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Ghazanfar AA, Gomez-Marin A. The central role of the individual in the history of brains. Neurosci Biobehav Rev 2024; 163:105744. [PMID: 38825259 PMCID: PMC11246226 DOI: 10.1016/j.neubiorev.2024.105744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 05/26/2024] [Accepted: 05/30/2024] [Indexed: 06/04/2024]
Abstract
Every species' brain, body and behavior is shaped by the contingencies of their evolutionary history; these exert pressures that change their developmental trajectories. There is, however, another set of contingencies that shape us and other animals: those that occur during a lifetime. In this perspective piece, we show how these two histories are intertwined by focusing on the individual. We suggest that organisms--their brains and behaviors--are not solely the developmental products of genes and neural circuitry but individual centers of action unfolding in time. To unpack this idea, we first emphasize the importance of variation and the central role of the individual in biology. We then go over "errors in time" that we often make when comparing development across species. Next, we reveal how an individual's development is a process rather than a product by presenting a set of case studies. These show developmental trajectories as emerging in the contexts of the "the actual now" and "the presence of the past". Our consideration reveals that individuals are slippery-they are never static; they are a set of on-going, creative activities. In light of this, it seems that taking individual development seriously is essential if we aspire to make meaningful comparisons of neural circuits and behavior within and across species.
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Affiliation(s)
- Asif A Ghazanfar
- Princeton Neuroscience Institute, and Department of Psychology, Princeton University, Princeton, NJ 08544, USA.
| | - Alex Gomez-Marin
- Behavior of Organisms Laboratory, Instituto de Neurociencias CSIC-UMH, Alicante 03550, Spain.
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2
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Ferreira RC, Rodrigues CR, Broach JR, Briones MRS. Convergent Mutations and Single Nucleotide Variants in Mitochondrial Genomes of Modern Humans and Neanderthals. Int J Mol Sci 2024; 25:3785. [PMID: 38612593 PMCID: PMC11012180 DOI: 10.3390/ijms25073785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/12/2024] [Accepted: 03/13/2024] [Indexed: 04/14/2024] Open
Abstract
The genetic contributions of Neanderthals to the modern human genome have been evidenced by the comparison of present-day human genomes with paleogenomes. Neanderthal signatures in extant human genomes are attributed to intercrosses between Neanderthals and archaic anatomically modern humans (AMHs). Although Neanderthal signatures are well documented in the nuclear genome, it has been proposed that there is no contribution of Neanderthal mitochondrial DNA to contemporary human genomes. Here we show that modern human mitochondrial genomes contain 66 potential Neanderthal signatures, or Neanderthal single nucleotide variants (N-SNVs), of which 36 lie in coding regions and 7 result in nonsynonymous changes. Seven N-SNVs are associated with traits such as cycling vomiting syndrome, Alzheimer's disease and Parkinson's disease, and two N-SNVs are associated with intelligence quotient. Based on recombination tests, principal component analysis (PCA) and the complete absence of these N-SNVs in 41 archaic AMH mitogenomes, we conclude that convergent evolution, and not recombination, explains the presence of N-SNVs in present-day human mitogenomes.
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Affiliation(s)
- Renata C. Ferreira
- Center for Medical Bioinformatics, Federal University of São Paulo, São Paulo 04039032, SP, Brazil;
| | - Camila R. Rodrigues
- Graduate Program in Microbiology and Immunology, Federal University of São Paulo, São Paulo 04039032, SP, Brazil;
| | - James R. Broach
- Department of Biochemistry, Institute for Personalized Medicine, Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA 17033, USA;
| | - Marcelo R. S. Briones
- Center for Medical Bioinformatics, Federal University of São Paulo, São Paulo 04039032, SP, Brazil;
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3
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Mao Y, Harvey WT, Porubsky D, Munson KM, Hoekzema K, Lewis AP, Audano PA, Rozanski A, Yang X, Zhang S, Yoo D, Gordon DS, Fair T, Wei X, Logsdon GA, Haukness M, Dishuck PC, Jeong H, Del Rosario R, Bauer VL, Fattor WT, Wilkerson GK, Mao Y, Shi Y, Sun Q, Lu Q, Paten B, Bakken TE, Pollen AA, Feng G, Sawyer SL, Warren WC, Carbone L, Eichler EE. Structurally divergent and recurrently mutated regions of primate genomes. Cell 2024; 187:1547-1562.e13. [PMID: 38428424 PMCID: PMC10947866 DOI: 10.1016/j.cell.2024.01.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 11/26/2023] [Accepted: 01/31/2024] [Indexed: 03/03/2024]
Abstract
We sequenced and assembled using multiple long-read sequencing technologies the genomes of chimpanzee, bonobo, gorilla, orangutan, gibbon, macaque, owl monkey, and marmoset. We identified 1,338,997 lineage-specific fixed structural variants (SVs) disrupting 1,561 protein-coding genes and 136,932 regulatory elements, including the most complete set of human-specific fixed differences. We estimate that 819.47 Mbp or ∼27% of the genome has been affected by SVs across primate evolution. We identify 1,607 structurally divergent regions wherein recurrent structural variation contributes to creating SV hotspots where genes are recurrently lost (e.g., CARD, C4, and OLAH gene families) and additional lineage-specific genes are generated (e.g., CKAP2, VPS36, ACBD7, and NEK5 paralogs), becoming targets of rapid chromosomal diversification and positive selection (e.g., RGPD gene family). High-fidelity long-read sequencing has made these dynamic regions of the genome accessible for sequence-level analyses within and between primate species.
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Affiliation(s)
- Yafei Mao
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China.
| | - William T Harvey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Alexandra P Lewis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Peter A Audano
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Allison Rozanski
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Xiangyu Yang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Shilong Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - DongAhn Yoo
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - David S Gordon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Tyler Fair
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - Xiaoxi Wei
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Glennis A Logsdon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Marina Haukness
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Philip C Dishuck
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Hyeonsoo Jeong
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Ricardo Del Rosario
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vanessa L Bauer
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Bouder, CO, USA
| | - Will T Fattor
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Bouder, CO, USA
| | - Gregory K Wilkerson
- Department of Veterinary Sciences, Michale E. Keeling Center for Comparative Medicine and Research, The University of Texas MD Anderson Cancer Center, Bastrop, TX, USA; Department of Clinical Sciences, North Carolina State University, Raleigh, NC, USA
| | - Yuxiang Mao
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, Shanghai, China; Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China
| | - Yongyong Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China; Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, Shanghai, China; Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China
| | - Qiang Sun
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, Shanghai, China; Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China
| | - Qing Lu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | | | - Alex A Pollen
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Guoping Feng
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sara L Sawyer
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Bouder, CO, USA
| | - Wesley C Warren
- Department of Animal Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA; Department of Surgery, School of Medicine, University of Missouri, Columbia, MO, USA; Institute of Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Lucia Carbone
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA; Division of Genetics, Oregon National Primate Research Center, Beaverton, OR, USA; Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA; Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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Buffalo V, Kern AD. A quantitative genetic model of background selection in humans. PLoS Genet 2024; 20:e1011144. [PMID: 38507461 PMCID: PMC10984650 DOI: 10.1371/journal.pgen.1011144] [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: 09/17/2023] [Revised: 04/01/2024] [Accepted: 01/19/2024] [Indexed: 03/22/2024] Open
Abstract
Across the human genome, there are large-scale fluctuations in genetic diversity caused by the indirect effects of selection. This "linked selection signal" reflects the impact of selection according to the physical placement of functional regions and recombination rates along chromosomes. Previous work has shown that purifying selection acting against the steady influx of new deleterious mutations at functional portions of the genome shapes patterns of genomic variation. To date, statistical efforts to estimate purifying selection parameters from linked selection models have relied on classic Background Selection theory, which is only applicable when new mutations are so deleterious that they cannot fix in the population. Here, we develop a statistical method based on a quantitative genetics view of linked selection, that models how polygenic additive fitness variance distributed along the genome increases the rate of stochastic allele frequency change. By jointly predicting the equilibrium fitness variance and substitution rate due to both strong and weakly deleterious mutations, we estimate the distribution of fitness effects (DFE) and mutation rate across three geographically distinct human samples. While our model can accommodate weaker selection, we find evidence of strong selection operating similarly across all human samples. Although our quantitative genetic model of linked selection fits better than previous models, substitution rates of the most constrained sites disagree with observed divergence levels. We find that a model incorporating selective interference better predicts observed divergence in conserved regions, but overall our results suggest uncertainty remains about the processes generating fitness variation in humans.
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Affiliation(s)
- Vince Buffalo
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America
- Institute of Ecology and Evolution and Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Andrew D. Kern
- Institute of Ecology and Evolution and Department of Biology, University of Oregon, Eugene, Oregon, United States of America
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5
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Zhang Y, Shen SX, Bibic A, Wang X. Evolutionary continuity and divergence of auditory dorsal and ventral pathways in primates revealed by ultra-high field diffusion MRI. Proc Natl Acad Sci U S A 2024; 121:e2313831121. [PMID: 38377216 PMCID: PMC10907247 DOI: 10.1073/pnas.2313831121] [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: 08/10/2023] [Accepted: 01/22/2024] [Indexed: 02/22/2024] Open
Abstract
Auditory dorsal and ventral pathways in the human brain play important roles in supporting speech and language processing. However, the evolutionary root of the dual auditory pathways in the primate brain is unclear. By parcellating the auditory cortex of marmosets (a New World monkey species), macaques (an Old World monkey species), and humans using the same individual-based analysis method and tracking the pathways from the auditory cortex based on multi-shell diffusion-weighted MRI (dMRI), homologous auditory dorsal and ventral fiber tracks were identified in these primate species. The ventral pathway was found to be well conserved in all three primate species analyzed but extend to more anterior temporal regions in humans. In contrast, the dorsal pathway showed a divergence between monkey and human brains. First, frontal regions in the human brain have stronger connections to the higher-level auditory regions than to the lower-level auditory regions along the dorsal pathway, while frontal regions in the monkey brain show opposite connection patterns along the dorsal pathway. Second, the left lateralization of the dorsal pathway is only found in humans. Moreover, the connectivity strength of the dorsal pathway in marmosets is more similar to that of humans than macaques. These results demonstrate the continuity and divergence of the dual auditory pathways in the primate brains along the evolutionary path, suggesting that the putative neural networks supporting human speech and language processing might have emerged early in primate evolution.
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Affiliation(s)
- Yang Zhang
- Laboratory of Auditory Neurophysiology, Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Sherry Xinyi Shen
- Laboratory of Auditory Neurophysiology, Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Adnan Bibic
- Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, MD21205
- Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, F. M. Kirby Center, Baltimore, MD21205
| | - Xiaoqin Wang
- Laboratory of Auditory Neurophysiology, Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD21205
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6
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Lei H, Li J, Zhao B, Kou SH, Xiao F, Chen T, Wang SM. Evolutionary origin of germline pathogenic variants in human DNA mismatch repair genes. Hum Genomics 2024; 18:5. [PMID: 38287404 PMCID: PMC10823654 DOI: 10.1186/s40246-024-00573-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 01/17/2024] [Indexed: 01/31/2024] Open
Abstract
BACKGROUND Mismatch repair (MMR) system is evolutionarily conserved for genome stability maintenance. Germline pathogenic variants (PVs) in MMR genes that lead to MMR functional deficiency are associated with high cancer risk. Knowing the evolutionary origin of germline PVs in human MMR genes will facilitate understanding the biological base of MMR deficiency in cancer. However, systematic knowledge is lacking to address the issue. In this study, we performed a comprehensive analysis to know the evolutionary origin of human MMR PVs. METHODS We retrieved MMR gene variants from the ClinVar database. The genomes of 100 vertebrates were collected from the UCSC genome browser and ancient human sequencing data were obtained through comprehensive data mining. Cross-species conservation analysis was performed based on the phylogenetic relationship among 100 vertebrates. Rescaled ancient sequencing data were used to perform variant calling for archeological analysis. RESULTS Using the phylogenetic approach, we traced the 3369 MMR PVs identified in modern humans in 99 non-human vertebrate genomes but found no evidence for cross-species conservation as the source for human MMR PVs. Using the archeological approach, we searched the human MMR PVs in over 5000 ancient human genomes dated from 45,045 to 100 years before present and identified a group of MMR PVs shared between modern and ancient humans mostly within 10,000 years with similar quantitative patterns. CONCLUSION Our study reveals that MMR PVs in modern humans were arisen within the recent human evolutionary history.
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Affiliation(s)
- Huijun Lei
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, 999078, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310018, Zhejiang, China
- Department of Cancer Prevention, Zhejiang Cancer Hospital, Hangzhou, 310022, Zhejiang, China
| | - Jiaheng Li
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, 999078, China
| | - Bojin Zhao
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, 999078, China
| | - Si Hoi Kou
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, 999078, China
| | - Fengxia Xiao
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, 999078, China
| | - Tianhui Chen
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310018, Zhejiang, China.
