FDR) < 0.05] although the degree of transcriptional changes was not high due to experimental conditions or blunted transcriptional reaction in saliva to cold stress. As a result, differential gene expression analyses detected the cathepsin L (CTSL) gene to be significantly upregulated, with FDR < 0.05 and log2 fold change value > 1; thus, this gene was identified as a differentially expressed gene. Given that the cathepsin L protein is related to invasion of the novel coronavirus (SARS-CoV-2), mild cold stress might alter the susceptibility to coronavirus disease-19 in humans. The gene ontology enrichment analysis for 14 genes with FDR < 0.05 suggested that immune-related molecules could be activated by mild cold stress. Conclusions The results obtained from this study indicate that CTSL expression levels can be altered by acute mild cold stress. Supplementary Information The online version contains supplementary material available at 10.1186/s40101-021-00267-9.
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Affiliation(s)
- Yoshiki Yasukochi
- Department of Human Functional Genomics, Advanced Science Research Promotion Center, Organization for the Promotion of Regional Innovation, Mie University, 1577 Kurima-machiya, Tsu, Mie, 514-8507, Japan. .,Department of Genome Analysis, Institute of Biomedical Science, Kansai Medical University, 2-5-1 Shinmachi, Hirakata, Osaka, 573-1010, Japan.
| | - Sora Shin
- Department of Human Science, Graduate School of Design, Kyushu University, 4-9-1 Shiobaru, Minami-ku, Fukuoka, 815-8540, Japan
| | - Hitoshi Wakabayashi
- Faculty of Engineering, Hokkaido University, N13 W8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
| | - Takafumi Maeda
- Department of Human Science, Faculty of Design, Kyushu University, 4-9-1 Shiobaru, Minami-ku, Fukuoka, 815-8540, Japan.,Physiological Anthropology Research Center, Faculty of Design, Kyushu University, 4-9-1 Shiobaru, Minami-ku, Fukuoka, 815-8540, Japan
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27
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Kramer KL, Campbell BC, Achenbach A, Hackman JV. Sex differences in adipose development in a hunter-gatherer population. Am J Hum Biol 2021; 34:e23688. [PMID: 34655448 DOI: 10.1002/ajhb.23688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 09/09/2021] [Accepted: 09/28/2021] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVE Humans are unusually sexually dimorphic in body composition, with adult females having on average nearly twice the fat mass as males. The development of adipose sex differences has been well characterized for children growing up in food-abundant environments, with less known about cross-cultural variation, particularly in populations without exposure to market foods, mechanized technologies, schooling, vaccination, or other medical interventions. METHODS To add to the existing cross-cultural data, we fit multiple growth curves to body composition and anthropometric data to describe adipose development for the Savanna Pumé, South American hunter-gatherers. RESULTS (1) Little evidence is found for an adiposity 'rebound' at the end of early childhood among either Savanna Pumé girls or boys. (2) Rather, fat deposition fluctuates during childhood, from age ~4 to ~9 years, with no appreciable accumulation until the onset of puberty, a pattern also observed among Congo Baka hunter-gatherers. (3) Body fat fluctuations are more pronounced for girls than boys. (4) The age of peak skeletal, weight, and adipose gains are staggered to a much greater extent among the Savanna Pumé compared to the National Health and Nutrition Examination Survey (NHANES III) reference, suggesting this is an important developmental strategy in lean populations. CONCLUSION Documenting growth patterns under diverse preindustrial energetic conditions provides an important baseline for understanding sex differences in body fat emerging today under food abundance.
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Affiliation(s)
- Karen L Kramer
- Department of Anthropology, University of Utah, Salt Lake City, Utah, USA
| | - Benjamin C Campbell
- Department of Anthropology, University of Wisconsin, Milwaukee, Wisconsin, USA
| | - Alan Achenbach
- Department of Anthropology, University of Utah, Salt Lake City, Utah, USA
| | - Joseph V Hackman
- Department of Anthropology, University of Utah, Salt Lake City, Utah, USA
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28
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Kolmykov S, Vasiliev G, Osadchuk L, Kleschev M, Osadchuk A. Whole-Exome Sequencing Analysis of Human Semen Quality in Russian Multiethnic Population. Front Genet 2021; 12:662846. [PMID: 34178030 PMCID: PMC8232892 DOI: 10.3389/fgene.2021.662846] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 04/19/2021] [Indexed: 01/12/2023] Open
Abstract
The global trend toward the reduction of human spermatogenic function observed in many countries, including Russia, raised the problem of extensive screening and monitoring of male fertility and elucidation of its genetic and ethnic mechanisms. Recently, whole-exome sequencing (WES) was developed as a powerful tool for genetic analysis of complex traits. We present here the first Russian WES study for identification of new genes associated with semen quality. The experimental 3 × 2 design of the WES study was based on the analysis of 157 samples including three ethnic groups—Slavs (59), Buryats (n = 49), and Yakuts (n = 49), and two different semen quality groups—pathozoospermia (n = 95) and normospermia (n = 62). Additionally, our WES study group was negative for complete AZF microdeletions of the Y-chromosome. The normospermia group included men with normal sperm parameters in accordance with the WHO-recommended reference limit. The pathozoospermia group included men with impaired semen quality, namely, with any combined parameters of sperm concentration <15 × 106/ml, and/or progressive motility <32%, and/or normal morphology <4%. The WES was performed for all 157 samples. Subsequent calling and filtering of variants were carried out according to the GATK Best Practices recommendations. On the genotyping stage, the samples were combined into four cohorts: three sets corresponded to three ethnic groups, and the fourth set contained all the 157 whole-exome samples. Association of the obtained polymorphisms with semen quality parameters was investigated using the χ2 test. To prioritize the obtained variants associated with pathozoospermia, their effects were determined using Ensembl Variant Effect Predictor. Moreover, polymorphisms located in genes expressed in the testis were revealed based on the genomic annotation. As a result, the nine potential SNP markers rs6971091, rs557806, rs610308, rs556052, rs1289658, rs278981, rs1129172, rs12268007, and rs17228441 were selected for subsequent verification on our previously collected population sample (about 1,500 males). The selected variants located in seven genes FAM71F1, PPP1R15A, TRIM45, PRAME, RBM47, WDFY4, and FSIP2 that are expressed in the testis and play an important role in cell proliferation, meiosis, and apoptosis.
