The Magnitude of Global Marine Species Diversity

Background: The question of how many marine species exist is important because it provides a metric for how much we do and do not know about life in the oceans. We have compiled the first register of the marine species of the world and used this baseline to estimate how many more species, partitioned among all major eukaryotic groups, may be discovered. Results: There are ∼226,000 eukaryotic marine species described. More species were described in the past decade (∼20,000) than in any previous one. The number of authors describing new species has been increasing at a faster rate than the number of new species described in the past six decades. We report that there are ∼170,000 synonyms, that 58,000–72,000 species are collected but not yet described, and that 482,000–741,000 more species have yet to be sampled. Molecular methods may add tens of thousands of cryptic species. Thus, there may be 0.7–1.0 million marine species. Past rates of description of new species indicate there may be 0.5 ± 0.2 million marine species. On average 37% (median 31%) of species in over 100 recent field studies around the world might be new to science. Conclusions: Currently, between one-third and two-thirds of marine species may be undescribed, and previous estimates of there being well over one million marine species appear highly unlikely. More species than ever before are being described annually by an increasing number of authors. If the current trend continues, most species will be discovered this century

The James Webb Space Telescope Mission

Twenty-six years ago a small committee report, building on earlier studies, expounded a compelling and poetic vision for the future of astronomy, calling for an infrared-optimized space telescope with an aperture of at least $4m$. With the support of their governments in the US, Europe, and Canada, 20,000 people realized that vision as the $6.5m$ James Webb Space Telescope. A generation of astronomers will celebrate their accomplishments for the life of the mission, potentially as long as 20 years, and beyond. This report and the scientific discoveries that follow are extended thank-you notes to the 20,000 team members. The telescope is working perfectly, with much better image quality than expected. In this and accompanying papers, we give a brief history, describe the observatory, outline its objectives and current observing program, and discuss the inventions and people who made it possible. We cite detailed reports on the design and the measured performance on orbit.Comment: Accepted by PASP for the special issue on The James Webb Space Telescope Overview, 29 pages, 4 figure

Curation of microarray oligonucleotides and corresponding ESTs/cDNAs used for gene expression analysis in zebra finches

Abstract Objectives Zebra finches are a major model organism for investigating mechanisms of vocal learning, a trait that enables spoken language in humans. The development of cDNA collections with expressed sequence tags (ESTs) and microarrays has allowed for extensive molecular characterizations of circuitry underlying vocal learning and production. However, poor database curation can lead to errors in transcriptome and bioinformatics analyses, limiting the impact of these resources. Here we used genomic alignments and synteny analysis for orthology verification to curate and reannotate ~ 35% of the oligonucleotides and corresponding ESTs/cDNAs that make-up Agilent microarrays for gene expression analysis in finches. Data description We found that: (1) 5475 out of 43,084 oligos (a) failed to align to the zebra finch genome, (b) aligned to multiple loci, or (c) aligned to Chr_un only, and thus need to be flagged until a better genome assembly is available, or (d) reflect cloning artifacts; (2) Out of 9635 valid oligos examined further, 3120 were incorrectly named, including 1533 with no known orthologs; and (3) 2635 oligos required name update. The resulting curated dataset provides a reference for correcting gene identification errors in previous finch microarrays studies, and avoiding such errors in future studies

Oligonucleotide annotations from the Agilent Songbird Oligonucleotide Array V2: data file 5

This dataset contains a single MS Excel <b>.xlsx</b> file, documenting the curation of a large set of oligonucleotide (oligo) annotations from the Agilent Songbird Oligonucleotide Array V2.<div><div><br></div><div><b>Tables 3-13</b> provide a list of subsets of oligos that were curated at each step of the analysis, including subsets of oligos that were removed because they were deemed uninformative (<b>Tables 3-6</b>), or subjected to a name verification and/or reannotation effort (<b>Tables 8-13</b>). The step-by-step curation of these oligos is described in the manuscript associated with this dataset.</div><div><br></div><div>Oligos in various categories are identified by 'oligo IDs' given by Duke University. Those subject to name verification and/or reannotation effort also have recorded the most recent oligo consensus symbols and names applied in two studies referenced in the related paper, Chromosomal and strand information to which the oligo aligns, and related HGNC ID Gene Description and HGNC Symbol Status, where relevant.</div><div><br></div><div><b>Background</b></div><div>Zebra finches are a major model organism for investigating mechanisms of vocal learning, a trait that enables spoken language in humans. The development of EST/cDNA database collections and microarrays has allowed extensive molecular characterizations of the vocal learning and production circuitry. However, poor curation of these databases can lead to errors in transcriptome and bioinformatics analyses, limiting the impact of these resources. Here we used genomic alignments and synteny analysis for orthology verification to curate and reannotate a large set of oligonucleotides and corresponding ESTs/cDNAs that make-up Agilent microarrays for gene expression analysis in finches.<br></div><div><br></div></div