- Department of Cancer Prevention, Zhejiang Cancer Hospital, Hangzhou, 310022, Zhejiang, China.
| | - San Ming Wang
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, 999078, China.
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7
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Shao Y, Zhou L, Li F, Zhao L, Zhang BL, Shao F, Chen JW, Chen CY, Bi X, Zhuang XL, Zhu HL, Hu J, Sun Z, Li X, Wang D, Rivas-González I, Wang S, Wang YM, Chen W, Li G, Lu HM, Liu Y, Kuderna LFK, Farh KKH, Fan PF, Yu L, Li M, Liu ZJ, Tiley GP, Yoder AD, Roos C, Hayakawa T, Marques-Bonet T, Rogers J, Stenson PD, Cooper DN, Schierup MH, Yao YG, Zhang YP, Wang W, Qi XG, Zhang G, Wu DD. Phylogenomic analyses provide insights into primate evolution. Science 2023; 380:913-924. [PMID: 37262173 DOI: 10.1126/science.abn6919] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 01/26/2023] [Indexed: 06/03/2023]
Abstract
Comparative analysis of primate genomes within a phylogenetic context is essential for understanding the evolution of human genetic architecture and primate diversity. We present such a study of 50 primate species spanning 38 genera and 14 families, including 27 genomes first reported here, with many from previously less well represented groups, the New World monkeys and the Strepsirrhini. Our analyses reveal heterogeneous rates of genomic rearrangement and gene evolution across primate lineages. Thousands of genes under positive selection in different lineages play roles in the nervous, skeletal, and digestive systems and may have contributed to primate innovations and adaptations. Our study reveals that many key genomic innovations occurred in the Simiiformes ancestral node and may have had an impact on the adaptive radiation of the Simiiformes and human evolution.
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Affiliation(s)
- Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Long Zhou
- Center of Evolutionary & Organismal Biology, and Women's Hospital at Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Fang Li
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- Institute of Animal Sex and Development, ZhejiangWanli University, Ningbo 315100, China
| | - Lan Zhao
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Bao-Lin Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Feng Shao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, China
| | | | - Chun-Yan Chen
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Xupeng Bi
- Center of Evolutionary & Organismal Biology, and Women's Hospital at Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xiao-Lin Zhuang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming 650204, China
| | | | - Jiang Hu
- Grandomics Biosciences, Beijing 102206, China
| | - Zongyi Sun
- Grandomics Biosciences, Beijing 102206, China
| | - Xin Li
- Grandomics Biosciences, Beijing 102206, China
| | - Depeng Wang
- Grandomics Biosciences, Beijing 102206, China
| | | | - Sheng Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Yun-Mei Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Wu Chen
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou 510070, China
| | - Gang Li
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Hui-Meng Lu
- School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Yang Liu
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Lukas F K Kuderna
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain
- Illumina Artificial Intelligence Laboratory, Illumina Inc, San Diego, CA 92122, USA
| | - Kyle Kai-How Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc, San Diego, CA 92122, USA
| | - Peng-Fei Fan
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Ming Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhi-Jin Liu
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - George P Tiley
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Takashi Hayakawa
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
- Japan Monkey Centre, Inuyama, Aichi 484-0081, Japan
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Peter D Stenson
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | | | - Yong-Gang Yao
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming 650204, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650107, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650107, China
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China
| | - Xiao-Guang Qi
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- Center of Evolutionary & Organismal Biology, and Women's Hospital at Zhejiang University School of Medicine, Hangzhou 310058, China
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311121, China
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650107, China
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650204, China
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8
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Mao Y, Harvey WT, Porubsky D, Munson KM, Hoekzema K, Lewis AP, Audano PA, Rozanski A, Yang X, Zhang S, Gordon DS, Wei X, Logsdon GA, Haukness M, Dishuck PC, Jeong H, Del Rosario R, Bauer VL, Fattor WT, Wilkerson GK, Lu Q, Paten B, Feng G, Sawyer SL, Warren WC, Carbone L, Eichler EE. Structurally divergent and recurrently mutated regions of primate genomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.07.531415. [PMID: 36945442 PMCID: PMC10028934 DOI: 10.1101/2023.03.07.531415] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
To better understand the pattern of primate genome structural variation, we sequenced and assembled using multiple long-read sequencing technologies the genomes of eight nonhuman primate species, including New World monkeys (owl monkey and marmoset), Old World monkey (macaque), Asian apes (orangutan and gibbon), and African ape lineages (gorilla, bonobo, and chimpanzee). Compared to the human genome, we identified 1,338,997 lineage-specific fixed structural variants (SVs) disrupting 1,561 protein-coding genes and 136,932 regulatory elements, including the most complete set of human-specific fixed differences. Across 50 million years of primate evolution, we estimate that 819.47 Mbp or ~27% of the genome has been affected by SVs based on analysis of these primate lineages. We identify 1,607 structurally divergent regions (SDRs) wherein recurrent structural variation contributes to creating SV hotspots where genes are recurrently lost (CARDs, ABCD7, OLAH) and new lineage-specific genes are generated (e.g., CKAP2, NEK5) and have become targets of rapid chromosomal diversification and positive selection (e.g., RGPDs). High-fidelity long-read sequencing has made these dynamic regions of the genome accessible for sequence-level analyses within and between primate species for the first time.
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Affiliation(s)
- Yafei Mao
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - William T Harvey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Alexandra P Lewis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Peter A Audano
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Allison Rozanski
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Xiangyu Yang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Shilong Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - David S Gordon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Xiaoxi Wei
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Glennis A Logsdon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Marina Haukness
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Philip C Dishuck
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Hyeonsoo Jeong
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Ricardo Del Rosario
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vanessa L Bauer
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Will T Fattor
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Gregory K Wilkerson
- Department of Veterinary Sciences, Michale E. Keeling Center for Comparative Medicine and Research, The University of Texas MD Anderson Cancer Center, Bastrop, TX, USA
- Department of Clinical Sciences, North Carolina State University, Raleigh, NC, USA
| | - Qing Lu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Guoping Feng
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sara L Sawyer
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Wesley C Warren
- Department of Animal Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Department of Surgery, School of Medicine, University of Missouri, Columbia, MO, USA
- Institute of Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Lucia Carbone
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA
- Division of Genetics, Oregon National Primate Research Center, Beaverton, OR, USA
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
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9
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Vallender EJ, Hotchkiss CE, Lewis AD, Rogers J, Stern JA, Peterson SM, Ferguson B, Sayers K. Nonhuman primate genetic models for the study of rare diseases. Orphanet J Rare Dis 2023; 18:20. [PMID: 36721163 PMCID: PMC9887761 DOI: 10.1186/s13023-023-02619-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 01/15/2023] [Indexed: 02/01/2023] Open
Abstract
Pre-clinical research and development relies heavily upon translationally valid models of disease. A major difficulty in understanding the biology of, and developing treatments for, rare disease is the lack of animal models. It is important that these models not only recapitulate the presentation of the disease in humans, but also that they share functionally equivalent underlying genetic causes. Nonhuman primates share physiological, anatomical, and behavioral similarities with humans resulting from close evolutionary relationships and high genetic homology. As the post-genomic era develops and next generation sequencing allows for the resequencing and screening of large populations of research animals, naturally occurring genetic variation in nonhuman primates with clinically relevant phenotypes is regularly emerging. Here we review nonhuman primate models of multiple rare genetic diseases with a focus on the similarities and differences in manifestation and etiologies across species. We discuss how these models are being developed and how they can offer new tools and opportunities for researchers interested in exploring novel therapeutics for these and other genetic diseases. Modeling human genetic diseases in translationally relevant nonhuman primates presents new prospects for development of therapeutics and a better understanding of rare diseases. The post-genomic era offers the opportunity for the discovery and further development of more models like those discussed here.
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Affiliation(s)
- Eric J. Vallender
- University of Mississippi Medical Center, Jackson, MS USA
- Tulane National Primate Research Center, Covington, LA USA
| | - Charlotte E. Hotchkiss
- University of Washington, Seattle, WA USA
- Washington National Primate Research Center, Seattle, WA USA
| | - Anne D. Lewis
- Oregon Health and Sciences University, Beaverton, OR USA
- Oregon National Primate Research Center, Beaverton, OR USA
| | - Jeffrey Rogers
- Baylor College of Medicine, Houston, TX USA
- Wisconsin National Primate Research Center, Madison, WI USA
| | - Joshua A. Stern
- University of California-Davis, Davis, CA USA
- California National Primate Research Center, Davis, CA USA
| | - Samuel M. Peterson
- Oregon Health and Sciences University, Beaverton, OR USA
- Oregon National Primate Research Center, Beaverton, OR USA
| | - Betsy Ferguson
- Oregon Health and Sciences University, Beaverton, OR USA
- Oregon National Primate Research Center, Beaverton, OR USA
| | - Ken Sayers
- Texas Biomedical Research Institute, San Antonio, TX USA
- Southwest National Primate Research Center, San Antonio, TX USA
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10
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Galili U. Paleo-immunology of human anti-carbohydrate antibodies preventing primate extinctions. Immunology 2023; 168:18-29. [PMID: 36161654 DOI: 10.1111/imm.13582] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 09/16/2022] [Indexed: 12/27/2022] Open
Abstract
Two human natural anti-carbohydrate antibodies appeared in critical evolutionary events that brought primates and hominins to brink of extinction. The first is the anti-Gal antibody, produced in Old-World monkeys (OWM), apes and humans. It binds the carbohydrate-antigen 'α-gal epitope' (Galα1-3Galβ1-4GlcNAc-R) on carbohydrate-chains (glycans) synthesized by non-primate mammals, lemurs and New-World monkeys (NWM). The second is anti-N-glycolylneuraminic-acid (anti-Neu5Gc) antibody binding Neu5Gc on glycans synthesized by OWM, apes and most non-primate mammals. Ancestral OWM and apes synthesized α-gal epitopes and were eliminated ~20-30 million-years-ago (mya). Only few accidentally mutated offspring lacking α-gal epitopes, produced anti-Gal and survived. Hominin-populations living ~3 mya synthesized Neu5Gc and were eliminated, but few mutated offspring that accidently lost their ability to synthesize Neu5Gc, produced natural anti-Neu5Gc antibody. These hominins survived and ultimately evolved into present-day humans. It is argued that these two near-extinction events were likely to be the result of epidemics caused by highly virulent and lethal enveloped viruses that killed parental-populations. These viruses presented α-gal epitopes or Neu5Gc synthesized in host-cells of the parental-populations. Mutated offspring survived the epidemics because they were protected from the lethal virus by the natural anti-Gal or anti-Neu5Gc antibodies they produced due to loss of immune-tolerance to α-gal epitopes or to Neu5Gc, respectively.
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Affiliation(s)
- Uri Galili
- Department of Medicine/Division of Cardiology, Rush University Medical College, Chicago, Illinois, USA
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11
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Alagöz G, Molz B, Eising E, Schijven D, Francks C, Stein JL, Fisher SE. Using neuroimaging genomics to investigate the evolution of human brain structure. Proc Natl Acad Sci U S A 2022; 119:e2200638119. [PMID: 36161899 PMCID: PMC9546597 DOI: 10.1073/pnas.2200638119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 08/15/2022] [Indexed: 01/16/2023] Open
Abstract
Alterations in brain size and organization represent some of the most distinctive changes in the emergence of our species. Yet, there is limited understanding of how genetic factors contributed to altered neuroanatomy during human evolution. Here, we analyze neuroimaging and genetic data from up to 30,000 people in the UK Biobank and integrate with genomic annotations for different aspects of human evolution, including those based on ancient DNA and comparative genomics. We show that previously reported signals of recent polygenic selection for cortical anatomy are not replicable in a more ancestrally homogeneous sample. We then investigate relationships between evolutionary annotations and common genetic variants shaping cortical surface area and white-matter connectivity for each hemisphere. Our analyses identify single-nucleotide polymorphism heritability enrichment in human-gained regulatory elements that are active in early brain development, affecting surface areas of several parts of the cortex, including left-hemispheric speech-associated regions. We also detect heritability depletion in genomic regions with Neanderthal ancestry for connectivity of the uncinate fasciculus; this is a white-matter tract involved in memory, language, and socioemotional processing with relevance to neuropsychiatric disorders. Finally, we show that common genetic loci associated with left-hemispheric pars triangularis surface area overlap with a human-gained enhancer and affect regulation of ZIC4, a gene implicated in neurogenesis. This work demonstrates how genomic investigations of present-day neuroanatomical variation can help shed light on the complexities of our evolutionary past.
