Aleksander SA, Balhoff J, Carbon S, Cherry JM, Drabkin HJ, Ebert D et al. (2023) The Gene Ontology knowledgebase in 2023. Genetics 224:iyad031
Anders S, Tanaka M, Kinney DK (2013) Depression as an evolutionary strategy for defense against infection. Brain Behav Immun 31:9–22
Google Scholar
Anisimova M, Yang Z (2007) Multiple hypothesis testing to detect lineages under positive selection that affects only a few sites. Mol Biol Evol 24:1219–28
Google Scholar
Ardlie KG, Deluca DS, Segrè AV, Sullivan TJ, Young TR, Gelfand ET et al. (2015) The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans. Science 348:648–660
Google Scholar
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25:25–29
Google Scholar
Aspden JL, Wallace EWJ, Whiffin N (2023) Not all exons are protein coding: Addressing a common misconception. Cell Genomics 3:100296
Google Scholar
Bakewell MA, Shi P, Zhang J (2007) More genes underwent positive selection in chimpanzee evolution than in human evolution. Proc Natl Acad Sci USA 104:7489–7494
Google Scholar
Begni V, Riva MA, Cattaneo A (2017) Cellular and molecular mechanisms of the brain-derived neurotrophic factor in physiological and pathological conditions. Clin Sci 131:123–138
Google Scholar
Benton ML, Abraham A, LaBella AL, Abbot P, Rokas A, Capra JA (2021) The influence of evolutionary history on human health and disease. Nat Rev Genet 22:269–283
Google Scholar
Bersaglieri T, Sabeti PC, Patterson N, Vanderploeg T, Schaffner SF, Drake JA et al. (2004) Genetic signatures of strong recent positive selection at the lactase gene. Am J Hum Genet 74:1111–20
Google Scholar
Beurel E, Toups M, Nemeroff CB (2020) The Bidirectional Relationship of Depression and Inflammation: Double Trouble. Neuron 107:234–256
Google Scholar
Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S et al. (2009) AmiGO: online access to ontology and annotation data. Bioinformatics 25:288–289
Google Scholar
Chang CC, Chow CC, Tellier LC, Vattikuti S, Purcell SM, Lee JJ (2015) Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience 4:7
Google Scholar
Chen H, Lin R, Lu Y, Zhang R, Gao Y, He Y et al. (2022) Tracing Bai-Yue Ancestry in Aboriginal Li People on Hainan Island. Mol Biol Evol 39:msac210
Google Scholar
Chen X, Huang Y, Huang L, Huang Z, Hao Z-Z, Xu L et al. (2024) A brain cell atlas integrating single-cell transcriptomes across human brain regions. Nat Med 30:2679–2691
Google Scholar
Cunningham F, Allen JE, Allen J, Alvarez-Jarreta J, Amode MR, Armean IM et al. (2022) Ensembl 2022. Nucleic Acids Res 50:D988–D995
Google Scholar
Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA et al. (2011) The variant call format and VCFtools. Bioinformatics 27:2156–8
Google Scholar
Dosari M, AlDayel SK, Alduraibi KM, AlTurki AA, Aljehaiman F, Alamri S et al. (2023) Prevalence of Highly Sensitive Personality and Its Relationship With Depression, and Anxiety in the Saudi General Population. Cureus 15:e49834
Google Scholar
Dumas G, Malesys S, Bourgeron T (2021) Systematic detection of brain protein-coding genes under positive selection during primate evolution and their roles in cognition. Genome Res 31:484–496
Google Scholar
Fedeli C, Filadi R, Rossi A, Mammucari C, Pizzo P (2019) PSEN2 (presenilin 2) mutants linked to familial Alzheimer disease impair autophagy by altering Ca(2+) homeostasis. Autophagy 15:2044–2062
Google Scholar
Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER et al. (2007) Evolutionary and biomedical insights from the rhesus macaque genome. Science 316:222–234
Google Scholar
Gu L, Xia C (2019) Cluster expansion of apolipoprotein D (ApoD) genes in teleost fishes. BMC Evol Biol 19:9
Google Scholar
Gu L, Xia C, Yang S, Yang G (2023) The adaptive evolution of cancer driver genes. BMC Genomics 24:215
Google Scholar
Han B, Eskin E (2011) Random-effects model aimed at discovering associations in meta-analysis of genome-wide association studies. Am J Hum Genet 88:586–98
Google Scholar
Han B, Eskin E (2012) Interpreting meta-analyses of genome-wide association studies. PLoS Genet 8:e1002555
