Undirected Song Encourages the Breeding Female Zebra Finch to Remain in the Nest

AbstractVocal behavior can be dramatically changed by both neural circuit development and postnatal maturation of the body. During song learning in songbirds, both the song system and syringeal muscles are functionally changing, but it is unknown if maturation of sound generators within the syrinx contributes to vocal development. Here we densely sample the respiratory pressure control space of the zebra finch syrinx in vitro. We show that the syrinx produces sound very efficiently and that key acoustic parameters, minimal fundamental frequency, entropy and source level, do not change over development in both sexes. Thus, our data suggest that the observed acoustic changes in vocal development must be attributed to changes in the motor control pathway, from song system circuitry to muscle force, and not by material property changes in the avian analog of the vocal folds. We propose that in songbirds, muscle use and training driven by the sexually dimorphic song system are the crucial drivers that lead to sexual dimorphism of the syringeal skeleton and musculature. The size and properties of the instrument are thus not changing, while its player is.

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Differences in Depredation by Small Predators Limit the Use of Plasticine and Zebra Finch Eggs in Artificial-Nest Studies

The Condor ◽

10.1093/condor/103.1.180 ◽

2001 ◽

Vol 103 (1) ◽

pp. 180-183 ◽

Cited By ~ 2

Author(s):

Thomas J. Maier ◽

Richard M. Degraaf

Keyword(s):

Small Mammals ◽

Zebra Finch ◽

House Sparrow ◽

Peromyscus Leucopus ◽

Passer Domesticus ◽

Field Studies ◽

Taeniopygia Guttata ◽

Artificial Nest ◽

Neotropical Migrant ◽

Passerine Species

Abstract Small mammals, such as mice and voles, have been implicated as major egg predators of Neotropical migrant passerines by field studies using soft plasticine eggs or the very small eggs of Zebra Finch (Taeniopygia guttata). Nevertheless, the effort required to depredate these commonly used egg surrogates may be less than that required to depredate the larger, thicker-shelled eggs of most passerine species. To compare the depredation of these surrogates to that of the eggs of a mid-sized passerine by a ubiquitous small predator, we exposed dissimilar pairs of plasticine, Zebra Finch, and House Sparrow (Passer domesticus) eggs to captive white-footed mice (Peromyscus leucopus). Plasticine eggs were marked by mice more than either kind of real egg, and Zebra Finch eggs were breached more often than House Sparrow eggs. We conclude that the use of either plasticine or Zebra Finch eggs may lead to overestimation of the ability or proclivity of small mammals to actually depredate the eggs of most passerines.

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Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C

Nature Communications ◽

10.1038/s41467-020-20536-y ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Zev N. Kronenberg ◽

Arang Rhie ◽

Sergey Koren ◽

Gregory T. Concepcion ◽

Paul Peluso ◽

...

Keyword(s):

Zebra Finch ◽

Cultured Cells ◽

De Novo ◽

Single Cells ◽

Variant Calling ◽

Chromatin Interaction ◽

Extended Haplotype ◽

Benchmark Datasets ◽

And Performance ◽

Genome Assemblies

AbstractHaplotype-resolved genome assemblies are important for understanding how combinations of variants impact phenotypes. To date, these assemblies have been best created with complex protocols, such as cultured cells that contain a single-haplotype (haploid) genome, single cells where haplotypes are separated, or co-sequencing of parental genomes in a trio-based approach. These approaches are impractical in most situations. To address this issue, we present FALCON-Phase, a phasing tool that uses ultra-long-range Hi-C chromatin interaction data to extend phase blocks of partially-phased diploid assembles to chromosome or scaffold scale. FALCON-Phase uses the inherent phasing information in Hi-C reads, skipping variant calling, and reduces the computational complexity of phasing. Our method is validated on three benchmark datasets generated as part of the Vertebrate Genomes Project (VGP), including human, cow, and zebra finch, for which high-quality, fully haplotype-resolved assemblies are available using the trio-based approach. FALCON-Phase is accurate without having parental data and performance is better in samples with higher heterozygosity. For cow and zebra finch the accuracy is 97% compared to 80–91% for human. FALCON-Phase is applicable to any draft assembly that contains long primary contigs and phased associate contigs.

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