Detecting signatures of positive selection associated with musical aptitude in the human genome

Chromosome-scale assembly and analysis of Melilotus officinalis genome for SSR development and nodulation genes analysis

Melilotus officinalis is an important legume crop with forage and Chinese medicinal value. The unknown genome of M. officinalis restricted the domestication and utilization of the species and its germplasm resource diversity. A chromosome-scale assembly of the M. officinalis genome was assembled and analysed. The 976.27 Mb of genome was divided into eight chromosomes covering 99.16% of the whole genome. A total of 50022 genes were predicted in the genome. M. officinalis and Melilotus albus shared a common ancestor 0.5-5.65 million years ago (MYA). A genome-wide doubling event occurred 68.93 MYA according to the synonymous nucleotide-substitution values. A total of 552102 tandem repeats were predicted, and 46004 SSR primers of TRs with 10 or more base pairs were developed and designed. The elucidation of the M. officinalis genome provides a compelling model system for studying the genetic, evolutionary and biosynthesis of this legume.

Sensogenomics of music and Alzheimer's disease: An interdisciplinary view from neuroscience, transcriptomics, and epigenomics

Introduction

The relationship between music and Alzheimer's disease (AD) has been approached by different disciplines, but most of our outstanding comes from neuroscience.

Methods

First, we systematically reviewed the state-of-the-art of neuroscience and cognitive sciences research on music and AD (>100 studies), and the progress made on the therapeutic impact of music stimuli in memory. Next, we meta-analyzed transcriptomic and epigenomic data of AD patients to search for commonalities with genes and pathways previously connected to music in genome association, epigenetic, and gene expression studies.

Results

Our findings indicate that >93% of the neuroscience/ cognitive sciences studies indicate at least one beneficial effect of music on patients with neurodegenerative diseases, being improvements on memory and cognition the most frequent outcomes; other common benefits were on social behavior, mood and emotion, anxiety and agitation, quality of life, and depression. Out of the 334 music-related genes, 127 (38%) were found to be linked to epigenome/transcriptome analysis in AD (vs. healthy controls); some of them (SNCA, SLC6A4, ASCC2, FTH1, PLAUR and ARHGAP26) have been reported to be associated e.g. with musical aptitude and music effect on the transcriptome. Other music-related genes (GMPR, SELENBP1 and ADIPOR1) associated to neuropsychiatric, neurodegenerative diseases and music performance, emerged as hub genes in consensus co-expression modules detected between AD and music estimulated transcriptomes. In addition, we found connections between music, AD and dopamine related genes, with SCNA being the most remarkable - a gene previously associated with learning and memory, and neurodegenerative disorders (e.g., Parkinson's disease and AD).

Discussion

The present study indicate that the vast majority of neuroscientific studies unambiguously show that music has a beneficial effect on health, being the most common benefits relevant to Alzheimer's disease. These findings illuminate a new roadmap for genetic research in neurosciences, and musical interventions in AD and other neurodegenerative conditions.

Ventral tegmental area dopaminergic action in music therapy for post-traumatic stress disorder: A literature review

Post-traumatic stress disorder (PTSD) is a debilitating sequela of extraordinary traumatic sufferings that threaten personal health and dramatically attenuate the patient's quality of life. Accumulating lines of evidence suggest that functional disorders in the ventral tegmental area (VTA) dopaminergic system contribute substantially to PTSD symptomatology. Notably, music therapy has been shown to greatly ameliorate PTSD symptoms. In this literature review, we focused on whether music improved PTSD symptoms, based on VTA dopaminergic action, including the effects of music on dopamine (DA)-related gene expression, the promotion of DA release and metabolism, and the activation of VTA functional activities. In addition, the strengths and limitations of the studies concerning the results of music therapy on PTSD are discussed. Collectively, music therapy is an effective approach for PTSD intervention, in which the VTA dopaminergic system may hold an important position.