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Affiliation(s)
- Gökberk Alagöz
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6500 AH Nijmegen, The Netherlands
| | - Barbara Molz
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6500 AH Nijmegen, The Netherlands
| | - Else Eising
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6500 AH Nijmegen, The Netherlands
| | - Dick Schijven
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6500 AH Nijmegen, The Netherlands
| | - Clyde Francks
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6500 AH Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6500 HB Nijmegen, The Netherlands
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Jason L. Stein
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Simon E. Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6500 AH Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6500 HB Nijmegen, The Netherlands
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12
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Baehren L, Carvalho S. Yet Another Non-Unique Human Behaviour: Leave-Taking in Wild Chacma Baboons (Papio ursinus). Animals (Basel) 2022; 12:ani12192577. [PMID: 36230318 PMCID: PMC9559683 DOI: 10.3390/ani12192577] [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: 08/17/2022] [Revised: 09/18/2022] [Accepted: 09/19/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Although greeting is well-studied across animal species, its counterpart, leave taking, is little studied in nonhumans. Here, we review the previous limitations of leave-taking research and use this to develop a new method for studying leave taking in nonhumans. Using videos of chacma baboons in Gorongosa National Park, Mozambique, we compared behaviours at the end of social departures to nonsocial departures. We found that shifting orientation towards the direction of parting was significantly more likely in social departures compared to nonsocial departures. As the first evidence of leave taking in a wild nonhuman species, we suggest that leave taking is not uniquely human as previously argued, and that our method could be used to further explore the presence of leave taking in other nonhuman species. Abstract Leave taking is a common, possibly universal, feature of human social behaviour that has undergone very little empirical research. Although the importance remains unknown, it has been suggested to play an important role in managing separations, mitigating the risk, and increasing social bonding beyond the interaction itself. In nonhuman species, the literature is virtually absent, but identifying leave taking beyond humans may provide unique insights into the evolutionary history of this behaviour and shed light onto its proximate and ultimate function(s). Methods to study leave taking are not well-established, and the variation in definitions, measures, and control variables presented in past studies poses additional challenges. Baboons are a valuable model for investigating human behavioural evolution: as a flexible, highly adaptable, and social primate whose radiation is, similarly to humans, associated with the emergence of the African savannah biome. Using the framework and definition proposed by Baehren, we investigated the presence of leave taking in a wild, generalist primate and tested a range of candidate behaviours on prerecorded video footage: (1) self-scratching, (2) eye gaze, and (3) orientation in the direction of parting. Using multivariate analysis, controlling for interaction duration and individual variation, our results show that orientation in the direction of parting occurs predominantly before social separation events. These results indicate evidence of leave taking in a wild nonhuman population and contrast with previous ideas that this is a uniquely human behaviour. The presence of leave taking in baboons suggests a deep evolutionary history of this behaviour, warranting further investigation into its function and presence across other nonhuman primate species.
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Affiliation(s)
- Lucy Baehren
- Primate Models for Behavioural Evolution Lab, Institute of Human Sciences, University of Oxford, Oxford OX2 6PR, UK
- Correspondence:
| | - Susana Carvalho
- Primate Models for Behavioural Evolution Lab, Institute of Human Sciences, University of Oxford, Oxford OX2 6PR, UK
- Gorongosa National Park, Beira 1983, Mozambique
- Interdisciplinary Centre for Archaeology and Evolution of Human Behaviour, Universidade do Algarve, 8005-139 Faro, Portugal
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13
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14
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Pozzi L, Penna A. Rocks and clocks revised: New promises and challenges in dating the primate tree of life. Evol Anthropol 2022; 31:138-153. [PMID: 35102633 DOI: 10.1002/evan.21940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 10/04/2021] [Accepted: 01/12/2022] [Indexed: 01/14/2023]
Abstract
In recent years, multiple technological and methodological advances have increased our ability to estimate phylogenies, leading to more accurate dating of the primate tree of life. Here we provide an overview of the limitations and potentials of some of these advancements and discuss how dated phylogenies provide the crucial temporal scale required to understand primate evolution. First, we review new methods, such as the total-evidence dating approach, that promise a better integration between the fossil record and molecular data. We then explore how the ever-increasing availability of genomic-level data for more primate species can impact our ability to accurately estimate timetrees. Finally, we discuss more recent applications of mutation rates to date divergence times. We highlight example studies that have applied these approaches to estimate divergence dates within primates. Our goal is to provide a critical overview of these new developments and explore the promises and challenges of their application in evolutionary anthropology.
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Affiliation(s)
- Luca Pozzi
- Department of Anthropology, The University of Texas at San Antonio, San Antonio, Texas, USA
| | - Anna Penna
- Department of Anthropology, The University of Texas at San Antonio, San Antonio, Texas, USA
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15
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Pugh KD. Phylogenetic analysis of Middle-Late Miocene apes. J Hum Evol 2022; 165:103140. [DOI: 10.1016/j.jhevol.2021.103140] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 12/28/2021] [Accepted: 12/28/2021] [Indexed: 01/18/2023]
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16
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Arenson JL, Harrison T, Sargis EJ, Taboada HG, Gilbert CC. A new species of fossil guenon (Cercopithecini, Cercopithecidae) from the Early Pleistocene Lower Ngaloba Beds, Laetoli, Tanzania. J Hum Evol 2022; 163:103136. [PMID: 35033736 DOI: 10.1016/j.jhevol.2021.103136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 12/06/2021] [Accepted: 12/06/2021] [Indexed: 11/30/2022]
Abstract
The living guenons (Cercopithecini, Cercopithecidae) are speciose and widely distributed across sub-Saharan Africa but are poorly represented in the fossil record. In addition, the craniodental and skeletal similarity of the guenons has hampered the identification of fragmentary material, likely obscuring the taxonomic diversity represented in the fossil record. Here, we describe a new fossil guenon specimen (LAET 75-3703) from the Lower Ngaloba Beds, Laetoli in Tanzania, dated to ∼1.7-1.2 Ma and preserving the lower face and mandible. Comparison to 278 extant guenon specimens, representing all six extant genera, identified several informative traits for distinguishing between the morphologically similar Chlorocebus and Cercopithecus, and these support the attribution of LAET 75-3703 to Chlorocebus. A discriminant function analysis of seven craniodental indices on a subsample of Chlorocebus and Cercopithecus was robust with an overall correct classification rate of 80.4%, and it classified LAET 75-3703 as a member of Chlorocebus with a posterior probability of 92.7%. LAET 75-3703 shares with Chlorocebus the presence of small 'thumbprint' depressions on the maxilla; a tall, narrow, and diamond-shaped nasal aperture; a relatively longer and shallower face; relatively buccolingually broader molars; and a shallow mandible that decreases in depth posteriorly. In addition, LAET 75-3703 is distinguished from all extant guenons, including other species of Chlorocebus, in having a very small P3 relative to M1 area. As such, LAET 75-3703 is assigned to a new species, Chlorocebus ngedere sp. nov. This specimen represents the first cercopithecin from Laetoli, as well as the oldest fossil cercopithecin confidently attributed to a modern genus.
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Affiliation(s)
- Julia L Arenson
- PhD Program in Anthropology, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY, 10016, USA; New York Consortium in Evolutionary Primatology (NYCEP), New York, NY, 10016, USA.
| | - Terry Harrison
- New York Consortium in Evolutionary Primatology (NYCEP), New York, NY, 10016, USA; Center for the Study of Human Origins, Department of Anthropology, New York University, 25 Waverly Place, New York, NY, 10003, USA
| | - Eric J Sargis
- Department of Anthropology, Yale University, 10 Sachem Street, New Haven, CT, 06511, USA; Divisions of Vertebrate Paleontology and Vertebrate Zoology, Yale Peabody Museum of Natural History, 170 Whitney Avenue, New Haven, CT, 06511, USA; Yale Institute for Biospheric Studies, P.O. Box 208118, New Haven, CT, 06520, USA
| | - Hannah G Taboada
- Center for the Study of Human Origins, Department of Anthropology, New York University, 25 Waverly Place, New York, NY, 10003, USA
| | - Christopher C Gilbert
- PhD Program in Anthropology, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY, 10016, USA; New York Consortium in Evolutionary Primatology (NYCEP), New York, NY, 10016, USA; Department of Anthropology, Hunter College, CUNY, 695 Park Avenue, New York, NY, 10065, USA; Division of Paleontology, American Museum of Natural History, Central Park West, New York, NY, 10024, USA
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17
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Boso G, Fleck K, Carley S, Liu Q, Buckler-White A, Kozak CA. The Oldest Co-opted gag Gene of a Human Endogenous Retrovirus Shows Placenta-Specific Expression and Is Upregulated in Diffuse Large B-Cell Lymphomas. Mol Biol Evol 2021; 38:5453-5471. [PMID: 34410386 PMCID: PMC8662612 DOI: 10.1093/molbev/msab245] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Vertebrate genomes contain endogenous retroviruses (ERVs) that represent remnants of past germline infections by ancient retroviruses. Despite comprising 8% of the human genome, the human ERVs (HERVs) do not encode a replication competent retrovirus. However, some HERV genes have been co-opted to serve host functions, most notably the viral envelope-derived syncytins involved in placentation. Here, we identify the oldest HERV intact gag gene with an open reading frame, gagV1. Its provirus contains an intact env, envV1, and the first open reading frame found in an HERV gag leader, pre-gagV1, which encodes a novel protein. This HERV is linked to a related gag gene, gagV3, and these three genes all show patterns of evolutionary conservation in primates. gagV1 and pre-gagV1 orthologs are present in all simian primate lineages indicating that this HERV entered the germline of the common simian primate ancestor at least 43 Ma, whereas gagV3 is found in Old and New World monkeys. gagV1 and gagV3 have undergone recurrent gene conversion events and positive selection. Expression of gagV1, gagV3, and pre-gagV1 is restricted to the placenta in humans and macaques suggesting co-option for placenta-specific host functions. Transcriptomic analysis of human tumors also found upregulated levels of gagV1 transcripts in diffuse large B-cell lymphomas. These findings suggest that these HERV-V genes may be useful markers for the most common type of non-Hodgkin's lymphoma and that they may have contributed to the successive domestications of env and gag genes in eutherians involved in the ongoing ERV-driven evolution of the placenta.
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Affiliation(s)
- Guney Boso
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Katherine Fleck
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Samuel Carley
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Qingping Liu
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Alicia Buckler-White
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Christine A Kozak
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
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18
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Carn D, Lanaspa MA, Benner SA, Andrews P, Dudley R, Andres-Hernando A, Tolan DR, Johnson RJ. The role of thrifty genes in the origin of alcoholism: A narrative review and hypothesis. Alcohol Clin Exp Res 2021; 45:1519-1526. [PMID: 34120350 PMCID: PMC8429132 DOI: 10.1111/acer.14655] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 05/26/2021] [Accepted: 05/31/2021] [Indexed: 01/21/2023]
Abstract
In this narrative review, we present the hypothesis that key mutations in two genes, occurring 15 and 10 million years ago (MYA), were individually and then collectively adaptive for ancestral humans during periods of starvation, but are maladaptive in modern civilization (i.e., "thrifty genes"), with the consequence that these genes not only increase our risk today for obesity, but also for alcoholism. Both mutations occurred when ancestral apes were experiencing loss of fruit availability during periods of profound climate change or environmental upheaval. The silencing of uricase (urate oxidase) activity 15 MYA enhanced survival by increasing the ability for fructose present in dwindling fruit to be stored as fat, a consequence of enhanced uric acid production during fructose metabolism that stimulated lipogenesis and blocked fatty acid oxidation. Likewise, a mutation in class IV alcohol dehydrogenase ~10 MYA resulted in a remarkable 40-fold increase in the capacity to oxidize ethanol (EtOH), which allowed our ancestors to ingest fallen, fermenting fruit. In turn, the EtOH ingested could activate aldose reductase that stimulates the conversion of glucose to fructose, while uric acid produced during EtOH metabolism could further enhance fructose production and metabolism. By aiding survival, these mutations would have allowed our ancestors to generate more fat, primarily from fructose, to survive changing habitats due to the Middle Miocene disruption and also during the late-Miocene aridification of East Africa. Unfortunately, the enhanced ability to metabolize and utilize EtOH may now be acting to increase our risk for alcoholism, which may be yet another consequence of once-adaptive thrifty genes.