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Affiliation(s)
- Semyon Kolmykov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia.,Department of Computational Biology, Sirius University of Science and Technology, Sochi, Russia
| | - Gennady Vasiliev
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Ludmila Osadchuk
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Maxim Kleschev
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexander Osadchuk
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
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29
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Aguilar-Ordoñez I, Pérez-Villatoro F, García-Ortiz H, Barajas-Olmos F, Ballesteros-Villascán J, González-Buenfil R, Fresno C, Garcíarrubio A, Fernández-López JC, Tovar H, Hernández-Lemus E, Orozco L, Soberón X, Morett E. Whole genome variation in 27 Mexican indigenous populations, demographic and biomedical insights. PLoS One 2021; 16:e0249773. [PMID: 33831079 PMCID: PMC8031408 DOI: 10.1371/journal.pone.0249773] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 03/24/2021] [Indexed: 12/12/2022] Open
Abstract
There has been limited study of Native American whole genome diversity to date, which impairs effective implementation of personalized medicine and a detailed description of its demographic history. Here we report high coverage whole genome sequencing of 76 unrelated individuals, from 27 indigenous groups across Mexico, with more than 97% average Native American ancestry. On average, each individual has 3.26 million Single Nucleotide Variants and short indels, that together comprise a catalog of 9,737,152 variants, 44,118 of which are novel. We report 497 common Single Nucleotide Variants (with allele frequency > 5%) mapped to drug responses and 316,577 in enhancer or promoter elements; interestingly we found some of these enhancer variants in PPARG, a nuclear receptor involved in highly prevalent health problems in Mexican population, such as obesity, diabetes, and insulin resistance. By detecting signals of positive selection we report 24 enriched key pathways under selection, most of them related to immune mechanisms. No missense variants in ACE2, the receptor responsible for the entry of the SARS CoV-2 virus, were found in any individual. Population genomics and phylogenetic analyses demonstrated stratification in a Northern-Central-Southern axis, with major substructure in the Central region. The Seri, a northern group with the most genetic divergence in our study, showed a distinctive genomic context with the most novel variants, and the most population specific genotypes. Genome-wide analysis showed that the average haplotype blocks are longer in Native Mexicans than in other world populations. With this dataset we describe previously undetected population level variation in Native Mexicans, helping to reduce the gap in genomic data representation of such groups.
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Affiliation(s)
- Israel Aguilar-Ordoñez
- Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
- Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, México
| | - Fernando Pérez-Villatoro
- Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
- Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, México
- Winter Genomics, Mexico City, México
| | | | | | | | - Ram González-Buenfil
- Benemérita Universidad Autónoma de Puebla (BUAP), Puebla de Zaragoza, Puebla, México
| | - Cristobal Fresno
- Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, México
| | - Alejandro Garcíarrubio
- Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
| | | | - Hugo Tovar
- Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, México
| | | | - Lorena Orozco
- Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, México
| | - Xavier Soberón
- Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
- Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, México
| | - Enrique Morett
- Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
- * E-mail:
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Sun J, Ma PC, Cheng HZ, Wang CZ, Li YL, Cui YQ, Yao HB, Wen SQ, Wei LH. Post-last glacial maximum expansion of Y-chromosome haplogroup C2a-L1373 in northern Asia and its implications for the origin of Native Americans. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021; 174:363-374. [PMID: 33241578 DOI: 10.1002/ajpa.24173] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 10/10/2020] [Accepted: 11/04/2020] [Indexed: 02/05/2023]
Abstract
OBJECTIVES Subbranches of Y-chromosome haplogroup C2a-L1373 are founding paternal lineages in northern Asia and Native American populations. Our objective was to investigate C2a-L1373 differentiation in northern Asia and its implications for Native American origins. MATERIALS AND METHODS Sequences of rare subbranches (n = 43) and ancient individuals (n = 37) of C2a-L1373 (including P39 and MPB373), were used to construct phylogenetic trees with age estimation by BEAST software. RESULTS C2a-L1373 expanded rapidly approximately 17.7,000-14.3,000 years ago (kya) after the last glacial maximum (LGM), generating numerous sublineages which became founding paternal lineages of modern northern Asian and Native American populations (C2a-P39 and C2a-MPB373). The divergence pattern supports possible initiation of differentiation in low latitude regions of northern Asia and northward diffusion after the LGM. There is a substantial gap between the divergence times of C2a-MPB373 (approximately 22.4 or 17.7 kya) and C2a-P39 (approximately 14.3 kya), indicating two possible migration waves. DISCUSSION We discussed the decreasing time interval of "Beringian standstill" (2.5 ky or smaller) and its reduced significance. We also discussed the multiple possibilities for the peopling of the Americas: the "Long-term Beringian standstill model," the "Short-term Beringian standstill model," and the "Multiple waves of migration model." Our results support the argument from ancient DNA analyses that the direct ancestor group of Native Americans is an admixture of "Ancient Northern Siberians" and Paleolithic communities from the Amur region, which appeared during the post-LGM era, rather than ancient populations in greater Beringia, or an adjacent region, before the LGM.
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Affiliation(s)
- Jin Sun
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China
- Xingyi Normal University for Nationalities, Xingyi, China
| | - Peng-Cheng Ma
- School of Life Sciences, Jilin University, Changchun, China
| | - Hui-Zhen Cheng
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China
| | - Chi-Zao Wang
- Department of Radiology, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Yong-Lan Li
- School of Ethnology and Anthropology, Inner Mongolia Normal University, Hohhot, China
| | - Yin-Qiu Cui
- School of Life Sciences, Jilin University, Changchun, China
| | - Hong-Bin Yao
- Key Laboratory of Evidence Science of Gansu Province, Gansu University of Political Science and Law, Lanzhou, China
| | - Shao-Qing Wen
- Institute of Archaeological Science, Fudan University, Shanghai, China
- B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, Shanghai, China
| | - Lan-Hai Wei
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China
- B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, Shanghai, China
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31
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Abstract
As human populations spread across the world, they adapted genetically to local conditions. So too did the resident microorganism communities that everyone carries with them. However, the collective influence of the diverse and dynamic community of resident microbes on host evolution is poorly understood. The taxonomic composition of the microbiota varies among individuals and displays a range of sometimes redundant functions that modify the physicochemical environment of the host and may alter selection pressures. Here we review known human traits and genes for which the microbiota may have contributed or responded to changes in host diet, climate, or pathogen exposure. Integrating host–microbiota interactions in human adaptation could offer new approaches to improve our understanding of human health and evolution.
