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Zug R, Uller T. Evolution and dysfunction of human cognitive and social traits: A transcriptional regulation perspective. EVOLUTIONARY HUMAN SCIENCES 2022; 4:e43. [PMID: 37588924 PMCID: PMC10426018 DOI: 10.1017/ehs.2022.42] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 08/11/2022] [Accepted: 09/11/2022] [Indexed: 11/07/2022] Open
Abstract
Evolutionary changes in brain and craniofacial development have endowed humans with unique cognitive and social skills, but also predisposed us to debilitating disorders in which these traits are disrupted. What are the developmental genetic underpinnings that connect the adaptive evolution of our cognition and sociality with the persistence of mental disorders with severe negative fitness effects? We argue that loss of function of genes involved in transcriptional regulation represents a crucial link between the evolution and dysfunction of human cognitive and social traits. The argument is based on the haploinsufficiency of many transcriptional regulator genes, which makes them particularly sensitive to loss-of-function mutations. We discuss how human brain and craniofacial traits evolved through partial loss of function (i.e. reduced expression) of these genes, a perspective compatible with the idea of human self-domestication. Moreover, we explain why selection against loss-of-function variants supports the view that mutation-selection-drift, rather than balancing selection, underlies the persistence of psychiatric disorders. Finally, we discuss testable predictions.
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Affiliation(s)
- Roman Zug
- Department of Biology, Lund University, Lund, Sweden
| | - Tobias Uller
- Department of Biology, Lund University, Lund, Sweden
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Babaian C, Kumar S. How to Build a Super Predator: From Genotype to Phenotype. THE AMERICAN BIOLOGY TEACHER 2021; 83:138-146. [PMID: 34012167 PMCID: PMC8130183 DOI: 10.1525/abt.2021.83.3.138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We present a drawing discovery lab that crosscuts multiple disciplines in biology and links concepts in genetics and evolutionary thinking to enhance understanding of the genotype-to-phenotype transformation. These combined concepts are also linked to ecological frameworks in nature through the model of biological plasticity. Students and teachers explore drawing skills to flesh out the future of a predator while engaging with the computational software MEGA, which introduces students and teachers to nucleotide changes, mutations, variation, phylogenetics, and molecular evolution.
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Albers PK, McVean G. Dating genomic variants and shared ancestry in population-scale sequencing data. PLoS Biol 2020; 18:e3000586. [PMID: 31951611 PMCID: PMC6992231 DOI: 10.1371/journal.pbio.3000586] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 01/30/2020] [Accepted: 01/02/2020] [Indexed: 12/31/2022] Open
Abstract
The origin and fate of new mutations within species is the fundamental process underlying evolution. However, while much attention has been focused on characterizing the presence, frequency, and phenotypic impact of genetic variation, the evolutionary histories of most variants are largely unexplored. We have developed a nonparametric approach for estimating the date of origin of genetic variants in large-scale sequencing data sets. The accuracy and robustness of the approach is demonstrated through simulation. Using data from two publicly available human genomic diversity resources, we estimated the age of more than 45 million single-nucleotide polymorphisms (SNPs) in the human genome and release the Atlas of Variant Age as a public online database. We characterize the relationship between variant age and frequency in different geographical regions and demonstrate the value of age information in interpreting variants of functional and selective importance. Finally, we use allele age estimates to power a rapid approach for inferring the ancestry shared between individual genomes and to quantify genealogical relationships at different points in the past, as well as to describe and explore the evolutionary history of modern human populations.
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Affiliation(s)
- Patrick K. Albers
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
- * E-mail:
| | - Gil McVean
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
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Srikanth K, Kim NY, Park W, Kim JM, Kim KD, Lee KT, Son JH, Chai HH, Choi JW, Jang GW, Kim H, Ryu YC, Nam JW, Park JE, Kim JM, Lim D. Comprehensive genome and transcriptome analyses reveal genetic relationship, selection signature, and transcriptome landscape of small-sized Korean native Jeju horse. Sci Rep 2019; 9:16672. [PMID: 31723199 PMCID: PMC6853925 DOI: 10.1038/s41598-019-53102-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 10/18/2019] [Indexed: 12/16/2022] Open
Abstract
The Jeju horse, indigenous to the Jeju Island in Korea may have originated from Mongolian horses. Adaptations to the local harsh environment have conferred Jeju horse with unique traits such as small-sized body, stocky head, and shorter limbs. These characteristics have not been studied previously at the genomic level. Therefore, we sequenced and compared the genome of 41 horses belonging to 6 breeds. We identified numerous breed-specific non-synonymous SNPs and loss-of-function mutants. Demographic and admixture analyses showed that, though Jeju horse is genetically the closest to the Mongolian breeds, its genetic ancestry is independent of that of the Mongolian breeds. Genome wide selection signature analysis revealed that genes such as LCORL, MSTN, HMGA2, ZFAT, LASP1, PDK4, and ACTN2, were positively selected in the Jeju horse. RNAseq analysis showed that several of these genes were also differentially expressed in Jeju horse compared to Thoroughbred horse. Comparative muscle fiber analysis showed that, the type I muscle fibre content was substantially higher in Jeju horse compared to Thoroughbred horse. Our results provide insights about the selection of complex phenotypic traits in the small-sized Jeju horse and the novel SNPs identified will aid in designing high-density SNP chip for studying other native horse breeds.
