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1. Exploring the genetics of rhythmic perception and musical engagement in the Vanderbilt Online Musicality Study

   https://doi.org/10.1111/nyas.14964  

   Gustavson, Daniel E.; Coleman, Peyton L.; Wang, Youjia; Nitin, Rachana; Petty, Lauren E.; Bush, Catherine T.; Mosing, Miriam A.; Wesseldijk, Laura W.; Ullén, Fredrik; 23 and Me Research Team; et al (January 2023, Annals of the New York Academy of Sciences)

   Abstract Uncovering the genetic underpinnings of musical ability and engagement is a foundational step for exploring their wide‐ranging associations with cognition, health, and neurodevelopment. Prior studies have focused on using twin and family designs, demonstrating moderate heritability of musical phenotypes. The current study used genome‐wide complex trait analysis and polygenic score (PGS) approaches utilizing genotype data to examine genetic influences on two musicality traits (rhythmic perception and music engagement) inN= 1792 unrelated adults in the Vanderbilt Online Musicality Study. Meta‐analyzed heritability estimates (including a replication sample of Swedish individuals) were 31% for rhythmic perception and 12% for self‐reported music engagement. A PGS derived from a recent study on beat synchronization ability predicted both rhythmic perception (β= 0.11) and music engagement (β= 0.19) in our sample, suggesting that genetic influences underlying self‐reported beat synchronization ability also influence individuals’ rhythmic discrimination aptitude and the degree to which they engage in music. Cross‐trait analyses revealed a modest contribution of PGSs from several nonmusical traits (from the cognitive, personality, and circadian chronotype domains) to individual differences in musicality (β= −0.06 to 0.07). This work sheds light on the complex relationship between the genetic architecture of musical rhythm processing, beat synchronization, music engagement, and other nonmusical traits. 

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2. Song Preference in Female and Juvenile Songbirds: Proximate and Ultimate Questions

   https://doi.org/10.3389/fphys.2022.876205  

   Fujii, Tomoko G.; Coulter, Austin; Lawley, Koedi S.; Prather, Jonathan F.; Okanoya, Kazuo (April 2022, Frontiers in Physiology)

   Birdsong has long been a subject of extensive research in the fields of ethology as well as neuroscience. Neural and behavioral mechanisms underlying song acquisition and production in male songbirds are particularly well studied, mainly because birdsong shares some important features with human speech such as critical dependence on vocal learning. However, birdsong, like human speech, primarily functions as communication signals. The mechanisms of song perception and recognition should also be investigated to attain a deeper understanding of the nature of complex vocal signals. Although relatively less attention has been paid to song receivers compared to signalers, recent studies on female songbirds have begun to reveal the neural basis of song preference. Moreover, there are other studies of song preference in juvenile birds which suggest possible functions of preference in social context including the sensory phase of song learning. Understanding the behavioral and neural mechanisms underlying the formation, maintenance, expression, and alteration of such song preference in birds will potentially give insight into the mechanisms of speech communication in humans. To pursue this line of research, however, it is necessary to understand current methodological challenges in defining and measuring song preference. In addition, consideration of ultimate questions can also be important for laboratory researchers in designing experiments and interpreting results. Here we summarize the current understanding of song preference in female and juvenile songbirds in the context of Tinbergen’s four questions, incorporating results ranging from ethological field research to the latest neuroscience findings. We also discuss problems and remaining questions in this field and suggest some possible solutions and future directions. 

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3. Genomic Diversity in the Endosymbiotic Bacteria of Human Head Lice

   https://doi.org/10.1093/molbev/msae064  

   Boyd, Bret M.; House, Niyomi; Carduck, Christopher W.; Reed, David L.; Yoder, ed., Anne (March 2024, Molecular Biology and Evolution)

   Abstract Insects have repeatedly forged symbioses with heritable microbes, gaining novel traits. For the microbe, the transition to symbioses can lead to the degeneration of the symbiont's genome through transmission bottlenecks, isolation, and the loss of DNA repair enzymes. However, some insect-microbial symbioses have persisted for millions of years, suggesting that natural selection slows genetic drift and maintains functional consistency between symbiont populations. By sampling in multiple countries, we examine genomic diversity within a symbiont species, a heritable symbiotic bacterium found only in human head lice. We find that human head louse symbionts contain genetic diversity that appears to have arisen contemporaneously with the appearance of anatomically modern humans within Africa and/or during the colonization of Eurasia by humans. We predict that the observed genetic diversity underlies functional differences in extant symbiont lineages, through the inactivation of genes involved in symbiont membrane construction. Furthermore, we find evidence of additional gene losses prior to the appearance of modern humans, also impacting the symbiont membrane. From this, we conclude that symbiont genome degeneration is proceeding, via gene inactivation and subsequent loss, in human head louse symbionts, while genomic diversity is maintained. Collectively, our results provide a look into the genomic diversity within a single symbiont species and highlight the shared evolutionary history of humans, lice, and bacteria. 

