Vireo philadelphicus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA814984 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Many species of animals deliver vocalizations in sequences presumed to be governed by internal rules, though the nature and complexity of these syntactical rules have been investigated in relatively few species. Here I present an investigation into the song syntax of fourteen male Cassin's Vireos (Vireo cassinii), a species whose song sequences are highly temporally structured. I compare their song sequences to three candidate models of varying levels of complexity-zero-order, first-order and second-order Markov models-and employ novel methods to interpolate between these three models. A variety of analyses, including sequence simulations, Fisher's exact tests, and model likelihood analyses, showed that the songs of this species are too complex to be described by a zero-order or first-order Markov model. The model that best fit the data was intermediate in complexity between a first- and second-order model, though I also present evidence that some transition probabilities are conditioned on up to three preceding phrases. In addition, sequences were shown to be predictable with more than 54% accuracy overall, and predictability was positively correlated with the rate of song delivery. An assessment of the time homogeneity of syntax showed that transition probabilities between phrase types are largely stable over time, but that there was some evidence for modest changes in syntax within and between breeding seasons, a finding that I interpret to represent changes in breeding stage and social context rather than irreversible, secular shifts in syntax over time. These findings constitute a valuable addition to our understanding of bird song syntax in free-living birds, and will contribute to future attempts to understand the evolutionary importance of bird song syntax in avian communication.
| S-EPMC4822860 | biostudies-literature
Project description:Anthropogenic alterations in the natural environment can be a potent evolutionary force. For species that have specific habitat requirements, habitat loss can result in substantial genetic effects, potentially impeding future adaptability and evolution. The endangered black-capped vireo (Vireo atricapilla) suffered a substantial contraction of breeding habitat and population size during much of the 20th century. In a previous study, we reported significant differentiation between remnant populations, but failed to recover a strong genetic signal of bottlenecks. In this study, we used a combination of historical and contemporary sampling from Oklahoma and Texas to (i) determine whether population structure and genetic diversity have changed over time and (ii) evaluate alternate demographic hypotheses using approximate Bayesian computation (ABC). We found lower genetic diversity and increased differentiation in contemporary samples compared to historical samples, indicating nontrivial impacts of fragmentation. ABC analysis suggests a bottleneck having occurred in the early part of the 20th century, resulting in a magnitude decline in effective population size. Genetic monitoring with temporally spaced samples, such as used in this study, can be highly informative for assessing the genetic impacts of anthropogenic fragmentation on threatened or endangered species, as well as revealing the dynamics of small populations over time.
| S-EPMC3461138 | biostudies-literature
Project description:Habitat fragmentation can produce metapopulations or source-sink systems in which dispersal in crucial for population maintenance. Our objective was to investigate connectivity among black-capped vireo (Vireo atricapilla) populations in tandem with a demographic study (Biological Conservation, 2016, 203, 108-118) to elucidate if central Texas populations act as a source-sink system. We genotyped 343 individuals at 12 microsatellite loci to elucidate the movement ecology of the black-capped vireo in central Texas surrounding Fort Hood; the largest and most stable breeding population of black-capped vireos inhabit Fort Hood. To gain insight into gene flow among populations, we analyzed genetic differentiation, migration rates, number of migrants, and parentage. We found statistically significant, but low levels of genetic differentiation among several populations, suggesting some limited restriction to gene flow. Across approaches to estimate migration, we found consistent evidence for asymmetrical movement from Fort Hood to the other central Texas sites consistent with source-sink dynamics. Our results are complementary to black-capped vireo demographic studies done in tandem showing that portions of Fort Hood are acting as a source population to smaller central Texas populations.
| S-EPMC6342116 | biostudies-literature
Project description:Multiplexed single-cell RNA-seq analysis of multiple samples using pooling is a promising experimental design, offering increased throughput while allowing to overcome batch variation. To reconstruct the sample identify of each cell, genetic variants that segregate between the samples in the pool have been proposed as natural barcode for cell demultiplexing. Existing demultiplexing strategies rely on availability of complete genotype data from the pooled samples, which limits the applicability of such methods, in particular when genetic variation is not the primary object of study. To address this, we here present Vireo, a computationally efficient Bayesian model to demultiplex single-cell data from pooled experimental designs. Uniquely, our model can be applied in settings when only partial or no genotype information is available. Using pools based on synthetic mixtures and results on real data, we demonstrate the robustness of Vireo and illustrate the utility of multiplexed experimental designs for common expression analyses.
| S-EPMC6909514 | biostudies-literature
Project description:This dataset contains the raw sequencing data (Runs) from all of the 10x Genomics single-cell CITE-seq Experiments, as well as the demultiplexed cell-donor identities matrices which were generated with Vireo (Analysis).
| EGAD00001009820 | EGA
Project description:modENCODE_submission_5986 This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents. We will integrate information generated with existing knowledge on the biology of the targets and perform ChIP-seq analysis on mutant and RNAi extracts lacking selected target proteins. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: L3 Larva; Genotype: wild type; Sex: mixed Male and Hermaphrodite population; EXPERIMENTAL FACTORS: Developmental Stage L3 Larva; temp (temperature) 20 degree celsius; Strain N2; Antibody NURF-1 SDQ3525 (target is NURF-1)
2013-08-28 | E-GEOD-50296 | biostudies-arrayexpress