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Affiliation(s)
- Krishnamoorthy Srikanth
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Nam-Young Kim
- Subtropical Livestock Research Institute, National Institute of Animal Science, Rural Development Administration, Jeju-do, 63242, Republic of Korea
| | - WonCheoul Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Jae-Min Kim
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | | | - Kyung-Tai Lee
- Animal Breeding and Genetics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Ju-Hwan Son
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Han-Ha Chai
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Jung-Woo Choi
- College of Animal Life Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Gul-Won Jang
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | | | - Youn-Chul Ryu
- Division of Biotechnology, Jeju National University, Jeju, 63243, Republic of Korea
| | - Jin-Wu Nam
- Department of Life Science, Hanyang University, Seoul, 133-791, Republic of Korea
| | - Jong-Eun Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Jun-Mo Kim
- Department of Animal Science and Technology, College of Biotechnology and Natural Resources, Chung-Ang University, Ansung-si, 17546, Republic of Korea.
| | - Dajeong Lim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea.
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Lee LA, Karabina A, Broadwell LJ, Leinwand LA. The ancient sarcomeric myosins found in specialized muscles. Skelet Muscle 2019; 9:7. [PMID: 30836986 PMCID: PMC6402096 DOI: 10.1186/s13395-019-0192-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 02/22/2019] [Indexed: 12/17/2022] Open
Abstract
Striated muscles express an array of sarcomeric myosin motors that are tuned to accomplish specific tasks. Each myosin isoform found in muscle fibers confers unique contractile properties to the fiber in order to meet the demands of the muscle. The sarcomeric myosin heavy chain (MYH) genes expressed in the major cardiac and skeletal muscles have been studied for decades. However, three ancient myosins, MYH7b, MYH15, and MYH16, remained uncharacterized due to their unique expression patterns in common mammalian model organisms and due to their relatively recent discovery in these genomes. This article reviews the literature surrounding these three ancient sarcomeric myosins and the specialized muscles in which they are expressed. Further study of these ancient myosins and how they contribute to the functions of the specialized muscles may provide novel insight into the history of striated muscle evolution.
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Affiliation(s)
- Lindsey A. Lee
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO USA
- BioFrontiers Institute, University of Colorado, Boulder, CO USA
| | - Anastasia Karabina
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO USA
- BioFrontiers Institute, University of Colorado, Boulder, CO USA
| | - Lindsey J. Broadwell
- BioFrontiers Institute, University of Colorado, Boulder, CO USA
- Department of Biochemistry, University of Colorado, Boulder, CO USA
| | - Leslie A. Leinwand
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO USA
- BioFrontiers Institute, University of Colorado, Boulder, CO USA
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Park D, Goh CJ, Kim H, Lee JS, Hahn Y. Loss of conserved ubiquitylation sites in conserved proteins during human evolution. Int J Mol Med 2018; 42:2203-2212. [PMID: 30015863 DOI: 10.3892/ijmm.2018.3772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 07/06/2018] [Indexed: 11/06/2022] Open
Abstract
Ubiquitylation of lysine residues in proteins serves a pivotal role in the efficient removal of misfolded or unused proteins and in the control of various regulatory pathways by monitoring protein activity that may lead to protein degradation. The loss of ubiquitylated lysines may affect the ubiquitin‑mediated regulatory network and result in the emergence of novel phenotypes. The present study analyzed mouse ubiquitylation data and orthologous proteins from 62 mammals to identify 193 conserved ubiquitylation sites from 169 proteins that were lost in the Euarchonta lineage leading to humans. A total of 8 proteins, including betaine homocysteine S‑methyltransferase, clin and CBS domain divalent metal cation transport mediator 3, ribosome‑binding protein 1 and solute carrier family 37 member 4, lost 1 conserved lysine residue, which was ubiquitylated in the mouse ortholog, following the human‑chimpanzee divergence. A total of 17 of the lost ubiquitylated lysines are also known to be modified by acetylation and/or succinylation in mice. In 8 cases, a novel lysine evolved at positions flanking the lost conserved lysine residues, potentially as a method of compensation. We hypothesize that the loss of ubiquitylation sites during evolution may lead to the development of advantageous phenotypes, which are then fixed by selection. The ancestral ubiquitylation sites identified in the present study may be a useful resource for investigating the association between loss of ubiquitylation sites and the emergence of novel phenotypes during evolution towards modern humans.
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Affiliation(s)
- Dongbin Park
- Department of Life Science, Chung‑Ang University, Seoul 06974, Republic of Korea
| | - Chul Jun Goh
- Department of Life Science, Chung‑Ang University, Seoul 06974, Republic of Korea
| | - Hyein Kim
- Department of Life Science, Chung‑Ang University, Seoul 06974, Republic of Korea
| | - Ji Seok Lee
- Department of Life Science, Chung‑Ang University, Seoul 06974, Republic of Korea
| | - Yoonsoo Hahn
- Department of Life Science, Chung‑Ang University, Seoul 06974, Republic of Korea
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Heide M, Long KR, Huttner WB. Novel gene function and regulation in neocortex expansion. Curr Opin Cell Biol 2017; 49:22-30. [PMID: 29227861 DOI: 10.1016/j.ceb.2017.11.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 11/18/2017] [Accepted: 11/26/2017] [Indexed: 01/01/2023]
Abstract
The expansion of the neocortex during human evolution is due to changes in our genome that result in increased and prolonged proliferation of neural stem and progenitor cells during neocortex development. Three principal types of such genomic changes can be distinguished, first, novel gene regulation in human, second, novel function in human of genes existing in both human and non-human species, and third, novel, human-specific genes. The latter comprise both, increases in the copy number of genes existing also in non-human species, and the emergence of genes giving rise to unique, human-specific gene products. Examples of all these types of changes in the human genome have been identified, with ARHGAP11B constituting a paradigmatic example of a unique, human-specific protein.
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Affiliation(s)
- Michael Heide
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, D-01307 Dresden, Germany
| | - Katherine R Long
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, D-01307 Dresden, Germany
| | - Wieland B Huttner
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, D-01307 Dresden, Germany.
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