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Affiliation(s)
- Taichi A. Suzuki
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Ruth E. Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
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32
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Can the aging influence cold environment mediated cancer risk in the USA female population? J Therm Biol 2020; 92:102676. [PMID: 32888573 DOI: 10.1016/j.jtherbio.2020.102676] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/14/2020] [Accepted: 07/15/2020] [Indexed: 12/31/2022]
Abstract
Cancer is one of the most debilitating diseases worldwide. Cancer incidence and/or death depends on several intrinsic and extrinsic factors (e.g., dietary habits, socio-behavioral activities, physical inactivity, smoking, alcohol consumption, gender, races/ethnicities and age). Various studies have found that an inverse relationship subsists between environmental temperature and cancer risk. Furthermore, this negative relationship was found to be more consistent in the USA female population. This research mainly focuses on influence of aging on cold environment mediated cancer risk for overall and various anatomical site-specific cancers. Age-specific county-wise data of cancer incidence rate (CIR) in the USA female population was selected in this study. Statistical analysis found a negative correlation between the average annual temperature (AAT) and CIR in all anatomical sites (AAS; overall) as well as different anatomical site-specific cancers (e.g., breast, melanoma, leukaemia, pancreas, bladder, uterus, thyroid and non-Hodgkin's lymphoma (NHL), except for cervical cancer) in different age groups (e.g., less than 50 years, 50 plus years, less than 65 years and 65 plus years). In addition, an inverse relationship between the AAT and CIR was found in case of paediatric cancer. However, all the results obtained from the linear model based statistical analysis proposed that the older age-group of females particularly above 65 years seems to be more prone to cold temperature linked cancer risk. For example, age-specific cold linked cancer incidence appears to be more inclined in case of breast cancer in the age-group of 65 plus years. This study, for first time, proposes that aging may have a positive influence on the relationship between cancer incidence and environment temperature.
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Pre-extinction Demographic Stability and Genomic Signatures of Adaptation in the Woolly Rhinoceros. Curr Biol 2020; 30:3871-3879.e7. [PMID: 32795436 DOI: 10.1016/j.cub.2020.07.046] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/18/2020] [Accepted: 07/14/2020] [Indexed: 02/01/2023]
Abstract
Ancient DNA has significantly improved our understanding of the evolution and population history of extinct megafauna. However, few studies have used complete ancient genomes to examine species responses to climate change prior to extinction. The woolly rhinoceros (Coelodonta antiquitatis) was a cold-adapted megaherbivore widely distributed across northern Eurasia during the Late Pleistocene and became extinct approximately 14 thousand years before present (ka BP). While humans and climate change have been proposed as potential causes of extinction [1-3], knowledge is limited on how the woolly rhinoceros was impacted by human arrival and climatic fluctuations [2]. Here, we use one complete nuclear genome and 14 mitogenomes to investigate the demographic history of woolly rhinoceros leading up to its extinction. Unlike other northern megafauna, the effective population size of woolly rhinoceros likely increased at 29.7 ka BP and subsequently remained stable until close to the species' extinction. Analysis of the nuclear genome from a ∼18.5-ka-old specimen did not indicate any increased inbreeding or reduced genetic diversity, suggesting that the population size remained steady for more than 13 ka following the arrival of humans [4]. The population contraction leading to extinction of the woolly rhinoceros may have thus been sudden and mostly driven by rapid warming in the Bølling-Allerød interstadial. Furthermore, we identify woolly rhinoceros-specific adaptations to arctic climate, similar to those of the woolly mammoth. This study highlights how species respond differently to climatic fluctuations and further illustrates the potential of palaeogenomics to study the evolutionary history of extinct species.
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34
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Werren EA, Garcia O, Bigham AW. Identifying adaptive alleles in the human genome: from selection mapping to functional validation. Hum Genet 2020; 140:241-276. [PMID: 32728809 DOI: 10.1007/s00439-020-02206-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 07/07/2020] [Indexed: 12/19/2022]
Abstract
The suite of phenotypic diversity across geographically distributed human populations is the outcome of genetic drift, gene flow, and natural selection throughout human evolution. Human genetic variation underlying local biological adaptations to selective pressures is incompletely characterized. With the emergence of population genetics modeling of large-scale genomic data derived from diverse populations, scientists are able to map signatures of natural selection in the genome in a process known as selection mapping. Inferred selection signals further can be used to identify candidate functional alleles that underlie putative adaptive phenotypes. Phenotypic association, fine mapping, and functional experiments facilitate the identification of candidate adaptive alleles. Functional investigation of candidate adaptive variation using novel techniques in molecular biology is slowly beginning to unravel how selection signals translate to changes in biology that underlie the phenotypic spectrum of our species. In addition to informing evolutionary hypotheses of adaptation, the discovery and functional annotation of adaptive alleles also may be of clinical significance. While selection mapping efforts in non-European populations are growing, there remains a stark under-representation of diverse human populations in current public genomic databases, of both clinical and non-clinical cohorts. This lack of inclusion limits the study of human biological variation. Identifying and functionally validating candidate adaptive alleles in more global populations is necessary for understanding basic human biology and human disease.
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Affiliation(s)
- Elizabeth A Werren
- Department of Human Genetics, The University of Michigan, Ann Arbor, MI, USA
- Department of Anthropology, The University of Michigan, Ann Arbor, MI, USA
| | - Obed Garcia
- Department of Anthropology, The University of Michigan, Ann Arbor, MI, USA
| | - Abigail W Bigham
- Department of Anthropology, University of California Los Angeles, 341 Haines Hall, Los Angeles, CA, 90095, USA.