Google Scholar
Hawton K, Casañas I, Comabella C, Haw C, Saunders K (2013) Risk factors for suicide in individuals with depression: a systematic review. J Affect Disord 147:17–28
Google Scholar
Hoenicka J, Quiñones-Lombraña A, España-Serrano L, Alvira-Botero X, Kremer L, Pérez-González R et al. (2010) The ANKK1 gene associated with addictions is expressed in astroglial cells and upregulated by apomorphine. Biol Psychiatry 67:3–11
Google Scholar
Howard DM, Adams MJ, Shirali M, Clarke T-K, Marioni RE, Davies G et al. (2018a) Genome-wide association study of depression phenotypes in UK Biobank identifies variants in excitatory synaptic pathways. Nat Commun. 9:1470
Google Scholar
Howard DM, Adams MJ, Clarke T-K, Hafferty JD, Gibson J, Shirali M et al. (2019) Genome-wide meta-analysis of depression identifies 102 independent variants and highlights the importance of the prefrontal brain regions. Nat Neurosci 22:343–352
Google Scholar
Howard D, Adams M, Shirali M, Clarke T-K, Marioni R, Davies G et al. (2018b) Summary statistics for three depression phenotypes in UK Biobank, [dataset]. University of Edinburgh. https://doi.org/10.7488/ds/2350
Hu B, Zhuang X-L, Zhou L, Zhang G, Cooper DN, Wu D-D (2024) Deciphering the Role of Rapidly Evolving Conserved Elements in Primate Brain Development and Exploring Their Potential Involvement in Alzheimer’s Disease. Mol Biol Evol 41:msae001
Google Scholar
Huang DW, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4:44–57
Google Scholar
Innan H, Kim Y (2008) Detecting local adaptation using the joint sampling of polymorphism data in the parental and derived populations. Genetics 179:1713–20
Google Scholar
Klunk J, Vilgalys TP, Demeure CE, Cheng X, Shiratori M, Madej J et al. (2022) Evolution of immune genes is associated with the Black Death. Nature 611:312–319
Google Scholar
Kothapalli KSD, Ye K, Gadgil MS, Carlson SE, O’Brien KO, Zhang JY et al. (2016) Positive Selection on a Regulatory Insertion-Deletion Polymorphism in FADS2 Influences Apparent Endogenous Synthesis of Arachidonic Acid. Mol Biol Evol 33:1726–39
Google Scholar
Le François B, Zhang L, Mahajan GJ, Stockmeier CA, Friedman E, Albert PR (2018) A Novel Alternative Splicing Mechanism That Enhances Human 5-HT1A Receptor RNA Stability Is Altered in Major Depression. J Neurosci J Soc Neurosci 38:8200–8210
Google Scholar
Levey DF, Stein MB, Wendt FR, Pathak GA, Zhou H, Aslan M et al. (2021) Bi-ancestral depression GWAS in the Million Veteran Program and meta-analysis in >1.2 million individuals highlight new therapeutic directions. Nat Neurosci 24:954–963
Google Scholar
Lin W-J, Zhao Y, Li Z, Zheng S, Zou J-L, Warren NA et al. (2021) An increase in VGF expression through a rapid, transcription-independent, autofeedback mechanism improves cognitive function. Transl Psychiatry 11:383
Google Scholar
Lou DI, McBee RM, Le UQ, Stone AC, Wilkerson GK, Demogines AM et al. (2014) Rapid evolution of BRCA1 and BRCA2 in humans and other primates. BMC Evol Biol 14:155
Google Scholar
Narayanan R, Schratt G (2020) miRNA regulation of social and anxiety-related behaviour. Cell Mol Life Sci 77:4347–4364
Google Scholar
Nielsen R, Hellmann I, Hubisz M, Bustamante C, Clark AG (2007) Recent and ongoing selection in the human genome. Nat Rev Genet 8:857–68
Google Scholar
Notredame C, Higgins DG, Heringa J (2000) T-coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Biol 302:205–217
Google Scholar
Pang Y, Tan G, Yang X, Lin Y, Chen Y, Zhang J et al. (2021) Iron-sulphur cluster biogenesis factor LYRM4 is a novel prognostic biomarker associated with immune infiltrates in hepatocellular carcinoma. Cancer Cell Int 21:463
Google Scholar
Platt ML, Seyfarth RM, Cheney DL (2016) Adaptations for social cognition in the primate brain. Philos Trans R Soc Lond Ser B Biol Sci 371:20150096
Google Scholar
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D et al. (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81:559–75
Google Scholar
Raison CL, Miller AH (2013) The evolutionary significance of depression in Pathogen Host Defense (PATHOS-D). Mol Psychiatry 18:15–37