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Affiliation(s)
| | - Miguel A. Lanaspa
- Division of Nephrology, University of Colorado Anschutz Medical Center, Aurora, CO, USA
| | - Steven A. Benner
- The Foundation for Applied Molecular Evolution, Alachua, FL, USA
| | - Peter Andrews
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Robert Dudley
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Ana Andres-Hernando
- Division of Nephrology, University of Colorado Anschutz Medical Center, Aurora, CO, USA
| | - Dean R. Tolan
- Department of Biochemistry, Boston University, Boston, MA, USA
| | - Richard J. Johnson
- Division of Nephrology, University of Colorado Anschutz Medical Center, Aurora, CO, USA,The Rocky Mountain VA Medical Center, Aurora CO, USA
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19
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Varella TT, Ghazanfar AA. Cooperative care and the evolution of the prelinguistic vocal learning. Dev Psychobiol 2021; 63:1583-1588. [PMID: 33826142 PMCID: PMC8355020 DOI: 10.1002/dev.22108] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 01/12/2021] [Accepted: 01/17/2021] [Indexed: 11/06/2022]
Abstract
The development of the earliest vocalizations of human infants is influenced by social feedback from caregivers. As these vocalizations change, they increasingly elicit such feedback. This pattern of development is in stark contrast to that of our close phylogenetic relatives, Old World monkeys and apes, who produce mature-sounding vocalizations at birth. We put forth a scenario to account for this difference: Humans have a cooperative breeding strategy, which pressures infants to compete for the attention from caregivers. Humans use this strategy because large brained human infants are energetically costly and born altricial. An altricial brain accommodates vocal learning. To test this hypothetical scenario, we present findings from New World marmoset monkeys indicating that, through convergent evolution, this species adopted a largely identical developmental system-one that includes vocal learning and cooperative breeding.
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Affiliation(s)
- Thiago T. Varella
- Department of Psychology, Princeton University, Princeton NJ 08544, USA
- Princeton Neuroscience Institute, Princeton University, Princeton NJ 08544, USA
| | - Asif A. Ghazanfar
- Department of Psychology, Princeton University, Princeton NJ 08544, USA
- Princeton Neuroscience Institute, Princeton University, Princeton NJ 08544, USA
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton NJ 08544, USA
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20
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Morel B, Barbera P, Czech L, Bettisworth B, Hübner L, Lutteropp S, Serdari D, Kostaki EG, Mamais I, Kozlov AM, Pavlidis P, Paraskevis D, Stamatakis A. Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult. Mol Biol Evol 2021; 38:1777-1791. [PMID: 33316067 PMCID: PMC7798910 DOI: 10.1093/molbev/msaa314] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Numerous studies covering some aspects of SARS-CoV-2 data analyses are being published on a daily basis, including a regularly updated phylogeny on nextstrain.org. Here, we review the difficulties of inferring reliable phylogenies by example of a data snapshot comprising a quality-filtered subset of 8,736 out of all 16,453 virus sequences available on May 5, 2020 from gisaid.org. We find that it is difficult to infer a reliable phylogeny on these data due to the large number of sequences in conjunction with the low number of mutations. We further find that rooting the inferred phylogeny with some degree of confidence either via the bat and pangolin outgroups or by applying novel computational methods on the ingroup phylogeny does not appear to be credible. Finally, an automatic classification of the current sequences into subclasses using the mPTP tool for molecular species delimitation is also, as might be expected, not possible, as the sequences are too closely related. We conclude that, although the application of phylogenetic methods to disentangle the evolution and spread of COVID-19 provides some insight, results of phylogenetic analyses, in particular those conducted under the default settings of current phylogenetic inference tools, as well as downstream analyses on the inferred phylogenies, should be considered and interpreted with extreme caution.
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Affiliation(s)
- Benoit Morel
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Pierre Barbera
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Lucas Czech
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Ben Bettisworth
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Lukas Hübner
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Sarah Lutteropp
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Dora Serdari
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Evangelia-Georgia Kostaki
- Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Ioannis Mamais
- Department of Health Sciences, European University Cyprus, Nicosia, Cyprus
| | - Alexey M Kozlov
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Pavlos Pavlidis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, Crete, Greece
| | - Dimitrios Paraskevis
- Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Alexandros Stamatakis
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
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21
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Bettisworth B, Stamatakis A. Root Digger: a root placement program for phylogenetic trees. BMC Bioinformatics 2021; 22:225. [PMID: 33932975 PMCID: PMC8088003 DOI: 10.1186/s12859-021-03956-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/01/2021] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND In phylogenetic analysis, it is common to infer unrooted trees. However, knowing the root location is desirable for downstream analyses and interpretation. There exist several methods to recover a root, such as molecular clock analysis (including midpoint rooting) or rooting the tree using an outgroup. Non-reversible Markov models can also be used to compute the likelihood of a potential root position. RESULTS We present a software called RootDigger which uses a non-reversible Markov model to compute the most likely root location on a given tree and to infer a confidence value for each possible root placement. We find that RootDigger is successful at finding roots when compared to similar tools such as IQ-TREE and MAD, and will occasionally outperform them. Additionally, we find that the exhaustive mode of RootDigger is useful in quantifying and explaining uncertainty in rooting positions. CONCLUSIONS RootDigger can be used on an existing phylogeny to find a root, or to asses the uncertainty of the root placement. RootDigger is available under the MIT licence at https://www.github.com/computations/root_digger .
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Affiliation(s)
- Ben Bettisworth
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Alexandros Stamatakis
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- Institut für Theoretische Informatik, Karlsruhe Institute of Technology, Karslruhe, Germany
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22
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Amusa C, Rothman J, Odongo S, Matovu H, Ssebugere P, Baranga D, Sillanpää M. The endangered African Great Ape: Pesticide residues in soil and plants consumed by Mountain Gorillas (Gorilla beringei) in Bwindi Impenetrable National Park, East Africa. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 758:143692. [PMID: 33272601 DOI: 10.1016/j.scitotenv.2020.143692] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/31/2020] [Accepted: 10/31/2020] [Indexed: 06/12/2023]
Abstract
Bwindi Impenetrable National Park situated southwest of Uganda is a biodiversity hotspot that is home to about half of the world's endangered mountain gorilla (Gorilla beringei). Given its ecological significance and mounting pressures from agricultural activities such as tea growing, continuous monitoring of the levels of chemical toxins like pesticides in the park and surrounding areas is needed for effective conservation strategies. Furthermore, persistent organochlorine pesticides (OCPs) like DDT were used in agricultural gardens and indoor spraying in Kanungu district between the 1950s and 80s. The focus of this study was to explore the possible exposure of mountain gorillas to OCPs and cypermethrin used by the farmers in the areas near the park. Data from our interviews revealed that glyphosate is the most widely used pesticide by the farmers in areas surrounding the park, followed by cypermethrin, and mancozeb. Samples of leaves from plants consumed by mountain gorillas along the forest edges of the park and surficial soils (15-20 cm depths) were collected from three sites (Ruhija, Nkuringo and Buhoma) and analysed for the presence of cypermethrin and OCPs residues. Concentrations of total (∑) DDTs and ∑endosulfans were up to 0.34 and 9.89 mg/kg dry weight (d.w), respectively in soil samples. Concentrations of ∑DDTs and ∑endosulfans in samples of leaves ranged from 0.67 to 1.38 mg/kg d.w (mean = 1.07 mg/kg d.w) and 0.9 to 2.71 mg/kg d.w (mean = 1.68 mg/kg d.w), respectively. Mean concentration of ∑DDTs in leaves exceeded the European pharmacopeia and United States pharmacopeia recommended maximum residue limit values for DDTs in medicinal plants (1.0 mg/kg). In addition, calculated hazard indices for silverbacks (36.35), females (57.54) and juveniles (77.04) suggested potential health risks to the mountain gorillas. o,p'-DDT/p,p'-DDT ratios (0.5-0.63) in samples of leaves confirmed recent input of dicofol-DDT type in Bwindi rainforest.
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Affiliation(s)
- Chemonges Amusa
- Department of Chemistry, Makerere University, P. O Box 7062, Kampala, Uganda; Uganda Wildlife Authority and Primate Conservation, Kampala, Uganda
| | - Jessica Rothman
- Department of Anthropology, and New York Consortium in Evolutionary Primatology, Hunter College of the City University of New York, New York, NY, USA
| | - Silver Odongo
- Department of Chemistry, Makerere University, P. O Box 7062, Kampala, Uganda
| | - Henry Matovu
- Department of Chemistry, Makerere University, P. O Box 7062, Kampala, Uganda; Department of Chemistry, Gulu University, P. O Box 166, Gulu, Uganda
| | - Patrick Ssebugere
- Department of Chemistry, Makerere University, P. O Box 7062, Kampala, Uganda.
| | - Deborah Baranga
- Department of Zoology, Makerere University, P. O Box 7062, Kampala, Uganda
| | - Mika Sillanpää
- Institute of Research and Development, Duy Tan University, Da Nang 550000, Viet Nam; Faculty of Environment and Chemical Engineering, Duy Tan University, Da Nang 550000, Viet Nam; Department of Chemical Engineering, School of Mining, Metallurgy and Chemical Engineering, University of Johannesburg, P. O. Box 17011, Doornfontein 2028, South Africa
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23
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Sense-oriented AluYRa1 elements provide a lineage-specific transcription environment for polyadenylation. Sci Rep 2021; 11:3665. [PMID: 33574427 PMCID: PMC7878741 DOI: 10.1038/s41598-021-83360-4] [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: 10/15/2020] [Accepted: 01/29/2021] [Indexed: 11/08/2022] Open
Abstract
Transposable elements cause alternative splicing (AS) in different ways, contributing to transcript diversification. Alternative polyadenylation (APA), one of the AS events, is related to the generation of mRNA isoforms in 70% of human genes. In this study, we tried to investigate AluYRa1s located at the terminal region of cynomolgus monkey genes, utilizing both computational analysis and molecular experimentation. We found that ten genes had AluYRa1 at their 3' end, and nine of these AluYRa1s were sense-oriented. Furthermore, in seven genes, AluYRa1s were expected to have a similar consensus sequence for polyadenylation cleavage. Additional computational analysis using the annotation files from the UCSC database showed that AluYRa1 was more involved in polyadenylation than in open reading frame exon splicing. To examine the extent of AluYRa1 involvement in polyadenylation, RNA-seq data from 30 normal cynomolgus monkeys were analyzed using TAPAS, a recently devised software that detects all the promising polyadenylation sites including APA sites. We observed that approximately 74% of possible polyadenylation sites in the analyzed genes were provided by sense-oriented AluYRa1. In conclusion, AluYRa1 is an Old-World monkey-specific TE, and its sense-oriented insertion at the 3'UTR region tends to provide a favorable environment for polyadenylation, diversifying gene transcripts.
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24
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van der Kuyl AC. Contemporary Distribution, Estimated Age, and Prehistoric Migrations of Old World Monkey Retroviruses. EPIDEMIOLGIA (BASEL, SWITZERLAND) 2021; 2:46-67. [PMID: 36417189 PMCID: PMC9620922 DOI: 10.3390/epidemiologia2010005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/18/2021] [Accepted: 01/29/2021] [Indexed: 12/14/2022]
Abstract
Old World monkeys (OWM), simians inhabiting Africa and Asia, are currently affected by at least four infectious retroviruses, namely, simian foamy virus (SFV), simian immunodeficiency virus (SIV), simian T-lymphotropic virus (STLV), and simian type D retrovirus (SRV). OWM also show chromosomal evidence of having been infected in the past with four more retroviral species, baboon endogenous virus (BaEV), Papio cynocephalus endogenous virus (PcEV), simian endogenous retrovirus (SERV), and Rhesus endogenous retrovirus-K (RhERV-K/SERV-K1). For some of the viruses, transmission to other primates still occurs, resulting, for instance, in the HIV pandemic. Retroviruses are intimately connected with their host as they are normally spread by close contact. In this review, an attempt to reconstruct the distribution and history of OWM retroviruses will be made. A literature overview of the species infected by any of the eight retroviruses as well as an age estimation of the pathogens will be given. In addition, primate genomes from databases have been re-analyzed for the presence of endogenous retrovirus integrations. Results suggest that some of the oldest retroviruses, SERV and PcEV, have travelled with their hosts to Asia during the Miocene, when a higher global temperature allowed simian expansions. In contrast, younger viruses, such as SIV and SRV, probably due to the lack of a primate continuum between the continents in later times, have been restricted to Africa and Asia, respectively.
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Affiliation(s)
- Antoinette C van der Kuyl
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
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25
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Brito AF, Baele G, Nahata KD, Grubaugh ND, Pinney JW. Intrahost speciations and host switches played an important role in the evolution of herpesviruses. Virus Evol 2021; 7:veab025. [PMID: 33927887 PMCID: PMC8062258 DOI: 10.1093/ve/veab025] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In times when herpesvirus genomic data were scarce, the cospeciation between these viruses and their hosts was considered to be common knowledge. However, as more herpesviral sequences were made available, tree reconciliation analyses started to reveal topological incongruences between host and viral phylogenies, indicating that other cophylogenetic events, such as intrahost speciation and host switching, likely played important roles along more than 200 million years of evolutionary history of these viruses. Tree reconciliations performed with undated phylogenies can identify topological differences, but offer insufficient information to reveal temporal incongruences between the divergence timing of host and viral species. In this study, we performed cophylogenetic analyses using time-resolved trees of herpesviruses and their hosts, based on careful molecular clock modelling. This approach enabled us to infer cophylogenetic events over time and also integrate information on host biogeography to better understand host-virus evolutionary history. Given the increasing amount of sequence data now available, mismatches between host and viral phylogenies have become more evident, and to account for such phylogenetic differences, host switches, intrahost speciations and losses were frequently found in all tree reconciliations. For all subfamilies in Herpesviridae, under all scenarios we explored, intrahost speciation and host switching were more frequent than cospeciation, which was shown to be a rare event, restricted to contexts where topological and temporal patterns of viral and host evolution were in strict agreement.
