Evidence map›Paper›PMID 38401156›Full record

ArticleThe Journal of heredity2024

A highly contiguous genome assembly for the Yellow Warbler (Setophaga petechia).

Whitney L E Tsai, Merly Escalona, Kimball L Garrett, Ryan S Terrill, Ruta Sahasrabudhe, Oanh Nguyen, Eric Beraut, William Seligmann, Colin W Fairbairn, Ryan J Harrigan and 4 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in The Journal of heredity, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

14 authors.

Whitney L E TsaiDepartment of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, United States.ORCID 0000-0003-3274-2829
Merly EscalonaDepartment of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, United States.ORCID 0000-0003-0213-4777
Kimball L GarrettOrnithology Department, Natural History Museum of Los Angeles County, Los Angeles, CA 90007, United States.
Ryan S TerrillMoore Laboratory of Zoology, Biology Department, Occidental College, Los Angeles, CA 90041, United States.ORCID 0000-0003-3834-9761
Ruta SahasrabudheDNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA 95616, United States.ORCID 0000-0002-3285-6845
Oanh NguyenDNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA 95616, United States.ORCID 0000-0003-1492-2084
Eric BerautDepartment of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, United States.ORCID 0000-0002-4443-6282
William SeligmannDepartment of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, United States.ORCID 0000-0002-5762-3095
Colin W FairbairnDepartment of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, United States.
Ryan J HarriganDepartment of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, United States.ORCID 0000-0002-4504-7158
John E McCormackMoore Laboratory of Zoology, Biology Department, Occidental College, Los Angeles, CA 90041, United States.ORCID 0000-0002-0912-1461
Michael E AlfaroDepartment of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, United States.ORCID 0000-0002-8898-8230
Thomas B SmithDepartment of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, United States.ORCID 0000-0002-5978-6912
Rachael A BayDepartment of Evolution and Ecology, University of California, Davis, CA 95616, United States.ORCID 0000-0002-9516-5881

Funding

Pacific Biosciences PacBio RS Single Molecule Real Time SequencerS10OD018174 · OD · UNIVERSITY OF CALIFORNIA BERKELEY · PI ROKHSAR, DANIEL SOLEYMAN · 2014 to 2014
$600k
Acquisition of Covaris E220 and Sciclone G3 systems for high throughput sequencinS10OD010786 · OD · UNIVERSITY OF CALIFORNIA AT DAVIS · PI COMAI, LUCA · 2012 to 2012
$311k
NIH HHS S10 OD010786NIH HHS S10 OD018174
6 · The paper itself

Abstract

The Yellow Warbler (Setophaga petechia) is a small songbird in the wood-warbler family (Parulidae) that exhibits phenotypic and ecological differences across a widespread distribution and is important to California's riparian habitat conservation. Here, we present a high-quality de novo genome assembly of a vouchered female Yellow Warbler from southern California. Using HiFi long-read and Omni-C proximity sequencing technologies, we generated a 1.22 Gb assembly including 687 scaffolds with a contig N50 of 6.80 Mb, scaffold N50 of 21.18 Mb, and a BUSCO completeness score of 96.0%. This highly contiguous genome assembly provides an essential resource for understanding the history of gene flow, divergence, and local adaptation in Yellow Warblers and can inform conservation management of this charismatic bird species.

Indexed as

GenomeSongbirdsAnimalsCaliforniaFemaleGene FlowCalifornia Conservation Genomics ProjectParulidae

Identifiers

PMID38401156
PMCPMC11081134

What Socratic holds

Textmetadata
LicenceCC BY-NC
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.