Music Aptitude, Training, and Cognitive Transfer: A Mini-Review

In this mini-review, the genetic basis of music aptitude and the effects of music training are discussed. The review indicates that regardless of levels of innate ability, experience-induced neuroplasticity can occur as a result of music training. When that happens, it can be expressed as functional or structural brain changes. These changes are often accompanied by improvement in performance in tasks involving auditory analysis. Specifically, music training effects can transfer to a closely related cognitive domain such as auditory processing (near transfer). Music training can also affect more distantly related cognitive domains such as spatial and linguistic domains. Lastly, music training can affect general intelligence (“g”) (far transfer). Music training can mold behavioral brain development and confers cognitive benefits beyond music.

Hearing loss genes reveal patterns of adaptive evolution at the coding and non-coding levels in mammals

Background

Mammals possess unique hearing capacities that differ significantly from those of the rest of the amniotes. In order to gain insights into the evolution of the mammalian inner ear, we aim to identify the set of genetic changes and the evolutionary forces that underlie this process. We hypothesize that genes that impair hearing when mutated in humans or in mice (hearing loss (HL) genes) must play important roles in the development and physiology of the inner ear and may have been targets of selective forces across the evolution of mammals. Additionally, we investigated if these HL genes underwent a human-specific evolutionary process that could underlie the evolution of phenotypic traits that characterize human hearing.

Results

We compiled a dataset of HL genes including non-syndromic deafness genes identified by genetic screenings in humans and mice. We found that many genes including those required for the normal function of the inner ear such as LOXHD1, TMC1, OTOF, CDH23, and PCDH15 show strong signatures of positive selection. We also found numerous noncoding accelerated regions in HL genes, and among them, we identified active transcriptional enhancers through functional enhancer assays in transgenic zebrafish.

Conclusions

Our results indicate that the key inner ear genes and regulatory regions underwent adaptive evolution in the basal branch of mammals and along the human-specific branch, suggesting that they could have played an important role in the functional remodeling of the cochlea. Altogether, our data suggest that morphological and functional evolution could be attained through molecular changes affecting both coding and noncoding regulatory regions.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-021-01170-6.

Whole-Genome Resequencing to Study Brucellosis Susceptibility in Sheep

Brucellosis is a zoonotic disease and a major public health problem. However, the genetic mechanism of brucellosis in sheep remains unclear. In this study, serum samples were collected from 6,358 sheep from the F2 population (Dorper sheep ♂ × Hu sheep ♀), and antibody levels were continuously measured at 14 days and 1, 2, 3, 4, 5, 6, 7, 8, 9, and 10 months after administration of brucellosis vaccine. Finally, 19 brucellosis-resistant group (BRG) sheep and 22 brucellosis-susceptible group sheep (BSG) were screened for whole-genome sequencing. Using the fixation index, Fisher’s exact test, and chi-square test, a total of 205 candidate SNP sites were identified. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis suggested that 138 candidate genes were significantly enriched in adherens junction (CTNNA3, PARD3, and PTPRM), cell adhesion molecules (NLGN1, CNTNAP2, NCAM1, and PTPRM), salivary secretion (LOC101102109, PRKG1, and ADCY2), and hippo signaling pathway (CTNNA3, YAP1, and PARD3). These findings provide valuable molecular markers for brucellosis resistance breeding in sheep and novel insights into the genetic mechanism of brucellosis resistance.

Human Genomics and the Biocultural Origin of Music

Music is an exclusive feature of humankind. It can be considered as a form of universal communication, only partly comparable to the vocalizations of songbirds. Many trends of research in this field try to address music origins, as well as the genetic bases of musicality. On one hand, several hypotheses have been made on the evolution of music and its role, but there is still debate, and comparative studies suggest a gradual evolution of some abilities underlying musicality in primates. On the other hand, genome-wide studies highlight several genes associated with musical aptitude, confirming a genetic basis for different musical skills which humans show. Moreover, some genes associated with musicality are involved also in singing and song learning in songbirds, suggesting a likely evolutionary convergence between humans and songbirds. This comprehensive review aims at presenting the concept of music as a sociocultural manifestation within the current debate about its biocultural origin and evolutionary function, in the context of the most recent discoveries related to the cross-species genetics of musical production and perception.