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Affiliation(s)
- Anderson F Brito
- Department of Life Sciences, Imperial College London, South Kensington Campus. London SW7 2AZ, UK
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, CT 06510, USA
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven 3000, Belgium
| | - Kanika D Nahata
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven 3000, Belgium
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, CT 06510, USA
| | - John W Pinney
- Department of Life Sciences, Imperial College London, South Kensington Campus. London SW7 2AZ, UK
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26
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New Insights on the Evolution of the Sweet Taste Receptor of Primates Adapted to Harsh Environments. Animals (Basel) 2020; 10:ani10122359. [PMID: 33321745 PMCID: PMC7764350 DOI: 10.3390/ani10122359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/01/2020] [Accepted: 12/04/2020] [Indexed: 11/16/2022] Open
Abstract
Simple Summary A sense of taste is vital to an animal’s fitness. It enables animals to select and ingest beneficial foods and avoid harmful substances in their daily lives. There have been relatively few studies regarding the evolution of the taste receptor gene for sweetness, particularly in regard to endemic Bornean primates. We constructed TAS1R2 gene phylogenies for 20 anthropoid primate species using four different methods as well as established the phylogenic time divergence. The phylogenetic analysis successfully separated the primates into their taxonomic groups and as per their dietary preferences. Of note, the estimated time of divergence for the primate speciation pattern in this study was more recent than the previously published estimates. This difference may have been due to environmental changes, such as food scarcity and climate change, during the late Miocene epoch, which likely forced primates to adapt their dietary preferences. These findings establish a foundation for further investigations. Abstract Taste perception is an essential function that provides valuable dietary and sensory information, which is crucial for the survival of animals. Studies into the evolution of the sweet taste receptor gene (TAS1R2) are scarce, especially for Bornean endemic primates such as Nasalis larvatus (proboscis monkey), Pongo pygmaeus (Bornean orangutan), and Hylobates muelleri (Muller’s Bornean gibbon). Primates are the perfect taxa to study as they are diverse dietary feeders, comprising specialist folivores, frugivores, gummivores, herbivores, and omnivores. We constructed phylogenetic trees of the TAS1R2 gene for 20 species of anthropoid primates using four different methods (neighbor-joining, maximum parsimony, maximum-likelihood, and Bayesian) and also established the time divergence of the phylogeny. The phylogeny successfully separated the primates into their taxonomic groups as well as by their dietary preferences. Of note, the reviewed time of divergence estimation for the primate speciation pattern in this study was more recent than the previously published estimates. It is believed that this difference may be due to environmental changes, such as food scarcity and climate change, during the late Miocene epoch, which forced primates to change their dietary preferences. These findings provide a starting point for further investigation.
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Haass-Koffler CL, Cannella N, Ciccocioppo R. Translational dynamics of alcohol tolerance of preclinical models and human laboratory studies. Exp Clin Psychopharmacol 2020; 28:417-425. [PMID: 32212746 PMCID: PMC7390673 DOI: 10.1037/pha0000366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Increasing sensitivity due to alcohol intake has been explored using molecular and cellular mechanisms of sensitization and adaptive biobehavioral changes as well as through negative experiences of altered function during withdrawal. However, within both a preclinical and human laboratory setting, little has been elucidated toward understanding the neural substrates of decreased sensitivity to alcohol effects, that is, alcohol tolerance. More paradigms assessing alcohol tolerance are needed. Tolerance can be assessed through both self-reported response (subjective) and observed (objective) measurements. Therefore, sensitivity to alcohol is an exploitable variable that can be utilized to disentangle the diverse alcohol use disorder (AUD) phenotypical profile. This literature review focuses on preclinical models and human laboratory studies to evaluate alcohol tolerance and its modulating factors. Increased understanding of alcohol tolerance has the potential to reduce gaps between preclinical models and human laboratory studies to better evaluate the development of alcohol-related biobehavioral responses. Furthermore, alcohol tolerance can be used as an AUD phenotypic variable in randomized clinical trials designed for developing AUD therapies. (PsycInfo Database Record (c) 2020 APA, all rights reserved).
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Affiliation(s)
- Carolina L Haass-Koffler
- Center for Alcohol and Addiction Studies, Department of Psychiatry and Human Behavior, Warren Alpert Medical School, Brown University
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28
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Babarinde IA, Saitou N. The Dynamics, Causes, and Impacts of Mammalian Evolutionary Rates Revealed by the Analyses of Capybara Draft Genome Sequences. Genome Biol Evol 2020; 12:1444-1458. [PMID: 32835375 DOI: 10.1093/gbe/evaa157] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2020] [Indexed: 12/23/2022] Open
Abstract
Capybara (Hydrochoerus hydrochaeri) is the largest species among the extant rodents. The draft genome of capybara was sequenced with the estimated genome size of 2.6 Gb. Although capybara is about 60 times larger than guinea pig, comparative analyses revealed that the neutral evolutionary rates of the two species were not substantially different. However, analyses of 39 mammalian genomes revealed very heterogeneous evolutionary rates. The highest evolutionary rate, 8.5 times higher than the human rate, was found in the Cricetidae-Muridae common ancestor after the divergence of Spalacidae. Muridae, the family with the highest number of species among mammals, emerged after the rate acceleration. Factors responsible for the evolutionary rate heterogeneity were investigated through correlations between the evolutionary rate and longevity, gestation length, litter frequency, litter size, body weight, generation interval, age at maturity, and taxonomic order. The regression analysis of these factors showed that the model with three factors (taxonomic order, generation interval, and litter size) had the highest predictive power (R2 = 0.74). These three factors determine the number of meiosis per unit time. We also conducted transcriptome analysis and found that the evolutionary rate dynamics affects the evolution of gene expression patterns.
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Affiliation(s)
- Isaac Adeyemi Babarinde
- Department of Biological Sciences, Southern University of Science and Technology, Shenzhen, China.,Population Genetics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Naruya Saitou
- Population Genetics Laboratory, National Institute of Genetics, Mishima, Japan.,School of Medicine, University of the Ryukyus, Okinawa, Japan.,Department of Genetics, School of Life Science, Graduate University for Advanced Studies, Mishima, Japan.,Department of Biological Sciences, Graduate School of Science, University of Tokyo, Japan
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29
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Malassis R, Dehaene S, Fagot J. Baboons (Papio papio) Process a Context-Free but Not a Context-Sensitive Grammar. Sci Rep 2020; 10:7381. [PMID: 32355252 PMCID: PMC7193559 DOI: 10.1038/s41598-020-64244-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 04/10/2020] [Indexed: 01/29/2023] Open
Abstract
Language processing involves the ability to master supra-regular grammars, that go beyond the level of complexity of regular grammars. This ability has been hypothesized to be a uniquely human capacity. Our study probed baboons' capacity to learn two supra-regular grammars of different levels of complexity: a context-free grammar generating sequences following a mirror structure (e.g., AB | BA, ABC | CBA) and a context-sensitive grammar generating sequences following a repeat structure (e.g., AB | AB, ABC | ABC), the latter requiring greater computational power to be processed. Fourteen baboons were tested in a prediction task, requiring them to track a moving target on a touchscreen. In distinct experiments, sequences of target locations followed one of the above two grammars, with rare violations. Baboons showed slower response times when violations occurred in mirror sequences, but did not react to violations in repeat sequences, suggesting that they learned the context-free (mirror) but not the context-sensitive (repeat) grammar. By contrast, humans tested with the same task learned both grammars. These data suggest a difference in sensitivity in baboons between a context-free and a context-sensitive grammar.
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Affiliation(s)
- Raphaëlle Malassis
- Laboratoire de Psychologie Cognitive, Université d'Aix-Marseille, Marseille, France. .,School of Psychology and Neuroscience, University of St Andrews, St Andrews, Fife, Scotland, United Kingdom.
| | - Stanislas Dehaene
- Collège de France, Paris, France.,Cognitive Neuroimaging Unit, CEA DSV/I2BM, INSERM, Université Paris Sud, Université Paris-Saclay, NeuroSpin Center, 91191, Gif-sur-Yvette, France
| | - Joël Fagot
- Laboratoire de Psychologie Cognitive, Université d'Aix-Marseille, Marseille, France
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30
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Yin Y, Yang T, Liu H, Huang Z, Zhang Y, Song Y, Wang W, Guang X, Sahu SK, Kristiansen K. The draft genome of mandrill (Mandrillus sphinx): An Old World monkey. Sci Rep 2020; 10:2431. [PMID: 32051450 PMCID: PMC7016171 DOI: 10.1038/s41598-020-59110-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 12/02/2019] [Indexed: 11/15/2022] Open
Abstract
Mandrill (Mandrillus sphinx) is a primate species, which belongs to the Old World monkey (Cercopithecidae) family. It is closely related to human, serving as a model for human health related research. However, the genetic studies on and genomic resources of mandrill are limited, especially in comparison to other primate species. Here we produced 284 Gb data, providing 96-fold coverage (considering the estimated genome size of 2.9 Gb), to construct a reference genome for the mandrill. The assembled draft genome was 2.79 Gb with contig N50 of 20.48 Kb and scaffold N50 of 3.56 Mb. We annotated the mandrill genome to find 43.83% repeat elements, as well as 21,906 protein-coding genes. The draft genome was of good quality with 98% gene annotation coverage by Benchmarking Universal Single-Copy Orthologs (BUSCO). Based on comparative genomic analyses of the Major Histocompatibility Complex (MHC) of the immune system in mandrill and human, we found that 17 genes in the mandrill that have been associated with disease phenotypes in human such as Lung cancer, cranial volume and asthma, barbored amino acids changing mutations. Gene family analyses revealed expansion of several genes, and several genes associated with stress environmental adaptation and innate immunity responses exhibited signatures of positive selection. In summary, we established the first draft genome of the mandrill of value for studies on evolution and human health.
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Affiliation(s)
- Ye Yin
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, 2100, Denmark.
- BGI-Shenzhen, Shenzhen, 518083, China.
| | - Ting Yang
- BGI-Shenzhen, Shenzhen, 518083, China
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs., Lyngby, Denmark
| | - Huan Liu
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, 2100, Denmark
- BGI-Shenzhen, Shenzhen, 518083, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Ziheng Huang
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Yaolei Zhang
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Yue Song
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Wenliang Wang
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | | | - Sunil Kumar Sahu
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, 2100, Denmark.
- BGI-Shenzhen, Shenzhen, 518083, China.
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Grandi N, Pisano MP, Demurtas M, Blomberg J, Magiorkinis G, Mayer J, Tramontano E. Identification and characterization of ERV-W-like sequences in Platyrrhini species provides new insights into the evolutionary history of ERV-W in primates. Mob DNA 2020; 11:6. [PMID: 32021657 PMCID: PMC6995185 DOI: 10.1186/s13100-020-0203-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 01/13/2020] [Indexed: 11/29/2022] Open
Abstract
Background Endogenous Retroviruses (ERVs) constitute approximately 8% of every human genome and are relics of ancestral infections that affected the germ line cells. The ERV-W group contributed to primate physiology by providing an envelope protein (Syncytin-1) that has been adopted for placenta development in hominoids. Expression of Human ERV-W (HERV-W) sequences is investigated for a pathological role in various human diseases. Results We previously characterized ERV-W group genomic sequences in human and non-human Catarrhini species. We now investigated ERV-W-like sequences in the parvorder Platyrrhini, especially regarding two species with complete genome assemblies, namely marmoset (Callithrix jacchus) and squirrel monkey (Saimiri boliviensis). We identified in both species proviral sequences, annotated as ERV1–1 in respective genome assemblies, sharing high sequence similarities with Catarrhini ERV-W. A total of 130 relatively intact proviruses from the genomes of marmoset and squirrel monkey were characterized regarding their structural and evolutionarily relationships with Catarrhini ERV-W elements. Platyrrhini ERV-W sequences share several structural features with Catarrhini ERV-W elements and are closely related phylogenetically with the latter as well as with other ERV-W-related gammaretrovirus-like ERVs. The ERV-W group colonized Platyrrhini primates of both Callitrichidae and Atelidae lineages, with provirus formations having occurred mostly between 25 and 15 mya. Two LTR subgroups were associated with monophyletic proviral bodies. A pre-gag region appears to be a sequence feature common to the ERV-W group: it harbors a putative intron sequence that is missing in some ERV-W loci, holding a putative ORF as well. The presence of a long pre-gag portion was confirmed among all gammaretroviral ERV analyzed, suggesting a role in the latter biology. It is noteworthy that, contrary to Catarrhini ERV-W, there was no evidence of L1-mediated mobilization for Platyrrhini ERV-W sequences. Conclusions Our data establish that ERV-W is not exclusive to Catarrhini primates but colonized both parvorders of Simiiformes, providing further insight into the evolution of ERV-W and the colonization of primate genomes.
