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Gu L, Xia C, Yang S, Yang G. The adaptive evolution of cancer driver genes. BMC Genomics 2023; 24:215. [PMID: 37098512 PMCID: PMC10131384 DOI: 10.1186/s12864-023-09301-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 04/08/2023] [Indexed: 04/27/2023] Open
Abstract
BACKGROUND Cancer is a life-threatening disease in humans; yet, cancer genes are frequently reported to be under positive selection. This suggests an evolutionary-genetic paradox in which cancer evolves as a secondary product of selection in human beings. However, systematic investigation of the evolution of cancer driver genes is sparse. RESULTS Using comparative genomics analysis, population genetics analysis and computational molecular evolutionary analysis, the evolution of 568 cancer driver genes of 66 cancer types were evaluated at two levels, selection on the early evolution of humans (long timescale selection in the human lineage during primate evolution, i.e., millions of years), and recent selection in modern human populations (~ 100,000 years). Results showed that eight cancer genes covering 11 cancer types were under positive selection in the human lineage (long timescale selection). And 35 cancer genes covering 47 cancer types were under positive selection in modern human populations (recent selection). Moreover, SNPs associated with thyroid cancer in three thyroid cancer driver genes (CUX1, HERC2 and RGPD3) were under positive selection in East Asian and European populations, consistent with the high incidence of thyroid cancer in these populations. CONCLUSIONS These findings suggest that cancer can be evolved, in part, as a by-product of adaptive changes in humans. Different SNPs at the same locus can be under different selection pressures in different populations, and thus should be under consideration during precision medicine, especially for targeted medicine in specific populations.
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Affiliation(s)
- Langyu Gu
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, 510275, China.
| | - Canwei Xia
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Shiyu Yang
- The Affiliated Brain Hospital, Guangzhou Medical University, Guangzhou, 510180, Guangdong, China
| | - Guofen Yang
- Department of Gynecology, First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510060, Guangdong, China.
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Stamos PA, Alemseged Z. Hominin locomotion and evolution in the Late Miocene to Late Pliocene. J Hum Evol 2023; 178:103332. [PMID: 36947894 DOI: 10.1016/j.jhevol.2023.103332] [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: 05/10/2022] [Revised: 01/26/2023] [Accepted: 01/27/2023] [Indexed: 03/24/2023]
Abstract
In this review, we present on the evolution of the locomotor adaptation of hominins in the Late Miocene to Late Pliocene, with emphasis on some of the prominent advances and debates that have occurred over the past fifty years. We start with the challenging issue of defining hominin locomotor grades that are currently used liberally and offer our own working definitions of facultative, habitual, and obligate bipedalism. We then discuss the nature of the Pan-Homo last common ancestor and characterize the locomotor adaptation of Sahelanthropus, Orrorin, and Ardipithecus-often referred to as facultative bipeds-and examine the debates on the extent of bipedality and arboreality in these taxa. Moreover, the question of Middle Pliocene hominin locomotor diversity is addressed based on information derived from the 'Little Foot' specimen from Sterkfontein, footprints from Laetoli, and the Burtele Foot in Ethiopia. Our review suggests that the most convincing evidence for locomotor diversity comes from Burtele, whereas the evidence from Sterkfontein and Laetoli is unconvincing and equivocal, respectively. Finally, we address the decades old issue of the significance of arboreality in the otherwise habitual biped, Australopithecus, with emphasis on Australopithecus afarensis and its implications for the paleobiology of these creatures. We conclude that many of the apelike features encountered, mostly in the upper part of the Australopithecus skeleton, were retained for their significance in climbing. Approaches that have investigated character plasticity and those exploring internal bone structure have shown that the shoulder and limbs in Au. afarensis and Australopithecus africanus were involved in arboreal activities that are thought to be key for feeding, nesting, and predator avoidance. We conclude that many of the so-called retained ape-like features persisted due to stabilizing selection, that early hominins engaged in a considerable amount of arboreality even after Australopithecus had become a habitual biped, and arboreality only ceased to be an important component of hominin locomotor behavior after the emergence of Homo erectus.
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Affiliation(s)
- Peter A Stamos
- Department of Organismal Biology & Anatomy, The University of Chicago, Anatomy Bldg 201, 1027 E 57th Street, Chicago, IL 60637, USA
| | - Zeresenay Alemseged
- Department of Organismal Biology & Anatomy, The University of Chicago, Anatomy Bldg 201, 1027 E 57th Street, Chicago, IL 60637, USA.
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Young M, Richard D, Grabowski M, Auerbach BM, de Bakker BS, Hagoort J, Muthuirulan P, Kharkar V, Kurki HK, Betti L, Birkenstock L, Lewton KL, Capellini TD. The developmental impacts of natural selection on human pelvic morphology. SCIENCE ADVANCES 2022; 8:eabq4884. [PMID: 35977020 PMCID: PMC9385149 DOI: 10.1126/sciadv.abq4884] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
Evolutionary responses to selection for bipedalism and childbirth have shaped the human pelvis, a structure that differs substantially from that in apes. Morphology related to these factors is present by birth, yet the developmental-genetic mechanisms governing pelvic shape remain largely unknown. Here, we pinpoint and characterize a key gestational window when human-specific pelvic morphology becomes recognizable, as the ilium and the entire pelvis acquire traits essential for human walking and birth. We next use functional genomics to molecularly characterize chondrocytes from different pelvic subelements during this window to reveal their developmental-genetic architectures. We then find notable evidence of ancient selection and genetic constraint on regulatory sequences involved in ilium expansion and growth, findings complemented by our phenotypic analyses showing that variation in iliac traits is reduced in humans compared to African apes. Our datasets provide important resources for musculoskeletal biology and begin to elucidate developmental mechanisms that shape human-specific morphology.