Genetically related singers-acoustic feature analysis and impact on singer identification

Studies relating music with genetics have been one of the fascinating fields of research. In this study, we have attempted to answer the most curious question-how acoustically close are the genetically related singers? The present study has investigated this perception using two genetically different relations-three female sibling singers and father-son singer relation. These are famous Indian playback singers and the acoustic features are extracted using the songs of Bollywood films. Three different sets of self-developed cappella database are used for the experimentation. Positive correlations among the major musical aptitudes-pitch, vibrato, formant, and harmonic spectral envelope for both the singer relationships-revealed the genetic impact on the acoustic features. Also, the investigation of timbre spectral feature proved it a significant acoustic feature that differentiates similar voices. With Spearman's correlation coefficient, we conclude that strong acoustical association was observed between the acoustic features of genetically related singers, especially the female sibling singers. This was further validated by correlating these singers with genetically unrelated singers. A human perception test performed using cover songs indicated the genetic impact in voice similarity, while the automatic singer identification system discriminated singers more accurately than the human listeners.

Music-listening regulates human microRNA expression

Music-listening and performance have been shown to affect human gene expression. In order to further elucidate the biological basis of the effects of music on the human body, we studied the effects of music-listening on gene regulation by sequencing microRNAs of the listeners (Music Group) and their controls (Control Group) without music exposure. We identified upregulation of six microRNAs (hsa-miR-132-3p, hsa-miR-361-5p, hsa-miR-421, hsa-miR-23a-3p, hsa-miR-23b-3p, hsa-miR-25-3p) and downregulation of two microRNAs (hsa-miR-378a-3p, hsa-miR-16-2-3p) in Music Group with high musical aptitude. Some upregulated microRNAs were reported to be responsive to neuronal activity (miR-132, miR-23a, miR-23b) and modulators of neuronal plasticity, CNS myelination, and cognitive functions like long-term potentiation and memory. miR-132 plays a critical role in regulating TAU protein levels and is important for preventing tau protein aggregation that causes Alzheimer's disease. miR-132 and DICER, upregulated after music-listening, protect dopaminergic neurons and are important for retaining striatal dopamine levels. Some of the transcriptional regulators (FOS, CREB1, JUN, EGR1, and BDNF) of the upregulated microRNAs were immediate early genes and top candidates associated with musical traits. BDNF and SNCA, co-expressed and upregulated in music-listening and music-performance, are both are activated by GATA2, which is associated with musical aptitude. Several miRNAs were associated with song-learning, singing, and seasonal plasticity networks in songbirds. We did not detect any significant changes in microRNA expressions associated with music education or low musical aptitude. Our data thereby show the importance of inherent musical aptitude for music appreciation and for eliciting the human microRNA response to music-listening.

Links Between the Neurobiology of Oxytocin and Human Musicality

The human species possesses two complementary, yet distinct, universal communication systems—language and music. Functional imaging studies have revealed that some core elements of these two systems are processed in closely related brain regions, but there are also clear differences in brain circuitry that likely underlie differences in functionality. Music affects many aspects of human behavior, especially in encouraging prosocial interactions and promoting trust and cooperation within groups of culturally compatible but not necessarily genetically related individuals. Music, presumably via its impact on the limbic system, is also rewarding and motivating, and music can facilitate aspects of learning and memory. In this review these special characteristics of music are considered in light of recent research on the neuroscience of the peptide oxytocin, a hormone that has both peripheral and central actions, that plays a role in many complex human behaviors, and whose expression has recently been reported to be affected by music-related activities. I will first briefly discuss what is currently known about the peptide’s physiological actions on neurons and its interactions with other neuromodulator systems, then summarize recent advances in our knowledge of the distribution of oxytocin and its receptor (OXTR) in the human brain. Next, the complex links between oxytocin and various social behaviors in humans are considered. First, how endogenous oxytocin levels relate to individual personality traits, and then how exogenous, intranasal application of oxytocin affects behaviors such as trust, empathy, reciprocity, group conformity, anxiety, and overall social decision making under different environmental conditions. It is argued that many of these characteristics of oxytocin biology closely mirror the diverse effects that music has on human cognition and emotion, providing a link to the important role music has played throughout human evolutionary history and helping to explain why music remains a special prosocial human asset. Finally, it is suggested that there is a potential synergy in combining oxytocin- and music-based strategies to improve general health and aid in the treatment of various neurological dysfunctions.