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35
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Liu B, Ma P, Wang C, Yan S, Yao H, Li Y, Xie Y, Meng S, Sun J, Cai Y, Sarengaowa S, Li H, Cheng H, Wei L. Paternal origin of Tungusic‐speaking populations: Insights from the updated phylogenetic tree of Y‐chromosome haplogroup
C2a‐M86. Am J Hum Biol 2020; 33:e23462. [DOI: 10.1002/ajhb.23462] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 05/15/2020] [Accepted: 06/11/2020] [Indexed: 11/10/2022] Open
Affiliation(s)
- Bing‐Li Liu
- Institute of Chinese and Culture Education Studies Huaqiao University Xiamen China
| | - Peng‐Cheng Ma
- School of Life Sciences Jilin University Changchun China
| | - Chi‐Zao Wang
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences Fudan University Shanghai China
| | - Shi Yan
- Human Phenome Institute Fudan University Shanghai China
| | - Hong‐Bing Yao
- Key Laboratory of Evidence Science of Gansu Province Gansu University of Political Science and Law Lanzhou China
| | - Yong‐Lan Li
- Laboratory for Human Biology and Human Genetics Institute of Ethnology and Anthropology, School of Ethnology and Anthropology, Inner Mongolia Normal University Hohhot China
| | - Yong‐Mei Xie
- Laboratory for Human Biology and Human Genetics Institute of Ethnology and Anthropology, School of Ethnology and Anthropology, Inner Mongolia Normal University Hohhot China
| | - Song‐Lin Meng
- School of History and Ethnic Culture Hulunbuir University Hulunbuir China
| | - Jin Sun
- Department of Anthropology and Ethnology, Institute of Anthropology Xiamen University Xiamen China
| | - Yan‐Huan Cai
- Department of Anthropology and Ethnology, Institute of Anthropology Xiamen University Xiamen China
| | - Sarengaowa Sarengaowa
- Department of Anthropology and Ethnology, Institute of Anthropology Xiamen University Xiamen China
| | - Hui Li
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences Fudan University Shanghai China
- Human Phenome Institute Fudan University Shanghai China
- B&R International Joint Laboratory for Eurasian Anthropology Fudan University Shanghai China
| | - Hui‐Zhen Cheng
- Department of Anthropology and Ethnology, Institute of Anthropology Xiamen University Xiamen China
| | - Lan‐Hai Wei
- Department of Anthropology and Ethnology, Institute of Anthropology Xiamen University Xiamen China
- B&R International Joint Laboratory for Eurasian Anthropology Fudan University Shanghai China
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36
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Sinding MHS, Gopalakrishnan S, Ramos-Madrigal J, de Manuel M, Pitulko VV, Kuderna L, Feuerborn TR, Frantz LAF, Vieira FG, Niemann J, Samaniego Castruita JA, Carøe C, Andersen-Ranberg EU, Jordan PD, Pavlova EY, Nikolskiy PA, Kasparov AK, Ivanova VV, Willerslev E, Skoglund P, Fredholm M, Wennerberg SE, Heide-Jørgensen MP, Dietz R, Sonne C, Meldgaard M, Dalén L, Larson G, Petersen B, Sicheritz-Pontén T, Bachmann L, Wiig Ø, Marques-Bonet T, Hansen AJ, Gilbert MTP. Arctic-adapted dogs emerged at the Pleistocene-Holocene transition. Science 2020; 368:1495-1499. [PMID: 32587022 DOI: 10.1126/science.aaz8599] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 05/06/2020] [Indexed: 12/18/2022]
Abstract
Although sled dogs are one of the most specialized groups of dogs, their origin and evolution has received much less attention than many other dog groups. We applied a genomic approach to investigate their spatiotemporal emergence by sequencing the genomes of 10 modern Greenland sled dogs, an ~9500-year-old Siberian dog associated with archaeological evidence for sled technology, and an ~33,000-year-old Siberian wolf. We found noteworthy genetic similarity between the ancient dog and modern sled dogs. We detected gene flow from Pleistocene Siberian wolves, but not modern American wolves, to present-day sled dogs. The results indicate that the major ancestry of modern sled dogs traces back to Siberia, where sled dog-specific haplotypes of genes that potentially relate to Arctic adaptation were established by 9500 years ago.
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Affiliation(s)
- Mikkel-Holger S Sinding
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. .,Natural History Museum, University of Oslo, Oslo, Norway.,The Qimmeq Project, University of Greenland, Nuussuaq, Greenland.,Greenland Institute of Natural Resources, Nuuk, Greenland.,Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | | | | | - Marc de Manuel
- Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain
| | - Vladimir V Pitulko
- Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia
| | - Lukas Kuderna
- Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain
| | - Tatiana R Feuerborn
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,The Qimmeq Project, University of Greenland, Nuussuaq, Greenland.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Laurent A F Frantz
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.,School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Filipe G Vieira
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jonas Niemann
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,BioArch, Department of Archaeology, University of York, York, UK
| | | | - Christian Carøe
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Emilie U Andersen-Ranberg
- The Qimmeq Project, University of Greenland, Nuussuaq, Greenland.,Department of Clinical Veterinary Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Peter D Jordan
- Arctic Centre and Groningen Institute of Archaeology, University of Groningen, Netherlands
| | - Elena Y Pavlova
- Arctic and Antarctic Research Institute, St. Petersburg, Russia
| | | | - Aleksei K Kasparov
- Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia
| | - Varvara V Ivanova
- VNIIOkeangeologia Research Institute (The All-Russian Research Institute of Geology and Mineral Resources of the World Ocean), St. Petersburg, Russia
| | - Eske Willerslev
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Danish Institute for Advanced Study (D-IAS), University of Southern Denmark, Odense, Denmark.,Department of Zoology, University of Cambridge, Cambridge, UK.,Wellcome Trust Sanger Institute, University of Cambridge, Cambridge, UK
| | - Pontus Skoglund
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Francis Crick Institute, London, UK
| | - Merete Fredholm
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Sanne Eline Wennerberg
- Ministry of Fisheries, Hunting and Agriculture, Government of Greenland, Nuuk, Greenland
| | | | - Rune Dietz
- Department of Bioscience, Arctic Research Centre, Aarhus University, Roskilde, Denmark
| | - Christian Sonne
- The Qimmeq Project, University of Greenland, Nuussuaq, Greenland.,Department of Bioscience, Arctic Research Centre, Aarhus University, Roskilde, Denmark.,Henan Province Engineering Research Center for Biomass Value-added Products, School of Forestry, Henan Agricultural University, Zhengzhou, Henan, China
| | - Morten Meldgaard
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,The Qimmeq Project, University of Greenland, Nuussuaq, Greenland
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Greger Larson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Bent Petersen
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Thomas Sicheritz-Pontén
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Lutz Bachmann
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Øystein Wiig
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain. .,Catalan Institution of Research and Advanced Studies, Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Anders J Hansen
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. .,The Qimmeq Project, University of Greenland, Nuussuaq, Greenland
| | - M Thomas P Gilbert
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. .,University Museum, Norwegian University of Science and Technology, Trondheim, Norway
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Weldenegodguad M, Pokharel K, Ming Y, Honkatukia M, Peippo J, Reilas T, Røed KH, Kantanen J. Genome sequence and comparative analysis of reindeer (Rangifer tarandus) in northern Eurasia. Sci Rep 2020; 10:8980. [PMID: 32488117 PMCID: PMC7265531 DOI: 10.1038/s41598-020-65487-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 05/05/2020] [Indexed: 12/24/2022] Open
Abstract
Reindeer are semi-domesticated ruminants that have adapted to the challenging northern Eurasian environment characterized by long winters and marked annual fluctuations in daylight. We explored the genetic makeup behind their unique characteristics by de novo sequencing the genome of a male reindeer and conducted gene family analyses with nine other mammalian species. We performed a population genomics study of 23 additional reindeer representing both domestic and wild populations and several ecotypes from various geographic locations. We assembled 2.66 Gb (N50 scaffold of 5 Mb) of the estimated 2.92 Gb reindeer genome, comprising 27,332 genes. The results from the demographic history analysis suggested marked changes in the effective population size of reindeer during the Pleistocene period. We detected 160 reindeer-specific and expanded genes, of which zinc finger proteins (n = 42) and olfactory receptors (n = 13) were the most abundant. Comparative genome analyses revealed several genes that may have promoted the adaptation of reindeer, such as those involved in recombination and speciation (PRDM9), vitamin D metabolism (TRPV5, TRPV6), retinal development (PRDM1, OPN4B), circadian rhythm (GRIA1), immunity (CXCR1, CXCR2, CXCR4, IFNW1), tolerance to cold-triggered pain (SCN11A) and antler development (SILT2). The majority of these characteristic reindeer genes have been reported for the first time here. Moreover, our population genomics analysis suggested at least two independent reindeer domestication events with genetic lineages originating from different refugial regions after the Last Glacial Maximum. Taken together, our study has provided new insights into the domestication, evolution and adaptation of reindeer and has promoted novel genomic research of reindeer.