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Affiliation(s)
- Nicole Grandi
- 1Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS554, Monserrato, Cagliari Italy
| | - Maria Paola Pisano
- 1Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS554, Monserrato, Cagliari Italy
| | - Martina Demurtas
- 1Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS554, Monserrato, Cagliari Italy
| | - Jonas Blomberg
- 2Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | | | - Jens Mayer
- 4Department of Hygiene, Epidemiology, and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Enzo Tramontano
- 1Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS554, Monserrato, Cagliari Italy.,5Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Monserrato, Cagliari Italy
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Mayer A, Lewenfus G, Bittencourt-Navarrete RE, Clasca F, Franca JGD. Thalamic Inputs to Posterior Parietal Cortical Areas Involved in Skilled Forelimb Movement and Tool Use in the Capuchin Monkey. Cereb Cortex 2019; 29:5098-5115. [PMID: 30888415 DOI: 10.1093/cercor/bhz051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 02/09/2019] [Accepted: 02/22/2019] [Indexed: 12/27/2022] Open
Abstract
The posterior parietal cortex (PPC) is a central hub for the primate forebrain networks that control skilled manual behavior, including tool use. Here, we quantified and compared the sources of thalamic input to electrophysiologically-identified hand/forearm-related regions of several PPC areas, namely areas 5v, AIP, PFG, and PF, of the capuchin monkey (Sapajus sp). We found that these areas receive most of their thalamic connections from the Anterior Pulvinar (PuA), Lateral Posterior (LP) and Medial Pulvinar (PuM) nuclei. Each PPC area receives a specific combination of projections from these nuclei, and fewer additional projections from other nuclei. Moreover, retrograde labeling of the cells innervating different PPC areas revealed substantial intermingling of these cells within the thalamus. Differences in thalamic input may contribute to the different functional properties displayed by the PPC areas. Furthermore, the observed innervation of functionally-related PPC domains from partly intermingled thalamic cell populations accords with the notion that higher-order thalamic inputs may dynamically regulate functional connectivity between cortical areas.
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Affiliation(s)
- Andrei Mayer
- Department of Physiological Sciences, Federal University of Santa Catarina, 88040-900, Santa Catarina, Brazil
| | - Gabriela Lewenfus
- Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, 21941-902, Rio de Janeiro, Brazil
| | | | - Francisco Clasca
- Department of Anatomy & Neuroscience, Autonoma University, Madrid, 28029 Spain
| | - João Guedes da Franca
- Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, 21941-902, Rio de Janeiro, Brazil
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33
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Benson KK, Hu W, Weller AH, Bennett AH, Chen ER, Khetarpal SA, Yoshino S, Bone WP, Wang L, Rabinowitz JD, Voight BF, Soccio RE. Natural human genetic variation determines basal and inducible expression of PM20D1, an obesity-associated gene. Proc Natl Acad Sci U S A 2019; 116:23232-23242. [PMID: 31659023 PMCID: PMC6859347 DOI: 10.1073/pnas.1913199116] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
PM20D1 is a candidate thermogenic enzyme in mouse fat, with its expression cold-induced and enriched in brown versus white adipocytes. Thiazolidinedione (TZD) antidiabetic drugs, which activate the peroxisome proliferator-activated receptor-γ (PPARγ) nuclear receptor, are potent stimuli for adipocyte browning yet fail to induce Pm20d1 expression in mouse adipocytes. In contrast, PM20D1 is one of the most strongly TZD-induced transcripts in human adipocytes, although not in cells from all individuals. Two putative PPARγ binding sites exist near the gene's transcription start site (TSS) in human but not mouse adipocytes. The -4 kb upstream site falls in a segmental duplication of a nearly identical intronic region +2.5 kb downstream of the TSS, and this duplication occurred in the primate lineage and not in other mammals, like mice. PPARγ binding and gene activation occur via this upstream duplicated site, thus explaining the species difference. Furthermore, this functional upstream PPARγ site exhibits genetic variation among people, with 1 SNP allele disrupting a PPAR response element and giving less activation by PPARγ and TZDs. In addition to this upstream variant that determines PPARγ regulation of PM20D1 in adipocytes, distinct variants downstream of the TSS have strong effects on PM20D1 expression in human fat as well as other tissues. A haplotype of 7 tightly linked downstream SNP alleles is associated with very low PMD201 expression and correspondingly high DNA methylation at the TSS. These PM20D1 low-expression variants may account for human genetic associations in this region with obesity as well as neurodegenerative diseases.
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Affiliation(s)
- Kiara K Benson
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Division of Endocrinology, Diabetes, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Wenxiang Hu
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Division of Endocrinology, Diabetes, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Angela H Weller
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Division of Endocrinology, Diabetes, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Alexis H Bennett
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Division of Endocrinology, Diabetes, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Eric R Chen
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Division of Endocrinology, Diabetes, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Sumeet A Khetarpal
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Division of Endocrinology, Diabetes, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Satoshi Yoshino
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Division of Endocrinology, Diabetes, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - William P Bone
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Institute of Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Lin Wang
- Department of Chemistry, Princeton University, Princeton, NJ 08544
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Joshua D Rabinowitz
- Department of Chemistry, Princeton University, Princeton, NJ 08544
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Benjamin F Voight
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Institute of Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Raymond E Soccio
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104;
- Division of Endocrinology, Diabetes, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
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Gaska JM, Parsons L, Balev M, Cirincione A, Wang W, Schwartz RE, Ploss A. Conservation of cell-intrinsic immune responses in diverse nonhuman primate species. Life Sci Alliance 2019; 2:2/5/e201900495. [PMID: 31649152 PMCID: PMC6814850 DOI: 10.26508/lsa.201900495] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 10/14/2019] [Accepted: 10/15/2019] [Indexed: 02/03/2023] Open
Abstract
The transcriptomic response of diverse nonhuman primate (NHP) species to poly(I:C) is highly conserved, and this novel RNA sequencing dataset will help improve NHP genome annotations. Differences in immune responses across species can contribute to the varying permissivity of species to the same viral pathogen. Understanding how our closest evolutionary relatives, nonhuman primates (NHPs), confront pathogens and how these responses have evolved over time could shed light on host range barriers, especially for zoonotic infections. Here, we analyzed cell-intrinsic immunity of primary cells from the broadest panel of NHP species interrogated to date, including humans, great apes, and Old and New World monkeys. Our analysis of their transcriptomes after poly(I:C) transfection revealed conservation in the functional consequences of their response. In mapping reads to either the human or the species-specific genomes, we observed that with the current state of NHP annotations, the percent of reads assigned to a genetic feature was largely similar regardless of the method. Together, these data provide a baseline for the cell-intrinsic responses elicited by a potent immune stimulus across multiple NHP donors, including endangered species, and serve as a resource for refining and furthering the existing annotations of NHP genomes.
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Affiliation(s)
- Jenna M Gaska
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Lance Parsons
- Carl Icahn Laboratory, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Metodi Balev
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Ann Cirincione
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Wei Wang
- Carl Icahn Laboratory, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Robert E Schwartz
- Weill Cornell Medical College, Belfer Research Building, New York, NY, USA
| | - Alexander Ploss
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, NJ, USA
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35
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Macaques preferentially attend to visual patterns with higher fractal dimension contours. Sci Rep 2019; 9:10592. [PMID: 31332197 PMCID: PMC6646383 DOI: 10.1038/s41598-019-46799-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 05/15/2019] [Indexed: 11/09/2022] Open
Abstract
Animals' sensory systems evolved to efficiently process information from their environmental niches. Niches often include irregular shapes and rough textures (e.g., jagged terrain, canopy outlines) that must be navigated to find food, escape predators, and master other fitness-related challenges. For most primates, vision is the dominant sensory modality and thus, primates have evolved systems for processing complicated visual stimuli. One way to quantify information present in visual stimuli in natural scenes is evaluating their fractal dimension. We hypothesized that sensitivity to complicated geometric forms, indexed by fractal dimension, is an evolutionarily conserved capacity, and tested this capacity in rhesus macaques (Macaca mulatta). Monkeys viewed paired black and white images of simulated self-similar contours that systematically varied in fractal dimension while their attention to the stimuli was measured using noninvasive infrared eye tracking. They fixated more frequently on, dwelled for longer durations on, and had attentional biases towards images that contain boundary contours with higher fractal dimensions. This indicates that, like humans, they discriminate between visual stimuli on the basis of fractal dimension and may prefer viewing informationally rich visual stimuli. Our findings suggest that sensitivity to fractal dimension may be a wider ability of the vertebrate vision system.
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36
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Casanova MF, Casanova EL. The modular organization of the cerebral cortex: Evolutionary significance and possible links to neurodevelopmental conditions. J Comp Neurol 2019; 527:1720-1730. [PMID: 30303529 PMCID: PMC6784310 DOI: 10.1002/cne.24554] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 08/22/2018] [Accepted: 09/21/2018] [Indexed: 12/11/2022]
Abstract
The recognition of discernible anatomical regularities that appear to self-organize during development makes apparent the modular organization of the cerebral cortex. The metabolic cost engendered in sustaining interneuronal communications has emphasized the viability of short connections among neighboring neurons. This pattern of connectivity establishes a microcircuit which is repeated in parallel throughout the cerebral cortex. This canonical circuit is contained within the smallest module of information processing of the cerebral cortex; one which Vernon Mountcastle called the minicolumn. Plasticity within the brain is accounted, in part, by the presence of weak linkages that allow minicolumns to process information from a variety of sources and to quickly adapt to environmental exigencies without a need for genetic change. Recent research suggests that interlaminar correlated firing between minicolumns during the decision phase of target selection provides for the emergence of some executive functions. Bottlenecks of information processing within this modular minicolumnar organization may account for a variety of mental disorders observed in neurodevelopmental conditions.
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Affiliation(s)
- Manuel F Casanova
- Department of Biomedical Sciences, University of South Carolina School of Medicine Greenville, Greenville, South Carolina
| | - Emily L Casanova
- Department of Pediatrics, Greenville Health System, Greenville, South Carolina
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37
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Kunimatsu Y, Nakatsukasa M, Shimizu D, Nakano Y, Ishida H. Loss of the subarcuate fossa and the phylogeny of Nacholapithecus. J Hum Evol 2019. [DOI: 10.1016/j.jhevol.2019.03.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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38
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39
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Araújo Góis Morais PL, García-Amado M, Lima RRM, Córdoba-Claros A, Souza Cavalcante J, Clascá F, Nascimento ES. Cyto- and Myelo-Architecture of the Amygdaloid Complex of the Common Marmoset Monkey ( Callithrix jacchus). Front Neuroanat 2019; 13:36. [PMID: 30971903 PMCID: PMC6446959 DOI: 10.3389/fnana.2019.00036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 03/08/2019] [Indexed: 12/17/2022] Open
Abstract
The amygdaloid complex (AC) is a heterogeneous aggregate of nuclei located in the rostromedial region of the temporal lobe. In addition to being partly connected among themselves, the AC nuclei are strongly interconnected with the cerebral cortex, striatum, basal forebrain, hypothalamus and brainstem. Animal and human functional studies have established that the AC is a central hub of the neuronal networks supporting emotional responsivity, particularly its negative/aversive components. Dysfunction of AC circuits in humans has been implicated in anxiety, depression, schizophrenia and bipolar disorder. The small New-World marmoset monkey (Callithrix jacchus) has recently become a key model for neuroscience research. However, the nuclear and fiber tract organization of marmoset AC has not been examined in detail. Thus, the extent to which it can be compared to the AC of Old-World (human and macaque) primates is yet unclear. Here, using Nissl and acetylcholinesterase (AChE) histochemical stains as a reference, we analyzed the cytoarchitecture and nuclear parcellation of the marmoset AC. In addition, given the increasing relevance of tractographic localization for high-resolution in vivo imaging studies in non-human primates, we also identified the myelin fiber tracts present within and around the AC as revealed by the Gallyas method. The present study provides a detailed atlas of marmoset AC. Moreover, it reveals that, despite phylogenetic distance and brain size differences, every nucleus and myelinated axon bundle described in human and macaque studies can be confidently recognized in marmosets.