How far musicality and perfect pitch are derived from genetic factors?

There is an agreement about joint genetic and environmental background of musical reception and performance. Musical abilities tend to cluster in families. The studies done on a random population, twins and families of gifted musicians provided a strong support for genetic contribution. Modern biomolecular techniques exploring linkage analysis, variation of gene copy number, scanning for whole-genome expression helped to identify genes, or chromosome regions associated with musical aptitude. Some studies were focused on rare ability to recognize tone without reference that is known as a perfect pitch where a far ethnic differentiation was established. On the other hand, gene deletion leading to dysfunction in amusical individuals also indicated appropriate loci “by negation.” The strongest support for an association of genes with musicality was provided for genes: AVPR1 (12q14.2), SLC6A4 (17q11.2), GALM (2p22), PCDH7 (4p15.1), GATA2 (3q21.3), and few others as well for 4q22, 4q23, and 8q13–21 chromosome bands.

Music and the Meeting of Human Minds

Over tens of thousands of years of human genetic and cultural evolution, many types and varieties of music and language have emerged; however, the fundamental components of each of these modes of communication seem to be common to all human cultures and social groups. In this brief review, rather than focusing on the development of different musical techniques and practices over time, the main issues addressed here concern: (i) when, and speculations as to why, modern Homo sapiens evolved musical behaviors, (ii) the evolutionary relationship between music and language, and (iii) why humans, perhaps unique among all living species, universally continue to possess two complementary but distinct communication streams. Did music exist before language, or vice versa, or was there a common precursor that in some way separated into two distinct yet still overlapping systems when cognitively modern H. sapiens evolved? A number of theories put forward to explain the origin and persistent universality of music are considered, but emphasis is given, supported by recent neuroimaging, physiological, and psychological findings, to the role that music can play in promoting trust, altruistic behavior, social bonding, and cooperation within groups of culturally compatible but not necessarily genetically related humans. It is argued that, early in our history, the unique socializing and harmonizing power of music acted as an essential counterweight to the new and evolving sense of self, to an emerging sense of individuality and mortality that was linked to the development of an advanced cognitive capacity and articulate language capability.

Genomics studies on musical aptitude, music perception, and practice

When searching for genetic markers inherited together with musical aptitude, genes affecting inner ear development and brain function were identified. The alpha-synuclein gene (SNCA), located in the most significant linkage region of musical aptitude, was overexpressed when listening and performing music. The GATA-binding protein 2 gene (GATA2) was located in the best associated region of musical aptitude and regulates SNCA in dopaminergic neurons, thus linking DNA- and RNA-based studies of music-related traits together. In addition to SNCA, several other genes were linked to dopamine metabolism. Mutations in SNCA predispose to Lewy-body dementia and cause Parkinson disease in humans and affect song production in songbirds. Several other birdsong genes were found in transcriptome analysis, suggesting a common evolutionary background of sound perception and production in humans and songbirds. Regions of positive selection with musical aptitude contained genes affecting auditory perception, cognitive performance, memory, human language development, and song perception and production of songbirds. The data support the role of dopaminergic pathway and their link to the reward mechanism as a molecular determinant in positive selection of music. Integration of gene-level data from the literature across multiple species prioritized activity-dependent immediate early genes as candidate genes in musical aptitude and listening to and performing music.