Google Scholar
Roetker NS, Yonker JA, Lee C, Chang V, Basson JJ, Roan CL et al. (2012) Multigene interactions and the prediction of depression in the Wisconsin Longitudinal Study. BMJ Open 2:e000944
Google Scholar
Ryczek N, Łyś A, Makałowska I (2023) The Functional Meaning of 5’UTR in Protein-Coding Genes. Int J Mol Sci 24:2976
Google Scholar
Sabeti PC, Reich DE, Higgins JM, Levine HZP, Richter DJ, Schaffner SF et al. (2002) Detecting recent positive selection in the human genome from haplotype structure. Nature 419:832–7
Google Scholar
Sabeti PC, Varilly P, Fry B, Lohmueller J, Hostetter E, Cotsapas C et al. (2007) Genome-wide detection and characterization of positive selection in human populations. Nature 449:913–8
Google Scholar
Sherman BT, Hao M, Qiu J, Jiao X, Baseler MW, Lane HC et al. (2022) DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update). Nucleic Acids Res 50:W216–21
Google Scholar
Szpiech ZA, Hernandez RD (2014) selscan: an efficient multithreaded program to perform EHH-based scans for positive selection. Mol Biol Evol 31:2824–7
Google Scholar
Takahashi N, Coluccio A, Thorball CW, Planet E, Shi H, Offner S et al. (2019) ZNF445 is a primary regulator of genomic imprinting. Genes Dev 33:49–54
Google Scholar
Turner JD, Alt SR, Cao L, Vernocchi S, Trifonova S, Battello N et al. (2010) Transcriptional control of the glucocorticoid receptor: CpG islands, epigenetics and more. Biochem Pharm 80:1860–1868
Google Scholar
Upham NS, Esselstyn JA, Jetz W (2019) Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation. PLoS Biol 17:e3000494
Google Scholar
Vamathevan JJ, Hasan S, Emes RD, Amrine-Madsen H, Rajagopalan D, Topp SD et al. (2008) The role of positive selection in determining the molecular cause of species differences in disease. BMC Evol Biol 8:273
Google Scholar
Vicens A, Posada D (2018) Selective Pressures on Human Cancer Genes along the Evolution of Mammals. Genes 9:582
Google Scholar
Voight BF, Kudaravalli S, Wen X, Pritchard JK (2006) A Map of Recent Positive Selection in the Human Genome (L Hurst, Ed.). PLoS Biol 4:e72
Wang HY, Xie Y, Du H, Luo B, Li Z (2023) High LYRM4-AS1 predicts poor prognosis in patients with glioma and correlates with immune infiltration. PeerJ 11:e16104
Google Scholar
Wang WJ, Crompton RH (2004) Analysis of the human and ape foot during bipedal standing with implications for the evolution of the foot. J Biomech 37:1831–6
Google Scholar
Wingo TS, Liu Y, Gerasimov ES, Gockley J, Logsdon BA, Duong DM et al. (2021) Brain proteome-wide association study implicates novel proteins in depression pathogenesis. Nat Neurosci 24:810–817
Google Scholar
Xiao X, Zheng F, Chang H, Ma Y, Yao Y-G, Luo X-J et al. (2018) The Gene Encoding Protocadherin 9 (PCDH9), a Novel Risk Factor for Major Depressive Disorder. Neuropsychopharmacol Publ Am Coll Neuropsychopharmacol 43:1128–1137
Google Scholar
Yang Z (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13:555–6
Google Scholar
Yang Z (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24:1586–91
Google Scholar
Yang Z, Bai C, Pu Y, Kong Q, Guo Y, Ouzhuluobu L et al. (2022) Genetic adaptation of skin pigmentation in highland Tibetans. Proc Natl Acad Sci USA 119:e2200421119
Google Scholar
Ye K, Gao F, Wang D, Bar-Yosef O, Keinan A (2017) Dietary adaptation of FADS genes in Europe varied across time and geography. Nat Ecol Evol 1:167
Google Scholar
Yoo SS, Lee DW, Ham HJ, Yeo IJ, Chang JY, Yun J et al. (2024) Presenilin-2 knock-In mice show severe depressive behavior via DVL3 downregulation. CNS Neurosci Ther 30:e14370
Google Scholar
Zhang B, Zhao Y (2022) Novel variant of ETFDH leading to multiple acyl-CoA dehydrogenase deficiency by promoting protein degradation via ubiquitin proteasome pathway. Clin Chim Acta 530:104–112
Google Scholar
Zhuang X-L, Zhang J-J, Shao Y, Ye Y, Chen C-Y, Zhou L et al. (2023) Integrative Omics Reveals Rapidly Evolving Regulatory Sequences Driving Primate Brain Evolution. Mol Biol Evol 40:msad173
Google Scholar