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Affiliation(s)
- Paulo Leonardo Araújo Góis Morais
- Department of Morphology, Universidade Federal do Rio Grande do Norte, Natal, Brazil.,Department of Anatomy & Neuroscience, School of Medicine, Autonoma de Madrid University, Madrid, Spain
| | - María García-Amado
- Department of Anatomy & Neuroscience, School of Medicine, Autonoma de Madrid University, Madrid, Spain
| | | | - Angélica Córdoba-Claros
- Department of Anatomy & Neuroscience, School of Medicine, Autonoma de Madrid University, Madrid, Spain
| | | | - Francisco Clascá
- Department of Anatomy & Neuroscience, School of Medicine, Autonoma de Madrid University, Madrid, Spain
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40
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Rosa MGP, Soares JGM, Chaplin TA, Majka P, Bakola S, Phillips KA, Reser DH, Gattass R. Cortical Afferents of Area 10 in Cebus Monkeys: Implications for the Evolution of the Frontal Pole. Cereb Cortex 2019; 29:1473-1495. [PMID: 29697775 PMCID: PMC6676977 DOI: 10.1093/cercor/bhy044] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 01/12/2018] [Accepted: 02/07/2018] [Indexed: 01/26/2023] Open
Abstract
Area 10, located in the frontal pole, is a unique specialization of the primate cortex. We studied the cortical connections of area 10 in the New World Cebus monkey, using injections of retrograde tracers in different parts of this area. We found that injections throughout area 10 labeled neurons in a consistent set of areas in the dorsolateral, ventrolateral, orbital, and medial parts of the frontal cortex, superior temporal association cortex, and posterior cingulate/retrosplenial region. However, sites on the midline surface of area 10 received more substantial projections from the temporal lobe, including clear auditory connections, whereas those in more lateral parts received >90% of their afferents from other frontal areas. This difference in anatomical connectivity reflects functional connectivity findings in the human brain. The pattern of connections in Cebus is very similar to that observed in the Old World macaque monkey, despite >40 million years of evolutionary separation, but lacks some of the connections reported in the more closely related but smaller marmoset monkey. These findings suggest that the clearer segregation observed in the human frontal pole reflects regional differences already present in early simian primates, and that overall brain mass influences the pattern of cortico-cortical connectivity.
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Affiliation(s)
- Marcello G P Rosa
- Department of Physiology, Monash University, Clayton, VIC, Australia
- Neuroscience Program, Biomedicine Research Institute, Monash University, Clayton, VIC, Australia
- Australian Research Council, Centre of Excellence for Integrative Brain Function, Monash University Node, Clayton, VIC, Australia
| | - Juliana G M Soares
- Programa de Neurobiologia, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Tristan A Chaplin
- Department of Physiology, Monash University, Clayton, VIC, Australia
- Neuroscience Program, Biomedicine Research Institute, Monash University, Clayton, VIC, Australia
- Australian Research Council, Centre of Excellence for Integrative Brain Function, Monash University Node, Clayton, VIC, Australia
| | - Piotr Majka
- Department of Physiology, Monash University, Clayton, VIC, Australia
- Neuroscience Program, Biomedicine Research Institute, Monash University, Clayton, VIC, Australia
- Australian Research Council, Centre of Excellence for Integrative Brain Function, Monash University Node, Clayton, VIC, Australia
- Laboratory of Neuroinformatics, Department of Neurophysiology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 3 Pasteur Street, Warsaw, Poland
| | - Sophia Bakola
- Department of Physiology, Monash University, Clayton, VIC, Australia
- Neuroscience Program, Biomedicine Research Institute, Monash University, Clayton, VIC, Australia
- Australian Research Council, Centre of Excellence for Integrative Brain Function, Monash University Node, Clayton, VIC, Australia
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Kimberley A Phillips
- Department of Psychology, Trinity University, San Antonio, TX, USA
- USA Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - David H Reser
- Department of Physiology, Monash University, Clayton, VIC, Australia
- Neuroscience Program, Biomedicine Research Institute, Monash University, Clayton, VIC, Australia
- Australian Research Council, Centre of Excellence for Integrative Brain Function, Monash University Node, Clayton, VIC, Australia
- Monash Rural Health, Monash University, Churchill, VIC, Australia
| | - Ricardo Gattass
- Programa de Neurobiologia, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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41
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Xiong J, Jiang X, Ditsiou A, Gao Y, Sun J, Lowenstein ED, Huang S, Khaitovich P. Predominant patterns of splicing evolution on human, chimpanzee and macaque evolutionary lineages. Hum Mol Genet 2019; 27:1474-1485. [PMID: 29452398 DOI: 10.1093/hmg/ddy058] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 02/12/2018] [Indexed: 11/14/2022] Open
Abstract
Although splicing is widespread and evolves rapidly among species, the mechanisms driving this evolution, as well as its functional implications, are not yet fully understood. We analyzed the evolution of splicing patterns based on transcriptome data from five tissues of humans, chimpanzees, rhesus macaques and mice. In total, 1526 exons and exon sets from 1236 genes showed significant splicing differences among primates. More than 60% of these differences represent constitutive-to-alternative exon transitions while an additional 25% represent changes in exon inclusion frequency. These two dominant evolutionary patterns have contrasting conservation, regulation and functional features. The sum of these features indicates that, despite their prevalence, constitutive-to-alternative exon transitions do not substantially contribute to long-term functional transcriptome changes. Conversely, changes in exon inclusion frequency appear to be functionally relevant, especially for changes taking place in the brain on the human evolutionary lineage.
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Affiliation(s)
- Jieyi Xiong
- Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China.,Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Xi Jiang
- Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China
| | - Angeliki Ditsiou
- JBC/WTB Biocentre, University of Dundee, DD1 5EH Scotland, UK.,JMS Building, University of Sussex, BN1 9QG Brighton, UK
| | - Yang Gao
- Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China
| | - Jing Sun
- Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China
| | - Elijah D Lowenstein
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany.,Freie Universität Berlin, 14195 Berlin, Germany
| | - Shuyun Huang
- Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, 201210 Shanghai, China
| | - Philipp Khaitovich
- Skolkovo Institute of Science and Technology, 143025 Skolkovo, Russia.,Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China
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42
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Calcutt SE, Proctor D, Berman SM, de Waal FBM. Chimpanzees ( Pan troglodytes) Are More Averse to Social Than Nonsocial Risk. Psychol Sci 2018; 30:105-115. [PMID: 30511893 DOI: 10.1177/0956797618811877] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Social risk is a domain of risk in which the costs, benefits, and uncertainty of an action depend on the behavior of another individual. Humans overvalue the costs of a socially risky decision when compared with that of purely economic risk. Here, we played a trust game with 8 female captive chimpanzees ( Pan troglodytes) to determine whether this bias exists in one of our closest living relatives. A correlation between an individual's social- and nonsocial-risk attitudes indicated stable individual variation, yet the chimpanzees were more averse to social than nonsocial risk. This indicates differences between social and economic decision making and emotional factors in social risk taking. In another experiment using the same paradigm, subjects played with several partners with whom they had varying relationships. Preexisting relationships did not impact the subjects' choices. Instead, the apes used a tit-for-tat strategy and were influenced by the outcome of early interactions with a partner.
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Affiliation(s)
- Sarah E Calcutt
- 1 Living Links, Yerkes National Primate Research Center, Emory University.,2 Department of Psychology, Emory University
| | - Darby Proctor
- 1 Living Links, Yerkes National Primate Research Center, Emory University.,3 School of Psychology, Florida Institute of Technology
| | - Sarah M Berman
- 1 Living Links, Yerkes National Primate Research Center, Emory University
| | - Frans B M de Waal
- 1 Living Links, Yerkes National Primate Research Center, Emory University.,2 Department of Psychology, Emory University
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43
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Monson TA, Hlusko LJ. Breaking the rules: Phylogeny, not life history, explains dental eruption sequence in primates. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 167:217-233. [DOI: 10.1002/ajpa.23618] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 05/07/2018] [Accepted: 05/09/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Tesla A. Monson
- Department of Integrative Biology; University of California; Berkeley California 94720
- Museum of Vertebrate Zoology, Department of Integrative Biology; University of California; Berkeley California 94720
- Human Evolution Research Center, Department of Integrative Biology; University of California; Berkeley California 94720
| | - Leslea J. Hlusko
- Department of Integrative Biology; University of California; Berkeley California 94720
- Museum of Vertebrate Zoology, Department of Integrative Biology; University of California; Berkeley California 94720
- Human Evolution Research Center, Department of Integrative Biology; University of California; Berkeley California 94720
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44
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Reis MD, Gunnell GF, Barba-Montoya J, Wilkins A, Yang Z, Yoder AD. Using Phylogenomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Case. Syst Biol 2018; 67:594-615. [PMID: 29342307 PMCID: PMC6005039 DOI: 10.1093/sysbio/syy001] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Revised: 12/26/2017] [Accepted: 01/05/2018] [Indexed: 11/13/2022] Open
Abstract
Primates have long been a test case for the development of phylogenetic methods for divergence time estimation. Despite a large number of studies, however, the timing of origination of crown Primates relative to the Cretaceous-Paleogene (K-Pg) boundary and the timing of diversification of the main crown groups remain controversial. Here, we analysed a data set of 372 taxa (367 Primates and 5 outgroups, 3.4 million aligned base pairs) that includes nine primate genomes. We systematically explore the effect of different interpretations of fossil calibrations and molecular clock models on primate divergence time estimates. We find that even small differences in the construction of fossil calibrations can have a noticeable impact on estimated divergence times, especially for the oldest nodes in the tree. Notably, choice of molecular rate model (autocorrelated or independently distributed rates) has an especially strong effect on estimated times, with the independent rates model producing considerably more ancient age estimates for the deeper nodes in the phylogeny. We implement thermodynamic integration, combined with Gaussian quadrature, in the program MCMCTree, and use it to calculate Bayes factors for clock models. Bayesian model selection indicates that the autocorrelated rates model fits the primate data substantially better, and we conclude that time estimates under this model should be preferred. We show that for eight core nodes in the phylogeny, uncertainty in time estimates is close to the theoretical limit imposed by fossil uncertainties. Thus, these estimates are unlikely to be improved by collecting additional molecular sequence data. All analyses place the origin of Primates close to the K-Pg boundary, either in the Cretaceous or straddling the boundary into the Palaeogene.
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Affiliation(s)
- Mario Dos Reis
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Gregg F Gunnell
- Division of Fossil Primates, Duke University Lemur Center, Durham, 1013 Broad Street, NC 27705, USA
| | - Jose Barba-Montoya
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Alex Wilkins
- Division of Fossil Primates, Duke University Lemur Center, Durham, 1013 Broad Street, NC 27705, USA
- Department of Anthropology, The Ohio State University, Columbus, OH 43210, USA
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC 27708, USA
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45
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Oishi M, Ogihara N, Shimizu D, Kikuchi Y, Endo H, Une Y, Soeta S, Amasaki H, Ichihara N. Multivariate analysis of variations in intrinsic foot musculature among hominoids. J Anat 2018; 232:812-823. [PMID: 29327389 PMCID: PMC5879964 DOI: 10.1111/joa.12780] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2017] [Indexed: 11/28/2022] Open
Abstract
Comparative analysis of the foot muscle architecture among extant great apes is important for understanding the evolution of the human foot and, hence, human habitual bipedal walking. However, to our knowledge, there is no previous report of a quantitative comparison of hominoid intrinsic foot muscle dimensions. In the present study, we quantitatively compared muscle dimensions of the hominoid foot by means of multivariate analysis. The foot muscle mass and physiological cross-sectional area (PCSA) of five chimpanzees, one bonobo, two gorillas, and six orangutans were obtained by our own dissections, and those of humans were taken from published accounts. The muscle mass and PCSA were respectively divided by the total mass and total PCSA of the intrinsic muscles of the entire foot for normalization. Variations in muscle architecture among human and extant great apes were quantified based on principal component analysis. Our results demonstrated that the muscle architecture of the orangutan was the most distinctive, having a larger first dorsal interosseous muscle and smaller abductor hallucis brevis muscle. On the other hand, the gorilla was found to be unique in having a larger abductor digiti minimi muscle. Humans were distinguished from extant great apes by a larger quadratus plantae muscle. The chimpanzee and the bonobo appeared to have very similar muscle architecture, with an intermediate position between the human and the orangutan. These differences (or similarities) in architecture of the intrinsic foot muscles among humans and great apes correspond well to the differences in phylogeny, positional behavior, and locomotion.