Factors affecting pitch discrimination performance in a cohort of extensively phenotyped healthy volunteers

Despite efforts to characterize the different aspects of musical abilities in humans, many elements of this complex area remain unknown. Musical abilities are known to be associated with factors like intelligence, training, and sex, but a comprehensive evaluation of the simultaneous impact of multiple factors has not yet been performed. Here, we assessed 918 healthy volunteers for pitch discrimination abilities—their ability to tell two tones close in pitch apart. We identified the minimal threshold that the participants could detect, and we found that better performance was associated with higher intelligence, East Asian ancestry, male sex, younger age, formal music training–especially before age 6–and English as the native language. All these factors remained significant when controlling for the others, with general intelligence, musical training, and male sex having the biggest impacts. We also performed a small GWAS and gene-based collapsing analysis, identifying no significant associations. Future genetic studies of musical abilities should involve large sample sizes and an unbiased genome-wide approach, with the factors highlighted here included as important covariates.

Music genetics research: Association with musicality of a polymorphism in the AVPR1A gene

Musicality is defined as a natural tendency, sensibility, knowledge, or talent to create, perceive, and play music. Musical abilities involve a great range of social and cognitive behaviors, which are influenced by both environmental and genetic factors. Although a number of studies have yielded insights into music genetics research, genes and biological pathways related to these traits are not fully understood. Our hypothesis in the current study is that genes associated with different behaviors could also influence the musical phenotype. Our aim was to investigate whether polymorphisms in six genes (AVPR1A, SLC6A4, ITGB3, COMT, DRD2 and DRD4) related to social and cognitive traits are associated with musicality in a sample of children. Musicality was assessed through an individualized music therapy assessment profile (IMTAP) which has been validated in Brazil to measure musical ability. We show here that the RS1 microsatellite of the AVPR1A gene is nominally associated with musicality, corroborating previous results linking AVPR1A with musical activity. This study is one of the first to investigate musicality in a comprehensive way, and it contributes to better understand the genetic basis underlying musical ability.

Convergent evidence for the molecular basis of musical traits

To obtain aggregate evidence for the molecular basis of musical abilities and the effects of music, we integrated gene-level data from 105 published studies across multiple species including humans, songbirds and several other animals and used a convergent evidence method to prioritize the top candidate genes. Several of the identified top candidate genes like EGR1, FOS, ARC, BDNF and DUSP1 are known to be activity-dependent immediate early genes that respond to sensory and motor stimuli in the brain. Several other top candidate genes like MAPK10, SNCA, ARHGAP24, TET2, UBE2D3, FAM13A and NUDT9 are located on chromosome 4q21-q24, on the candidate genomic region for music abilities in humans. Functional annotation analyses showed the enrichment of genes involved in functions like cognition, learning, memory, neuronal excitation and apoptosis, long-term potentiation and CDK5 signaling pathway. Interestingly, all these biological functions are known to be essential processes underlying learning and memory that are also fundamental for musical abilities including recognition and production of sound. In summary, our study prioritized top candidate genes related to musical traits.

Parallel evolution of male germline epigenetic poising and somatic development in animals

Changes in gene regulation frequently underlie changes in morphology during evolution, and differences in chromatin state have been linked with changes in anatomical structure and gene expression across evolutionary time. Here we assess the relationship between evolution of chromatin state in germ cells and evolution of gene regulatory programs governing somatic development. We examined the poised (H3K4me3/H3K27me3 bivalent) epigenetic state in male germ cells from five mammalian and one avian species. We find that core genes poised in germ cells from multiple amniote species are ancient regulators of morphogenesis that sit at the top of transcriptional hierarchies controlling somatic tissue development, whereas genes that gain poising in germ cells from individual species act downstream of core poised genes during development in a species-specific fashion. We propose that critical regulators of animal development gained an epigenetically privileged state in germ cells, manifested in amniotes by H3K4me3/H3K27me3 poising, early in metazoan evolution.