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Affiliation(s)
- Melak Weldenegodguad
- Natural Resources Institute Finland, FI-31600, Jokioinen, Finland
- Department of Environmental and Biological Sciences, University of Eastern Finland, FI-70201, Kuopio, Finland
| | - Kisun Pokharel
- Natural Resources Institute Finland, FI-31600, Jokioinen, Finland
| | - Yao Ming
- BGI-Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Mervi Honkatukia
- Natural Resources Institute Finland, FI-31600, Jokioinen, Finland
- Nordic Genetic Resource Centre - NordGen, c/o NMBU - Biovit Box 5003, Ås, NO-1432, Norway
| | - Jaana Peippo
- Natural Resources Institute Finland, FI-31600, Jokioinen, Finland
| | - Tiina Reilas
- Natural Resources Institute Finland, FI-31600, Jokioinen, Finland
| | - Knut H Røed
- Department of Basic Sciences and Aquatic Medicine, Norwegian University of Life Sciences, P.O.Box 369 Centrum, 0102, Oslo, Norway
| | - Juha Kantanen
- Natural Resources Institute Finland, FI-31600, Jokioinen, Finland.
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38
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Bandyopadhayaya S, Ford B, Mandal CC. Cold-hearted: A case for cold stress in cancer risk. J Therm Biol 2020; 91:102608. [PMID: 32716858 DOI: 10.1016/j.jtherbio.2020.102608] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 04/25/2020] [Accepted: 04/25/2020] [Indexed: 02/07/2023]
Abstract
A negative correlation exists between environmental temperature and cancer risk based on both epidemiological and statistical analyses. Previously, cold stress was reported to be an effective cause of tumorigenesis. Several studies have demonstrated that cold temperature serves as a potential risk factor in cancer development. Most recently, a link was demonstrated between the effects of extreme cold climate on cancer incidence, pinpointing its impact on tumour suppressor genes by causing mutation. The underlying mechanism behind cold stress and its association with tumorigenesis is not well understood. Hence, this review intends to shed light on the role of associated factors, genetic and/or non-genetic, which are modulated by cold temperature, and eventually influence tumorigenic potential. While scrutinizing the effect of cold exposure on the body, the expression of certain genes, e.g. uncoupled proteins and heat-shock proteins, were elevated. Biological chemicals such as norepinephrine, thyroxine, and cholesterol were also elevated. Brown adipose tissue, which plays an essential role in thermogenesis, displayed enhanced activity upon cold exposure. Adaptive measures are utilized by the body to tolerate the cold, and in doing so, invites both epigenetic and genetic changes. Unknowingly, these adaptive strategies give rise to a lethal outcome i.e., genesis of cancer. Concisely, this review attempts to draw a link between cold stress, genetic and epigenetic changes, and tumorigenesis and aspires to ascertain the mechanism behind cold temperature-mediated cancer risk.
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Affiliation(s)
| | - Bridget Ford
- Department of Biology, University of the Incarnate Word, San Antonio, TX, 78209, USA
| | - Chandi C Mandal
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, 305817, India.
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39
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Abstract
Geographic patterns in human genetic diversity carry footprints of population history and provide insights for genetic medicine and its application across human populations. Summarizing and visually representing these patterns of diversity has been a persistent goal for human geneticists, and has revealed that genetic differentiation is frequently correlated with geographic distance. However, most analytical methods to represent population structure do not incorporate geography directly, and it must be considered post hoc alongside a visual summary of the genetic structure. Here, we estimate "effective migration" surfaces to visualize how human genetic diversity is geographically structured. The results reveal local patterns of differentiation in detail and emphasize that while genetic similarity generally decays with geographic distance, the relationship is often subtly distorted. Overall, the visualizations provide a new perspective on genetics and geography in humans and insight to the geographic distribution of human genetic variation.
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Affiliation(s)
- Benjamin M Peter
- Department of Human Genetics, University of Chicago, Chicago, IL
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Desislava Petkova
- Wellcome Trust Center for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - John Novembre
- Department of Human Genetics, University of Chicago, Chicago, IL
- Department of Ecology & Evolution, University of Chicago, Chicago, IL
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Hale N. Inuit metabolism revisited: what drove the selective sweep of CPT1a L479? Mol Genet Metab 2020; 129:255-271. [PMID: 32088118 DOI: 10.1016/j.ymgme.2020.01.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 01/30/2020] [Indexed: 12/31/2022]
Abstract
This article reassesses historical studies of Inuit metabolism in light of recent developments in evolutionary genetics. It discusses the possible selective advantage of a variant of CPT1a, which encodes the rate limiting enzyme in hepatic fatty acid oxidation. The L479 variant of CPT1a underwent one of the strongest known selective sweeps in human history and is specific to Inuit and Yu'pik populations. Recent hypotheses predict that this variant may have been selected in response to possible detrimental effects of chronic ketosis in communities with very low carbohydrate consumption. Assessing these hypotheses alongside several alternative explanations of the selective sweep, this article challenges the notion that the selection of L479 is linked to predicted detrimental effects of ketosis. Bringing together for the first time data from biochemical, metabolic, and physiological studies inside and outside the Inuit sphere, it aims to provide a broader interpretative framework and a more comprehensive way to understand the selective sweep. It suggests that L479 may have provided a selective advantage in glucose conservation as part of a metabolic adaptation to very low carbohydrate and high protein consumption, but not necessarily a ketogenic state, in an extremely cold environment. A high intake of n-3 fatty acids may be linked to selection through the mitigation of a detrimental effect of the mutation that arises in the fasted state. The implications of these conclusions for our broader understanding of very low carbohydrate metabolism, and for dietary recommendations for Inuit and non-Inuit populations, are discussed.