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Affiliation(s)
- Motoharu Oishi
- Laboratory of Anatomy 1School of Veterinary MedicineAzabu UniversityKanagawaJapan
| | - Naomichi Ogihara
- Department of Mechanical EngineeringFaculty of Science and TechnologyKeio UniversityKanagawaJapan
| | - Daisuke Shimizu
- Department of Physical TherapyFaculty of Nursing and RehabilitationChubu Gakuin UniversityGifuJapan
| | - Yasuhiro Kikuchi
- Division of Human Anatomy and Biological AnthropologyDepartment of Anatomy and PhysiologyFaculty of MedicineSaga UniversitySagaJapan
| | - Hideki Endo
- The University MuseumThe University of TokyoTokyoJapan
| | - Yumi Une
- Laboratory of Veterinary PathologySchool of Veterinary MedicineAzabu UniversityKanagawaJapan
| | - Satoshi Soeta
- Department of Veterinary AnatomySchool of Veterinary MedicineNippon Veterinary and Life Science UniversityTokyoJapan
| | - Hajime Amasaki
- Department of Veterinary AnatomySchool of Veterinary MedicineNippon Veterinary and Life Science UniversityTokyoJapan
| | - Nobutsune Ichihara
- Laboratory of Anatomy 1School of Veterinary MedicineAzabu UniversityKanagawaJapan
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46
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Lei R, Frasier CL, Hawkins MTR, Engberg SE, Bailey CA, Johnson SE, McLain AT, Groves CP, Perry GH, Nash SD, Mittermeier RA, Louis EE. Phylogenomic Reconstruction of Sportive Lemurs (genus Lepilemur) Recovered from Mitogenomes with Inferences for Madagascar Biogeography. J Hered 2018; 108:107-119. [PMID: 28173059 DOI: 10.1093/jhered/esw072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 09/30/2016] [Indexed: 11/12/2022] Open
Abstract
The family Lepilemuridae includes 26 species of sportive lemurs, most of which were recently described. The cryptic morphological differences confounded taxonomy until recent molecular studies; however, some species’ boundaries remain uncertain. To better understand the genus Lepilemur, we analyzed 35 complete mitochondrial genomes representing all recognized 26 sportive lemur taxa and estimated divergence dates. With our dataset we recovered 25 reciprocally monophyletic lineages, as well as an admixed clade containing Lepilemur mittermeieri and Lepilemur dorsalis. Using modern distribution data, an ancestral area reconstruction and an ecological vicariance analysis were performed to trace the history of diversification and to test biogeographic hypotheses. We estimated the initial split between the eastern and western Lepilemur clades to have occurred in the Miocene. Divergence of most species occurred from the Pliocene to the Pleistocene. The biogeographic patterns recovered in this study were better addressed with a combinatorial approach including climate, watersheds, and rivers. Generally, current climate and watershed hypotheses performed better for western and eastern clades, while speciation of northern clades was not adequately supported using the ecological factors incorporated in this study. Thus, multiple mechanisms likely contributed to the speciation and distribution patterns in Lepilemur.
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Affiliation(s)
- Runhua Lei
- Grewcock Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE, USA
| | - Cynthia L Frasier
- Grewcock Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE, USA
| | - Melissa T R Hawkins
- Grewcock Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE, USA
| | - Shannon E Engberg
- Grewcock Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE, USA
| | - Carolyn A Bailey
- Grewcock Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE, USA
| | - Steig E Johnson
- Department of Anthropology and Archaeology, University of Calgary, Calgary, AB, Canada
| | - Adam T McLain
- Department of Mathematics and Sciences, State University of New York Polytechnic Institute, Utica, NY, USA
| | - Colin P Groves
- School of Archaeology and Anthropology, Australian National University, Canberra, ACT, Australia
| | - George H Perry
- Departments of Anthropology and Biology, Pennsylvania State University, University Park, PA, USA
| | | | | | - Edward E Louis
- Grewcock Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE, USA
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47
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Grandi N, Tramontano E. HERV Envelope Proteins: Physiological Role and Pathogenic Potential in Cancer and Autoimmunity. Front Microbiol 2018; 9:462. [PMID: 29593697 PMCID: PMC5861771 DOI: 10.3389/fmicb.2018.00462] [Citation(s) in RCA: 145] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 02/27/2018] [Indexed: 12/29/2022] Open
Abstract
Human endogenous retroviruses (HERVs) are relics of ancient infections accounting for about the 8% of our genome. Despite their persistence in human DNA led to the accumulation of mutations, HERVs are still contributing to the human transcriptome, and a growing number of findings suggests that their expression products may have a role in various diseases. Among HERV products, the envelope proteins (Env) are currently highly investigated for their pathogenic properties, which could likely be participating to several disorders with complex etiology, particularly in the contexts of autoimmunity and cancer. In fact, HERV Env proteins have been shown, on the one side, to trigger both innate and adaptive immunity, prompting inflammatory, cytotoxic and apoptotic reactions; and, on the other side, to prevent the immune response activation, presenting immunosuppressive properties and acting as immune downregulators. In addition, HERV Env proteins have been shown to induce abnormal cell-cell fusion, possibly contributing to tumor development and metastasizing processes. Remarkably, even highly defective HERV env genes and alternative env splicing variants can provide further mechanisms of pathogenesis. A well-known example is the HERV-K(HML2) env gene that, depending on the presence or the absence of a 292-bp deletion, can originate two proteins of different length (Np9 and Rec) proposed to have oncogenic properties. The understanding of their involvement in complex pathological disorders made HERV Env proteins potential targets for therapeutic interventions. Of note, a monoclonal antibody directed against a HERV-W Env is currently under clinical trial as therapeutic approach for multiple sclerosis, representing the first HERV-based treatment. The present review will focus on the current knowledge of the HERV Env expression, summarizing its role in human physiology and its possible pathogenic effects in various cancer and autoimmune disorders. It moreover analyzes HERV Env possible exploitation for the development of innovative therapeutic strategies.
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Affiliation(s)
- Nicole Grandi
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Enzo Tramontano
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Cagliari, Italy
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48
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Gazes RP, Chee NW, Hampton RR. Monkeys choose, but do not learn, through exclusion. ANIMAL BEHAVIOR AND COGNITION 2018; 5:9-18. [PMID: 32864425 PMCID: PMC7450826 DOI: 10.26451/abc.05.01.02.2018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
Human children will select a novel object from among a group of known objects when presented with a novel object name. This disambiguation by exclusion may facilitate new name-object mappings and may play a role in the rapid word learning shown by young children. Animals including dogs, apes, monkeys, and birds make similar exclusion choices. However, evidence regarding whether children and nonhuman animals learn new associations through choice by exclusion is mixed. In the present study we dissociate choice by exclusion from learning by exclusion in rhesus monkeys using a paired-associate task. In experiment 1, monkeys demonstrated choice by exclusion by choosing a novel comparison image from among known comparison images when presented with a novel sample image. In experiment 2, monkeys failed to benefit from choice by exclusion in learning new sets of paired associates. Monkeys learned new sets of four paired associates by trial and error alone or by a combination of exclusion and trial and error. Despite choosing correctly by exclusion on almost 100% of opportunities, monkeys did not learn any faster by exclusion than by trial and error alone. These results indicate that monkeys chose, but do not learn, through exclusion, highlighting the importance of separately evaluating choice and learning in studies of exclusion in word learning.
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Affiliation(s)
- Regina Paxton Gazes
- Department of Psychology, Emory University, Atlanta, GA; Department of Psychology and Program in Animal Behavior Bucknell University, Lewisburg, PA
| | - Nicholas W Chee
- Department of Neuroscience and Behavioral Biology, Emory University, Atlanta, GA; NYU Langone Medical Center
| | - Robert R Hampton
- Department of Psychology, Emory University, Atlanta GA, Yerkes National Primate Research Center, Atlanta GA
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49
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Morimoto N, Nakatsukasa M, Ponce de León MS, Zollikofer CPE. Femoral ontogeny in humans and great apes and its implications for their last common ancestor. Sci Rep 2018; 8:1930. [PMID: 29386644 PMCID: PMC5792642 DOI: 10.1038/s41598-018-20410-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 01/18/2018] [Indexed: 11/09/2022] Open
Abstract
Inferring the morphology of the last common ancestor of humans, chimpanzees and gorillas is a matter of ongoing debate. Recent findings and reassessment of fossil hominins leads to the hypothesis that the last common ancestor was not extant African ape-like. However, an African great-ape-like ancestor with knuckle walking features still remains plausible and the most parsimonious scenario. Here we address this question via an evolutionary developmental approach, comparing taxon-specific patterns of shape change of the femoral diaphysis from birth to adulthood in great apes, humans, and macaques. While chimpanzees and gorillas exhibit similar locomotor behaviors, our data provide evidence for distinct ontogenetic trajectories, indicating independent evolutionary histories of femoral ontogeny. Our data further indicate that anthropoid primates share a basic pattern of femoral diaphyseal ontogeny that reflects shared developmental constraints. Humans escaped from these constraints via differential elongation of femur.
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Affiliation(s)
- Naoki Morimoto
- Laboratory of Physical Anthropology, Graduate School of Science, Kyoto University, Kyoto, Japan.
| | - Masato Nakatsukasa
- Laboratory of Physical Anthropology, Graduate School of Science, Kyoto University, Kyoto, Japan
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50
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Hoglen NEG, Larimer P, Phillips EAK, Malone BJ, Hasenstaub AR. Amplitude modulation coding in awake mice and squirrel monkeys. J Neurophysiol 2018; 119:1753-1766. [PMID: 29364073 DOI: 10.1152/jn.00101.2017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Both mice and primates are used to model the human auditory system. The primate order possesses unique cortical specializations that govern auditory processing. Given the power of molecular and genetic tools available in the mouse model, it is essential to understand the similarities and differences in auditory cortical processing between mice and primates. To address this issue, we directly compared temporal encoding properties of neurons in the auditory cortex of awake mice and awake squirrel monkeys (SQMs). Stimuli were drawn from a sinusoidal amplitude modulation (SAM) paradigm, which has been used previously both to characterize temporal precision and to model the envelopes of natural sounds. Neural responses were analyzed with linear template-based decoders. In both species, spike timing information supported better modulation frequency discrimination than rate information, and multiunit responses generally supported more accurate discrimination than single-unit responses from the same site. However, cortical responses in SQMs supported better discrimination overall, reflecting superior temporal precision and greater rate modulation relative to the spontaneous baseline and suggesting that spiking activity in mouse cortex was less strictly regimented by incoming acoustic information. The quantitative differences we observed between SQM and mouse cortex support the idea that SQMs offer advantages for modeling precise responses to fast envelope dynamics relevant to human auditory processing. Nevertheless, our results indicate that cortical temporal processing is qualitatively similar in mice and SQMs and thus recommend the mouse model for mechanistic questions, such as development and circuit function, where its substantial methodological advantages can be exploited. NEW & NOTEWORTHY To understand the advantages of different model organisms, it is necessary to directly compare sensory responses across species. Contrasting temporal processing in auditory cortex of awake squirrel monkeys and mice, with parametrically matched amplitude-modulated tone stimuli, reveals a similar role of timing information in stimulus encoding. However, disparities in response precision and strength suggest that anatomical and biophysical differences between squirrel monkeys and mice produce quantitative but not qualitative differences in processing strategy.
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Affiliation(s)
- Nerissa E G Hoglen
- Center for Integrative Neuroscience, University of California , San Francisco, California.,Department of Otolaryngology-Head and Neck Surgery, University of California , San Francisco, California.,Coleman Memorial Laboratory, University of California , San Francisco, California.,Kavli Institute for Fundamental Neuroscience, University of California , San Francisco, California.,Department of Psychiatry, University of California , San Francisco, California.,Neuroscience Graduate Program, University of California , San Francisco, California
| | - Phillip Larimer
- Center for Integrative Neuroscience, University of California , San Francisco, California.,Coleman Memorial Laboratory, University of California , San Francisco, California.,Department of Neurology, University of California , San Francisco, California
| | - Elizabeth A K Phillips
- Center for Integrative Neuroscience, University of California , San Francisco, California.,Department of Otolaryngology-Head and Neck Surgery, University of California , San Francisco, California.,Coleman Memorial Laboratory, University of California , San Francisco, California.,Neuroscience Graduate Program, University of California , San Francisco, California
| | - Brian J Malone
- Department of Otolaryngology-Head and Neck Surgery, University of California , San Francisco, California.,Coleman Memorial Laboratory, University of California , San Francisco, California.,Kavli Institute for Fundamental Neuroscience, University of California , San Francisco, California
| | - Andrea R Hasenstaub
- Center for Integrative Neuroscience, University of California , San Francisco, California.,Department of Otolaryngology-Head and Neck Surgery, University of California , San Francisco, California.,Coleman Memorial Laboratory, University of California , San Francisco, California.,Kavli Institute for Fundamental Neuroscience, University of California , San Francisco, California
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