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4. Matching human vocal imitations to birdsong: An exploratory analysis

   Oudyk, K; Wu, Y; Lostanlen, V; Salamon, J; Farnsworth, A; Bello, JP (August 2019, 2nd International Workshop on Vocal Interactivity in-and-between Humans, Animals and Robots)

   We explore computational strategies for matching human vocal imitations of birdsong to actual birdsong recordings. We recorded human vocal imitations of birdsong and subsequently analysed these data using three categories of audio features for matching imitations to original birdsong: spectral, temporal, and spectrotemporal. These exploratory analyses suggest that spectral features can help distinguish imitation strategies (e.g. whistling vs. singing) but are insufficient for distinguishing species. Similarly, whereas temporal features are correlated between human imitations and natural birdsong, they are also insufficient. Spectrotemporal features showed the greatest promise, in particular when used to extract a representation of the pitch contour of birdsong and human imitations. This finding suggests a link between the task of matching human imitations to birdsong to retrieval tasks in the music domain such as query-by-humming and cover song retrieval; we borrow from such existing methodologies to outline directions for future research. 

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5. Evolutionary constraint and innovation across hundreds of placental mammals

   https://doi.org/10.1126/science.abn3943  

   Christmas, Matthew J.; Kaplow, Irene M.; Genereux, Diane P.; Dong, Michael X.; Hughes, Graham M.; Li, Xue; Sullivan, Patrick F.; Hindle, Allyson G.; Andrews, Gregory; Armstrong, Joel C.; et al (April 2023, Science)

   INTRODUCTION A major challenge in genomics is discerning which bases among billions alter organismal phenotypes and affect health and disease risk. Evidence of past selective pressure on a base, whether highly conserved or fast evolving, is a marker of functional importance. Bases that are unchanged in all mammals may shape phenotypes that are essential for organismal health. Bases that are evolving quickly in some species, or changed only in species that share an adaptive trait, may shape phenotypes that support survival in specific niches. Identifying bases associated with exceptional capacity for cellular recovery, such as in species that hibernate, could inform therapeutic discovery. RATIONALE The power and resolution of evolutionary analyses scale with the number and diversity of species compared. By analyzing genomes for hundreds of placental mammals, we can detect which individual bases in the genome are exceptionally conserved (constrained) and likely to be functionally important in both coding and noncoding regions. By including species that represent all orders of placental mammals and aligning genomes using a method that does not require designating humans as the reference species, we explore unusual traits in other species. RESULTS Zoonomia’s mammalian comparative genomics resources are the most comprehensive and statistically well-powered produced to date, with a protein-coding alignment of 427 mammals and a whole-genome alignment of 240 placental mammals representing all orders. We estimate that at least 10.7% of the human genome is evolutionarily conserved relative to neutrally evolving repeats and identify about 101 million significantly constrained single bases (false discovery rate < 0.05). We cataloged 4552 ultraconserved elements at least 20 bases long that are identical in more than 98% of the 240 placental mammals. Many constrained bases have no known function, illustrating the potential for discovery using evolutionary measures. Eighty percent are outside protein-coding exons, and half have no functional annotations in the Encyclopedia of DNA Elements (ENCODE) resource. Constrained bases tend to vary less within human populations, which is consistent with purifying selection. Species threatened with extinction have few substitutions at constrained sites, possibly because severely deleterious alleles have been purged from their small populations. By pairing Zoonomia’s genomic resources with phenotype annotations, we find genomic elements associated with phenotypes that differ between species, including olfaction, hibernation, brain size, and vocal learning. We associate genomic traits, such as the number of olfactory receptor genes, with physical phenotypes, such as the number of olfactory turbinals. By comparing hibernators and nonhibernators, we implicate genes involved in mitochondrial disorders, protection against heat stress, and longevity in this physiologically intriguing phenotype. Using a machine learning–based approach that predicts tissue-specific cis - regulatory activity in hundreds of species using data from just a few, we associate changes in noncoding sequence with traits for which humans are exceptional: brain size and vocal learning. CONCLUSION Large-scale comparative genomics opens new opportunities to explore how genomes evolved as mammals adapted to a wide range of ecological niches and to discover what is shared across species and what is distinctively human. High-quality data for consistently defined phenotypes are necessary to realize this potential. Through partnerships with researchers in other fields, comparative genomics can address questions in human health and basic biology while guiding efforts to protect the biodiversity that is essential to these discoveries. Comparing genomes from 240 species to explore the evolution of placental mammals. Our new phylogeny (black lines) has alternating gray and white shading, which distinguishes mammalian orders (labeled around the perimeter). Rings around the phylogeny annotate species phenotypes. Seven species with diverse traits are illustrated, with black lines marking their branch in the phylogeny. Sequence conservation across species is described at the top left. IMAGE CREDIT: K. MORRILL 

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