Physiological constraints and cognitive chunking in Zebra Finch songs: Data and R script

Learned bird songs often have a hierarchical organization. In the case of zebra finches, each bird’s song is made up of a string of notes delivered in a stereotyped sequence to form a “motif”, and motifs are repeated to form a song bout. During song learning, young males copy “chunks” of two or more consecutive notes from their tutors’ songs. These chunks are represented as distinct units within memory (during learning) and within motor systems (during song production). During song performance, motifs may deviate from the learned sequence by stopping short, starting late, or by skipping, inserting or repeating notes. We measured acoustic and temporal variables related to the respiratory and vocal physiology of song production and asked how they related to deviations from each bird’s “canonical” sequence. The best predictor of deviations from that sequence was the duration of the silent interval between notes, when inspiration normally occurs. Deviations from the canonical motif occurred..., Subjects: The subjects were 50 adult male zebra finches (Taeniopygia guttata) bred and raised in the Williams College colony. Birds were hatched in aviaries that housed at least three breeding pairs, and so could copy songs from their fathers or from other adult males. Young males in their own and other broods could also influence song development (Tchernichovski & Nottebohm, 1998) or be the source of song material, and both young and older females were present and could influence song development (Carouso-Peck & Goldstein, 2019). When birds reached maturity (approximately 90 days) they were removed from their natal aviaries and housed in single-sex cages, grouped by age cohort, in a colony room that also housed females and older males. All procedures were approved by the Williams College Institutional Animal Care and Use Committee (Williams College IACUC protocol WH-A). Song Recording:  Recordings of female-directed song were obtained by placing a caged adult male (> 120 d..., R, with the following packages: ggplot2, Rcpp, Matrix, lme4, reshape2, sciplot, lattice, plyr, magrittr, MuMIn, Amelia, pscl, readr, performance, dplyr, tidyverse, ggeasy, car, glmmTMB, bbmle, GLMMadaptive, sandwich, lmtest, MASS, DescTools (all are open-source), \# **Physiological Constraints and Cognitive Chunking in Zebra Finch Songs: Data and R script** The data set for the associated paper was obtained by analyzing an average of more than 100 songs from each of 50 zebra finches. Zebra finches have a stereotyped song consisting of approximately ten notes, which are delivered in a stereotyped sequence called a motif. The full sequence is the canonical motif. To address the question of what physiological and cognitive factors are associated with deviations of the canonical motif sequence, we scored deviations as start, stop, and other (repeats, skips, insertions) and counted their occurrence at each transition between notes in each birds canonical motif. We then characterized the acoustic and temporal properties of each transition between notes. Finally, we characterized the cognitive chunks within the song by looking at 21 birds songs that were copies of the same motif, and noting where the copied songs did not match; the transitions where t...习得鸣唱的鸟类鸣曲通常具有层级化结构。就斑胸草雀（Zebra Finch）而言，每只个体的鸣曲由一系列遵循固定时序的鸣音串联而成，进而构成「鸣段（motif）」；多个鸣段重复排列则形成完整鸣唱串（song bout）。在鸣唱学习阶段，幼年雄鸟会从亲代导师的鸣曲中拷贝由两个及以上连续鸣音组成的「组块（chunk）」。这些组块会作为独立单元分别存储于学习阶段的记忆系统，以及鸣唱产生阶段的运动系统中。在鸣唱执行阶段，鸣段可能偏离习得的固定时序：例如提前终止、延迟起始，或是跳过、插入或重复鸣音。本研究测量了与鸣唱产生时呼吸及发声生理相关的声学与时序变量，并探究这些变量与每只个体「标准（canonical）」鸣曲序列偏离情况的关联。该序列偏离情况的最佳预测因子为鸣音间静默间隔的时长——此间隔通常为吸气过程的发生时段。标准鸣段的偏离情况包括…… 实验对象：本研究的实验对象为50只成年雄性斑胸草雀（Zebra Finch，*Taeniopygia guttata*），繁育饲养于威廉姆斯学院种群繁育基地。这些斑胸草雀孵化于至少配有3对繁殖种鸟的大型鸟舍，因此幼鸟可拷贝亲代或其他成年雄鸟的鸣曲。同窝或异窝的幼年雄鸟也可影响鸣唱发育（Tchernichovski & Nottebohm, 1998），或是成为鸣曲素材的来源；同时鸟舍内同时存在幼年与成年雌鸟，二者均可影响鸣唱发育（Carouso-Peck & Goldstein, 2019）。当斑胸草雀发育至性成熟（约90日龄）时，将其从出生鸟舍移出，按年龄组饲养于单性别笼舍中，饲养环境同时配有雌鸟与成年雄鸟。所有实验流程均通过威廉姆斯学院动物护理与使用委员会（Williams College IACUC）的伦理审批，审批编号为WH-A。 鸣唱录制：通过将日龄大于120天的成年雄性斑胸草雀置于笼中，获取其针对雌鸟的定向鸣唱录音。本研究使用R语言及以下开源软件包开展数据分析：ggplot2、Rcpp、Matrix、lme4、reshape2、sciplot、lattice、plyr、magrittr、MuMIn、Amelia、pscl、readr、performance、dplyr、tidyverse、ggeasy、car、glmmTMB、bbmle、GLMMadaptive、sandwich、lmtest、MASS、DescTools（所有包均为开源软件）。 # **斑胸草雀鸣曲中的生理限制与认知组块：数据集与R脚本** 本关联论文所使用的数据集，源自对50只斑胸草雀个体各平均100段以上鸣曲的分析。斑胸草雀的鸣曲具有固定模式，由约10个鸣音按固定时序排列构成「鸣段（motif）」，完整的固定时序序列即为「标准鸣段（canonical motif）」。为探究与标准鸣段序列偏离相关的生理及认知因素，本研究将偏离类型分为起始异常、终止异常及其他异常（包括重复、跳过、插入鸣音），并统计每只个体标准鸣段中各鸣音过渡节点处的偏离发生频次。随后，本研究对各鸣音过渡节点的声学与时序特征进行了表征。最后，本研究通过分析21只个体拷贝自同一标准鸣段的鸣曲，识别拷贝鸣曲与原序列不匹配的位置，以此表征鸣曲中的认知组块；在各过渡节点处……