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Zhang L, Wang Z, Wang X, Chen Z, Shao L, Tian Y, Zheng C, Li S, Zhu M, Gao R. Prevalence of overweight and obesity in China: Results from a cross-sectional study of 441 thousand adults, 2012-2015. Obes Res Clin Pract 2020; 14:119-126. [PMID: 32139330 DOI: 10.1016/j.orcp.2020.02.005] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/16/2020] [Accepted: 02/20/2020] [Indexed: 10/24/2022]
Abstract
OBJECTIVES Obesity has become a global health public problem. The study aims to examine the latest prevalence of overweight and obesity in China. METHODS Data came from the China Hypertension Survey (CHS), a nationally representative cross-sectional study among residents aged ≥18 years from October 2012 to December 2015. Overweight and obesity were defined as 25≤BMI<30kg/m2 and BMI≥30kg/m2 according to the WHO classifications, respectively. RESULTS The data of 441 306 participants were analyzed. The prevalence of overweight and obesity was 28.1% and 5.2% respectively. The prevalence of overweight and obesity varied considerably across provinces. The prevalence of overweight was the highest in Beijing, which was 2.8 fold of the lowest in Guangxi (40.9% vs. 14.6%). The prevalence of obesity was the highest in Tianjin, which was 9.4 fold of the lowest in Hainan (12.2% vs. 1.3%). There was a striking north-south gradient with the prevalence higher in Northeast and Northwest China and lower in Southeast China. Multivariate logistic regression analysis indicated that sex, age, education, smoking, marital status and family history of cardiovascular disease were significantly associated with overweight and obesity. CONCLUSIONS Overweight and obesity are highly prevalent among Chinese adults, and their prevalence varies greatly among different population subgroups and provinces. National and provincial obesity control and prevention strategies should be public health priorities in China.
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Affiliation(s)
- Linfeng Zhang
- Division of Prevention and Community Health, National Center for Cardiovascular Disease, Fuwai Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, No. 15 (Lin), Fengcunxili,Mentougou District, Beijing 102308, China.
| | - Zengwu Wang
- Division of Prevention and Community Health, National Center for Cardiovascular Disease, Fuwai Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, No. 15 (Lin), Fengcunxili,Mentougou District, Beijing 102308, China.
| | - Xin Wang
- Division of Prevention and Community Health, National Center for Cardiovascular Disease, Fuwai Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, No. 15 (Lin), Fengcunxili,Mentougou District, Beijing 102308, China.
| | - Zuo Chen
- Division of Prevention and Community Health, National Center for Cardiovascular Disease, Fuwai Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, No. 15 (Lin), Fengcunxili,Mentougou District, Beijing 102308, China.
| | - Lan Shao
- Division of Prevention and Community Health, National Center for Cardiovascular Disease, Fuwai Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, No. 15 (Lin), Fengcunxili,Mentougou District, Beijing 102308, China.
| | - Ye Tian
- Division of Prevention and Community Health, National Center for Cardiovascular Disease, Fuwai Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, No. 15 (Lin), Fengcunxili,Mentougou District, Beijing 102308, China.
| | - Congyi Zheng
- Division of Prevention and Community Health, National Center for Cardiovascular Disease, Fuwai Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, No. 15 (Lin), Fengcunxili,Mentougou District, Beijing 102308, China.
| | - Suning Li
- Division of Prevention and Community Health, National Center for Cardiovascular Disease, Fuwai Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, No. 15 (Lin), Fengcunxili,Mentougou District, Beijing 102308, China.
| | - Manlu Zhu
- Division of Prevention and Community Health, National Center for Cardiovascular Disease, Fuwai Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, No. 15 (Lin), Fengcunxili,Mentougou District, Beijing 102308, China.
| | - Runlin Gao
- Department of Cardiology, National Center for Cardiovascular Disease, Fuwai Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, No. 167, Beilishilu, Xicheng District, Beijing, China.
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Eaaswarkhanth M, dos Santos ALC, Gokcumen O, Al-Mulla F, Thanaraj TA. Genome-Wide Selection Scan in an Arabian Peninsula Population Identifies a TNKS Haplotype Linked to Metabolic Traits and Hypertension. Genome Biol Evol 2020; 12:77-87. [PMID: 32068798 PMCID: PMC7093833 DOI: 10.1093/gbe/evaa033] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/13/2020] [Indexed: 12/12/2022] Open
Abstract
Despite the extreme and varying environmental conditions prevalent in the Arabian Peninsula, it has experienced several waves of human migrations following the out-of-Africa diaspora. Eventually, the inhabitants of the peninsula region adapted to the hot and dry environment. The adaptation and natural selection that shaped the extant human populations of the Arabian Peninsula region have been scarcely studied. In an attempt to explore natural selection in the region, we analyzed 662,750 variants in 583 Kuwaiti individuals. We searched for regions in the genome that display signatures of positive selection in the Kuwaiti population using an integrative approach in a conservative manner. We highlight a haplotype overlapping TNKS that showed strong signals of positive selection based on the results of the multiple selection tests conducted (integrated Haplotype Score, Cross Population Extended Haplotype Homozygosity, Population Branch Statistics, and log-likelihood ratio scores). Notably, the TNKS haplotype under selection potentially conferred a fitness advantage to the Kuwaiti ancestors for surviving in the harsh environment while posing a major health risk to present-day Kuwaitis.
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Affiliation(s)
| | - Andre Luiz Campelo dos Santos
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo
- Department of Archeology, Federal University of Pernambuco, Recife, Brazil
| | - Omer Gokcumen
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo
| | - Fahd Al-Mulla
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Kuwait City, Kuwait
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Khrunin AV, Khvorykh GV, Fedorov AN, Limborska SA. Genomic landscape of the signals of positive natural selection in populations of Northern Eurasia: A view from Northern Russia. PLoS One 2020; 15:e0228778. [PMID: 32023328 PMCID: PMC7001972 DOI: 10.1371/journal.pone.0228778] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 01/23/2020] [Indexed: 12/15/2022] Open
Abstract
Natural selection of beneficial genetic variants played a critical role in human adaptation to a wide range of environmental conditions. Northern Eurasia, despite its severe climate, is home to lots of ethnically diverse populations. The genetic variants associated with the survival of these populations have hardly been analyzed. We searched for the genomic signatures of positive selection in (1) the genome-wide microarray data of 432 people from eight different northern Russian populations and (2) the whole-genome sequences of 250 people from Northern Eurasia from a public repository through testing the extended haplotype homozigosity (EHH) and direct comparison of allele frequency, respectively. The 20 loci with the strongest selection signals were characterized in detail. Among the top EHH hits were the NRG3 and NBEA genes, which are involved in the development and functioning of the neural system, the PTPRM gene, which mediates cell-cell interactions and adhesion, and a region on chromosome 4 (chr4:28.7-28.9 Mb) that contained several loci affiliated with different classes of non-coding RNAs (RN7SL101P, MIR4275, MESTP3, and LINC02364). NBEA and the region on chromosome 4 were novel selection targets that were identified for the first time in Western Siberian populations. Cross-population comparisons of EHH profiles suggested a particular role for the chr4:28.7-28.9 Mb region in the local adaptation of Western Siberians. The strongest selection signal identified in Siberian sequenced genomes was formed by six SNPs on chromosome 11 (chr11:124.9-125.2 Mb). This region included well-known genes SLC37A2 and PKNOX2. SLC37A2 is most-highly expressed in the gut. Its expression is regulated by vitamin D, which is often deficient in northern regions. The PKNOX2 gene is a transcription factor of the homeobox family that is expressed in the brain and many other tissues. This gene is associated with alcohol addiction, which is widespread in many Northern Eurasian populations.