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Affiliation(s)
- Mariel Young
- Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Daniel Richard
- Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Mark Grabowski
- Research Centre in Evolutionary Anthropology and Palaeoecology, Liverpool John Moores University, Liverpool L3 3AF, UK
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway
| | - Benjamin M. Auerbach
- Department of Anthropology, The University of Tennessee, Knoxville, TN, USA
- Department of Ecology and Evolutionary Biology, The University of Tennessee, Knoxville, TN, USA
| | - Bernadette S. de Bakker
- Department of Obstetrics and Gynecology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, Netherlands
- Amsterdam Reproduction and Development Research Institute, Amsterdam, Netherlands
| | - Jaco Hagoort
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, Netherlands
| | | | - Vismaya Kharkar
- Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Helen K. Kurki
- Department of Anthropology, University of Victoria, STN CSC, Victoria, BC V8W 2Y2, Canada
| | - Lia Betti
- School of Life and Health Sciences, University of Roehampton, London SW15 4JD, UK
| | | | - Kristi L. Lewton
- Department of Integrative Anatomical Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Terence D. Capellini
- Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
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Zirkle D, Meindl RS, Lovejoy CO. Upright walking has driven unique vascular specialization of the hominin ilium. PeerJ 2021; 9:e12240. [PMID: 34721969 PMCID: PMC8532992 DOI: 10.7717/peerj.12240] [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: 07/16/2021] [Accepted: 09/12/2021] [Indexed: 11/20/2022] Open
Abstract
Background A novel physis in hominins modulates broadening and shortening of the ilium. We report analysis of a vascular canal system whose origin may be associated with this physis and which appears to be also unique to hominins. Its presence is potentially identifiable in the fossil record by its association with a highly enlarged foramen that is consistently present in modern humans and hominin fossils. Methods We measured the diameter of this foramen in humans, fossil hominins, and African great apes and corrected for body size. Results The mean relative human foramen diameter is significantly greater than those of either Pan or Gorilla. Moreover, eight of the nine values of the Cohen’s d for these differences in ratios are highly significant and support the ordering of magnitudes: Pan < Gorilla < Homo. The relative foramen diameter of A.L. 288-1 is above the 75th percentile of all other hominoids and at the high end of humans. The foramen is also present in ARA-VP-6/500. Conclusions We posit that the presence and significant enlargement of this foramen in fossils can reasonably serve as an indicator that its anterior inferior iliac spine emerged via the unique hominin physis. The foramen can therefore serve as an indicator of hominin iliac ontogenetic specialization for bipedality in fossil taxa.
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Affiliation(s)
- Dexter Zirkle
- Division of Biomedical Sciences and Department of Anthropology, Kent State University, Kent, Ohio, United States
| | - Richard S Meindl
- Division of Biomedical Sciences and Department of Anthropology, Kent State University, Kent, Ohio, United States
| | - C Owen Lovejoy
- Division of Biomedical Sciences and Department of Anthropology, Kent State University, Kent, Ohio, United States
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Buck LT, Katz DC, Ackermann RR, Hlusko LJ, Kanthaswamy S, Weaver TD. Effects of hybridization on pelvic morphology: A macaque model. J Hum Evol 2021; 159:103049. [PMID: 34455262 DOI: 10.1016/j.jhevol.2021.103049] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 11/28/2022]
Abstract
Ancient DNA analyses have shown that interbreeding between hominin taxa occurred multiple times. Although admixture is often reflected in skeletal phenotype, the relationship between the two remains poorly understood, hampering interpretation of the hominin fossil record. Direct study of this relationship is often impossible due to the paucity of hominin fossils and difficulties retrieving ancient genetic material. Here, we use a sample of known ancestry hybrids between two closely related nonhuman primate taxa (Indian and Chinese Macaca mulatta) to investigate the effect of admixture on skeletal morphology. We focus on pelvic shape, which has potential fitness implications in hybrids, as mismatches between maternal pelvic and fetal cranial morphology are often fatal to mother and offspring. As the pelvis is also one of the skeletal regions that differs most between Homo sapiens and Neanderthals, investigating the pelvic consequences of interbreeding could be informative regarding the viability of their hybrids. We find that the effect of admixture in M. mulatta is small and proportional to the relatively small morphological difference between the parent taxa. Sexual dimorphism appears to be the main determinant of pelvic shape in M. mulatta. The lack of difference in pelvic shape between Chinese and Indian M. mulatta is in contrast to that between Neanderthals and H. sapiens, despite a similar split time (in generations) between the hybridizing pairs. Greater phenotypic divergence between hominins may relate to adaptations to disparate environments but may also highlight how the unique degree of cultural buffering in hominins allowed for greater neutral divergence. In contrast to some previous work identifying extreme morphologies in first- and second-generation hybrids, here the relationship between pelvic shape and admixture is linear. This linearity may be because most sampled animals have a multigenerational admixture history or because of relatively high constraints on the pelvis compared with other skeletal regions.
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Affiliation(s)
- Laura T Buck
- School of Biological and Environmental Sciences, Liverpool John Moores University, UK; Department of Anthropology, University of California Davis, USA.
| | - David C Katz
- Department of Anthropology, University of California Davis, USA; University of Calgary, Cumming School of Medicine, Canada
| | - Rebecca Rogers Ackermann
- Department of Archaeology, University of Cape Town, South Africa; Human Evolution Research Institute, University of Cape Town, South Africa
| | - Leslea J Hlusko
- Department of Integrative Biology, University of California Berkeley, USA; Centro Nacional de Investigación sobre la Evolución Humana (CENIEH), Burgos, Spain
| | - Sree Kanthaswamy
- School of Natural and Mathematical Sciences, Arizona State University, USA
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