Higher-Order Musical Temporal Structure in Bird Song.
Ontology highlight
ABSTRACT:
SUBMITTER: Bilger HT
PROVIDER: S-EPMC8044833 | biostudies-literature |
REPOSITORIES: biostudies-literature
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2013-08-09 | E-GEOD-41603 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below.
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Project description:Human social interactions are typically recorded as time-specific dyadic interactions, and represented as evolving (temporal) networks, where links are activated/deactivated over time. However, individuals can interact in groups of more than two people. Such group interactions can be represented as higher-order events of an evolving network. Here, we propose methods to characterize the temporal-topological properties of higher-order events to compare networks and identify their (dis)similarities. We analyzed 8 real-world physical contact networks, finding the following: (a) Events of different orders close in time tend to be also close in topology; (b) Nodes participating in many different groups (events) of a given order tend to involve in many different groups (events) of another order; Thus, individuals tend to be consistently active or inactive in events across orders; (c) Local events that are close in topology are correlated in time, supporting observation (a). Differently, in 5 collaboration networks, observation (a) is almost absent; Consistently, no evident temporal correlation of local events has been observed in collaboration networks. Such differences between the two classes of networks may be explained by the fact that physical contacts are proximity based, in contrast to collaboration networks. Our methods may facilitate the investigation of how properties of higher-order events affect dynamic processes unfolding on them and possibly inspire the development of more refined models of higher-order time-varying networks.
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Project description:Mammalian genomes contain several billion base pairs of DNA which are packaged in chromatin fibers. At selected gene loci, cohesin complexes have been proposed to arrange chromatin fibers into higher-order structures, but it is poorly understood how cohesin performs this task, how important this function is for determining the structure of chromosomes, and how this process is regulated to allow changes in gene expression. Here we show that the cohesin release factor Wapl controls chromatin structure and gene regulation at numerous loci throughout the mouse genome. Conditional deletion of the Wapl gene leads to stable accumulation of cohesin on chromatin, chromatin compaction, altered gene expression, cell cycle delay, chromosome segregation defects and embryonic lethality. In Wapl deficient chromosomes, cohesin accumulates in an axial domain, similar to how condensins form a M-bM-^@M-^\scaffoldM-bM-^@M-^] in mitotic chromosomes. We propose that Wapl controls chromatin structure and gene regulation by determining the residence time with which cohesin binds to DNA. 4 biological replicates for each genotype (Wapl +/F; Wapl -/F) treated with/without 4-OHT =16 samples
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Project description:Mammalian genomes contain several billion base pairs of DNA which are packaged in chromatin fibers. At selected gene loci, cohesin complexes have been proposed to arrange chromatin fibers into higher-order structures, but it is poorly understood how cohesin performs this task, how important this function is for determining the structure of chromosomes, and how this process is regulated to allow changes in gene expression. Here we show that the cohesin release factor Wapl controls chromatin structure and gene regulation at numerous loci throughout the mouse genome. Conditional deletion of the Wapl gene leads to stable accumulation of cohesin on chromatin, chromatin compaction, altered gene expression, cell cycle delay, chromosome segregation defects and embryonic lethality. In Wapl deficient chromosomes, cohesin accumulates in an axial domain, similar to how condensins form a “scaffold” in mitotic chromosomes. We propose that Wapl controls chromatin structure and gene regulation by determining the residence time with which cohesin binds to DNA. ChIP-Seq using two different antibodies (CTCF, Smc3); one (CTCF) and two (Smc3) replicates; two different genotypes (Wapl +/delta, Wapl -/delta). The control sample is a single-replicate INPUT for each genotype.
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Project description:Environmentally imposed selection pressures are well known to shape animal signals. Changes in these signals can result in recognition mismatches between individuals living in different habitats, leading to reproductive divergence and speciation. For example, numerous studies have shown that differences in avian song may be a potent prezygotic isolating mechanism. Typically, however, detailed studies of environmental pressures on variation in animal behavior have been conducted only at small spatial scales. Here, we use remote-sensing data to predict animal behavior, in this case, bird song, across vast spatial scales. We use remotely sensed data to predict the song characteristics of the little greenbul (Andropadus virens), a widely distributed African passerine, found across secondary and mature rainforest habitats and the rainforest-savanna ecotone. Satellite data that captured ecosystem structure and function explained up to 66% of the variation in song characteristics. Song differences observed across habitats, including those between human-altered and mature rainforest, have the potential to lead to reproductive divergence, and highlight the impacts that both natural and anthropogenic change may have on natural populations. Our approach offers a novel means to examine the ecological correlates of animal behavior across large geographic areas with potential applications to both evolutionary and conservation biology.
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Project description:The human capacity for speech and vocal music depends on vocal imitation. Songbirds, in contrast to non-human primates, share this vocal production learning with humans. The process through which birds and humans learn many of their vocalizations as well as the underlying neural system exhibit a number of striking parallels and have been widely researched. In contrast, rhythm, a key feature of language, and music, has received surprisingly little attention in songbirds. Investigating temporal periodicity in bird song has the potential to inform the relationship between neural mechanisms and behavioral output and can also provide insight into the biology and evolution of musicality. Here we present a method to analyze birdsong for an underlying rhythmic regularity. Using the intervals from one note onset to the next as input, we found for each bird an isochronous sequence of time stamps, a "signal-derived pulse," or pulse(S), of which a subset aligned with all note onsets of the bird's song. Fourier analysis corroborated these results. To determine whether this finding was just a byproduct of the duration of notes and intervals typical for zebra finches but not dependent on the individual duration of elements and the sequence in which they are sung, we compared natural songs to models of artificial songs. Note onsets of natural song deviated from the pulse(S) significantly less than those of artificial songs with randomized note and gap durations. Thus, male zebra finch song has the regularity required for a listener to extract a perceived pulse (pulse(P)), as yet untested. Strikingly, in our study, pulses(S) that best fit note onsets often also coincided with the transitions between sub-note elements within complex notes, corresponding to neuromuscular gestures. Gesture durations often equaled one or more pulse(S) periods. This suggests that gesture duration constitutes the basic element of the temporal hierarchy of zebra finch song rhythm, an interesting parallel to the hierarchically structured components of regular rhythms in human music.
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Project description:Human social interactions in local settings can be experimentally detected by recording the physical proximity and orientation of people. Such interactions, approximating face-to-face communications, can be effectively represented as time varying social networks with links being unceasingly created and destroyed over time. Traditional analyses of temporal networks have addressed mostly pairwise interactions, where links describe dyadic connections among individuals. However, many network dynamics are hardly ascribable to pairwise settings but often comprise larger groups, which are better described by higher-order interactions. Here we investigate the higher-order organizations of temporal social networks by analyzing five publicly available datasets collected in different social settings. We find that higher-order interactions are ubiquitous and, similarly to their pairwise counterparts, characterized by heterogeneous dynamics, with bursty trains of rapidly recurring higher-order events separated by long periods of inactivity. We investigate the evolution and formation of groups by looking at the transition rates between different higher-order structures. We find that in more spontaneous social settings, group are characterized by slower formation and disaggregation, while in work settings these phenomena are more abrupt, possibly reflecting pre-organized social dynamics. Finally, we observe temporal reinforcement suggesting that the longer a group stays together the higher the probability that the same interaction pattern persist in the future. Our findings suggest the importance of considering the higher-order structure of social interactions when investigating human temporal dynamics.
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