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Affiliation(s)
- Andrey V. Khrunin
- Department of Molecular Bases of Human Genetics, Institute of Molecular Genetics of Russian Academy of Sciences, Moscow, Russia
| | - Gennady V. Khvorykh
- Department of Molecular Bases of Human Genetics, Institute of Molecular Genetics of Russian Academy of Sciences, Moscow, Russia
| | - Alexei N. Fedorov
- Department of Molecular Bases of Human Genetics, Institute of Molecular Genetics of Russian Academy of Sciences, Moscow, Russia
- Department of Medicine, University of Toledo, Toledo, Ohio, United States of America
| | - Svetlana A. Limborska
- Department of Molecular Bases of Human Genetics, Institute of Molecular Genetics of Russian Academy of Sciences, Moscow, Russia
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Zhang L, Wang Z, Wang X, Chen Z, Shao L, Tian Y, Dong Y, Zheng C, Li S, Zhu M, Gao R. Prevalence of Abdominal Obesity in China: Results from a Cross-Sectional Study of Nearly Half a Million Participants. Obesity (Silver Spring) 2019; 27:1898-1905. [PMID: 31549787 DOI: 10.1002/oby.22620] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 07/19/2019] [Indexed: 12/27/2022]
Abstract
OBJECTIVE This study aimed to examine the latest prevalence of abdominal obesity in China based on nationally representative data. METHODS A stratified, multistage, random sampling method was used to obtain a nationally representative sample of residents aged ≥ 18 years from 31 provinces in mainland China from October 2012 to December 2015. Abdominal obesity was defined as a waist circumference ≥ 90 cm for men and a waist circumference ≥ 85 cm for women. RESULTS The data of 441,306 participants were analyzed. The prevalence of abdominal obesity was 29.1% (28.6% in men and 29.6% in women); the number of adults with abdominal obesity was estimated to be 277.8 million (approximately 140.1 million in men and 137.7 million in women). The prevalence of abdominal obesity varied considerably among provinces. In general, the prevalence of abdominal obesity was higher in the northern, lower in the southern, higher in the western, and lower in the eastern areas of China. Besides the regional disparities, the prevalence of abdominal obesity varied greatly among different population subgroups. CONCLUSIONS Abdominal obesity is highly prevalent among Chinese adults. National and provincial obesity control and prevention strategies should be public health priorities in China. To better control obesity, the underlying reasons for the regional disparities need to be addressed.
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Affiliation(s)
- Linfeng Zhang
- Division of Prevention and Community Health, National Center for Cardiovascular Disease, Fuwai Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Zengwu Wang
- Division of Prevention and Community Health, National Center for Cardiovascular Disease, Fuwai Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xin Wang
- Division of Prevention and Community Health, National Center for Cardiovascular Disease, Fuwai Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Zuo Chen
- Division of Prevention and Community Health, National Center for Cardiovascular Disease, Fuwai Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Lan Shao
- Division of Prevention and Community Health, National Center for Cardiovascular Disease, Fuwai Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Ye Tian
- Division of Prevention and Community Health, National Center for Cardiovascular Disease, Fuwai Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Ying Dong
- Division of Prevention and Community Health, National Center for Cardiovascular Disease, Fuwai Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Congyi Zheng
- Division of Prevention and Community Health, National Center for Cardiovascular Disease, Fuwai Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Suning Li
- Division of Prevention and Community Health, National Center for Cardiovascular Disease, Fuwai Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Manlu Zhu
- Division of Prevention and Community Health, National Center for Cardiovascular Disease, Fuwai Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Runlin Gao
- Department of Cardiology, National Center for Cardiovascular Disease, Fuwai Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
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Stepanov VA, Kharkov VN, Vagaitseva KV, Khitrinskaya IY, Bocharova AV, Kolesnikov NA, Zarubin AA, Popovich AA, Marusin AV, Swarovskaya MG, Triska P, Tatarinova TV. Signals of Positive Selection in Human Populations of Siberia and European Russia. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419100120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Yudin NS, Larkin DM. Whole genome studies of origin, selection and adaptation of the Russian cattle breeds. Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj19.525] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Our review presents several recent studies on the genetic history and signatures of selection in genomes of the native Russian cattle breeds. Most of these works are not easily accessible for the Russian-speaking audience. We describe the origins of appearance of the Russian cattle breeds from the genetics perspective. We point to the links between most of the Russian breeds with the taurine breeds of the European origin and for some Russian breeds with the breeds of the Asian origin. We describe major phylogenetic clusters of the Russian breeds and point to those that still maintain their unique genetics, meaning that their preservation is a priority. In addition, we review the results of the search for signatures of selection in genomes of the Russian cattle breeds. Some unique signatures of selection present in the genomes of so-called “turano-mongolian” cattle (i. e. the Yakut cattle) are described which allowed the Yakut cattle to adapt to harsh environments found above the Polar Circle. Signatures of selection which could help other cattle breeds of the Russian origin to adapt to various climatic condition of the Russian Federation are reviewed. The Russian cattle genomes also contain known signatures of selection related to cattle domestication about 8–10 thousand years ago. The most profound ones include genes related to changes of the coat colour. This phenotype in many cases could be related to the distinction of the first domesticated populations and lead to the formation of so-called land races (primitive breeds). Whole-genome association studies of Russian cattle breeds pointed to a novel gene which could be related to the “white-faced” phenotype and to a gene which is related to body temperature support under the acute cold stress. The data presented in our review could be used for identification of genetic markers to focus on in future efforts on designing new highly productive cattle breeds adapted to climates of the Russian Federation and other countries with similar climates.
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Affiliation(s)
| | - D. M. Larkin
- Royal Veterinary College, University of London; Institute of Cytology and Genetics, SB RAS
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Igoshin AV, Gunbin KV, Yudin NS, Voevoda MI. Searching for Signatures of Cold Climate Adaptation in TRPM8 Gene in Populations of East Asian Ancestry. Front Genet 2019; 10:759. [PMID: 31507633 PMCID: PMC6716346 DOI: 10.3389/fgene.2019.00759] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 07/17/2019] [Indexed: 12/14/2022] Open
Abstract
Dispersal of Homo sapiens across the globe during the last 200,000 years was accompanied by adaptation to local climatic conditions, with severe winter temperatures being probably one of the most significant selective forces. The TRPM8 gene codes for a cold-sensing ion channel, and adaptation to low temperatures is the major determinant of its molecular evolution. Here, our aim was to search for signatures of cold climate adaptation in TRPM8 gene using a combined data set of 19 populations of East Asian ancestry from the 1000 Genomes Project and Human Genome Diversity Project. As a result, out of a total of 60 markers under study, none showed significant association with the average winter temperatures at the locations of the studied populations considering the multiple testing thresholds. This might suggest that the principal mode of TRPM8 evolution may be different from widespread models, where adaptive alleles are additive, dominant or recessive, at least in populations with the predominant East Asian component. For example, evolution by means of selectively preferable epistatic interactions among amino acids may have taken place. Despite the lack of strong signals of association, however, a very promising single nucleotide polymorphism (SNP) was found. The SNP rs7577262 is considered the best candidate based on its allelic correlations with winter temperatures, signatures of selective sweep and physiological evidences. The second top SNP, rs17862920, may participate in adaptation as well. Additionally, to assist in interpreting the nominal associations, the other markers reached, we performed SNP prioritization based on functional evidences found in literature and on evolutionary conservativeness.
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Affiliation(s)
- Alexander V. Igoshin
- Sector of the Genetics of Industrial Microorganisms, The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch, The Russian Academy of Sciences, Novosibirsk, Russia
| | - Konstantin V. Gunbin
- Center of Brain Neurobiology and Neurogenetics, The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch, The Russian Academy of Sciences, Novosibirsk, Russia
- V. Zelman Institute for Medicine and Psychology Novosibirsk State University, Novosibirsk, Russia
- Center for Mitochondrial Functional Genomics, Institute of Living Systems, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Nikolay S. Yudin
- V. Zelman Institute for Medicine and Psychology Novosibirsk State University, Novosibirsk, Russia
- Laboratory of Livestock Molecular Genetics and Breeding, The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch, The Russian Academy of Sciences, Novosibirsk, Russia
| | - Mikhail I. Voevoda
- Laboratory of Human Molecular Genetics, The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch, The Russian Academy of Sciences, Novosibirsk, Russia
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Abstract
The Canadian Inuit have a distinct population background that may entail particular implications for the health of its individuals. However, the number of genetic studies examining this Inuit population is limited, and much remains to be discovered in regard to its genetic characteristics. In this study, we generated whole-exome sequences and genomewide genotypes for 170 Nunavik Inuit, a small and isolated founder population of Canadian Arctic indigenous people. Our study revealed the genetic background of Nunavik Inuit to be distinct from any known present-day population. The majority of Nunavik Inuit show little evidence of gene flow from European or present-day Native American peoples, and Inuit living around Hudson Bay are genetically distinct from those around Ungava Bay. We also inferred that Nunavik Inuit have a small effective population size of 3,000 and likely split from Greenlandic Inuit ∼10.5 kya. Nunavik Inuit went through a bottleneck at approximately the same time and might have admixed with a population related to the Paleo-Eskimos. Our study highlights population-specific genomic signatures in coding regions that show adaptations unique to Nunavik Inuit, particularly in pathways involving fatty acid metabolism and cellular adhesion (CPNE7, ICAM5, STAT2, and RAF1). Subsequent analyses in selection footprints and the risk of intracranial aneurysms (IAs) in Nunavik Inuit revealed an exonic variant under weak negative selection to be significantly associated with IA (rs77470587; P = 4.6 × 10-8).
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Szpak M, Xue Y, Ayub Q, Tyler‐Smith C. How well do we understand the basis of classic selective sweeps in humans? FEBS Lett 2019; 593:1431-1448. [DOI: 10.1002/1873-3468.13447] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/29/2019] [Accepted: 05/17/2019] [Indexed: 12/14/2022]
Affiliation(s)
| | - Yali Xue
- The Wellcome Sanger Institute Hinxton UK
| | - Qasim Ayub
- School of Science Monash University Malaysia Bandar Sunway Malaysia
- Tropical Medicine and Biology Multidisciplinary Platform Monash University Malaysia Genomics Facility Bandar Sunway Malaysia
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Edea Z, Dadi H, Dessie T, Kim KS. Genomic signatures of high-altitude adaptation in Ethiopian sheep populations. Genes Genomics 2019; 41:973-981. [PMID: 31119684 DOI: 10.1007/s13258-019-00820-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 04/11/2019] [Indexed: 12/18/2022]
Abstract
BACKGROUND Ethiopian sheep populations such as Arsi-Bale, Horro and Adilo (long fat-tailed, LFT) inhabit mid to high-altitude areas; and Menz sheep (MZ, short fat-tailed) are adapted to cool sub-alpine environments. In contrast, Blackhead Somali sheep (BHS, fat-rumped) thrive well in arid and semi-arid areas characterized by high temperature and low precipitation. The genomic investigation of Ethiopian sheep populations may help to identify genes and biological pathways enable to adapt to the different ecological conditions. OBJECTIVE To uncover genomic regions and genes showing evidence of positive selection for altitude adaptation in Ethiopian sheep populations. METHODS A total of 72 animals inhabiting high-versus low-altitude environments were genotyped on an Ovine Infinium HD array (~ 600 K). Pairwise genetic differentiation (Fst) was calculated in sliding windows of 20 SNPs and the upper 1% smoothed Fst values were considered to represent positive selection signatures. Genes within < 25 kb of the most differentiated SNPs were considered as selection candidates. RESULTS Signatures of selection were detected in genes known to be associated high with altitude adaptation in MZ-BHS pair comparison (PPP1R12A, RELN, PARP2, and DNAH9) and in LFT-BHS pair comparison (VAV3, MSRB3,EIF2AK4, MET, and TACR1). The candidate genes (MITF, FGF5, MTOR, TRHDE, and TUBB3) associated with altitude adaptation and shared between the MZ-BHS and LTF-BHS pair comparisons were also detected as under selection. Further functional analyses reveal that the candidate genes were involved in biological processes and pathways relevant to adaptation under extreme altitudes, including respiratory system development and smoothened signaling pathway. CONCLUSION The results of the present study could aid in-depth understanding and exploitation of the underlying genetic mechanisms for sheep and other livestock species adaptation to high-altitude environments.
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Affiliation(s)
- Zewdu Edea
- Department of Animal Science, Chungbuk National University, Cheongju, Korea
| | - Hailu Dadi
- Addis Ababa Science and Technology University, P. O. Box 2490, Addis Ababa, Ethiopia
| | - Tadelle Dessie
- International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Kwan-Suk Kim
- Department of Animal Science, Chungbuk National University, Cheongju, Korea.
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