Oligonucleotide annotations from the Agilent Songbird Oligonucleotide Array V2: data file 3

This dataset contains a single MS Excel <b>.xlsx</b> file, documenting the curation of a large set of oligonucleotide (oligo) annotations from the Agilent Songbird Oligonucleotide Array V2.<div><div><br></div><div><b>Tables 3-13</b> provide a list of subsets of oligos that were curated at each step of the analysis, including subsets of oligos that were removed because they were deemed uninformative (<b>Tables 3-6</b>), or subjected to a name verification and/or reannotation effort (<b>Tables 8-13</b>). The step-by-step curation of these oligos is described in the manuscript associated with this dataset.</div><div><br></div><div>Oligos in various categories are identified by 'oligo IDs' given by Duke University. Those subject to name verification and/or reannotation effort also have recorded the most recent oligo consensus symbols and names applied in two studies referenced in the related paper, Chromosomal and strand information to which the oligo aligns, and related HGNC ID Gene Description and HGNC Symbol Status, where relevant.</div><div><br></div><div><b>Background</b></div><div>Zebra finches are a major model organism for investigating mechanisms of vocal learning, a trait that enables spoken language in humans. The development of EST/cDNA database collections and microarrays has allowed extensive molecular characterizations of the vocal learning and production circuitry. However, poor curation of these databases can lead to errors in transcriptome and bioinformatics analyses, limiting the impact of these resources. Here we used genomic alignments and synteny analysis for orthology verification to curate and reannotate a large set of oligonucleotides and corresponding ESTs/cDNAs that make-up Agilent microarrays for gene expression analysis in finches.<br></div><div><br></div></div

Oligonucleotide annotations from the Agilent Songbird Oligonucleotide Array V2: data file 11

This dataset contains a single MS Excel <b>.xlsx</b> file, documenting the curation of a large set of oligonucleotide (oligo) annotations from the Agilent Songbird Oligonucleotide Array V2.<div><div><br></div><div><b>Tables 3-13</b> provide a list of subsets of oligos that were curated at each step of the analysis, including subsets of oligos that were removed because they were deemed uninformative (<b>Tables 3-6</b>), or subjected to a name verification and/or reannotation effort (<b>Tables 8-13</b>). The step-by-step curation of these oligos is described in the manuscript associated with this dataset.</div><div><br></div><div>Oligos in various categories are identified by 'oligo IDs' given by Duke University. Those subject to name verification and/or reannotation effort also have recorded the most recent oligo consensus symbols and names applied in two studies referenced in the related paper, Chromosomal and strand information to which the oligo aligns, and related HGNC ID Gene Description and HGNC Symbol Status, where relevant.</div><div><br></div><div><b>Background</b></div><div>Zebra finches are a major model organism for investigating mechanisms of vocal learning, a trait that enables spoken language in humans. The development of EST/cDNA database collections and microarrays has allowed extensive molecular characterizations of the vocal learning and production circuitry. However, poor curation of these databases can lead to errors in transcriptome and bioinformatics analyses, limiting the impact of these resources. Here we used genomic alignments and synteny analysis for orthology verification to curate and reannotate a large set of oligonucleotides and corresponding ESTs/cDNAs that make-up Agilent microarrays for gene expression analysis in finches.<br></div><div><br></div></div

Oligonucleotide annotations from the Agilent Songbird Oligonucleotide Array V2: data file 7

This dataset contains a single MS Excel <b>.xlsx</b> file, documenting the curation of a large set of oligonucleotide (oligo) annotations from the Agilent Songbird Oligonucleotide Array V2.<div><div><br></div><div><b>Tables 3-13</b> provide a list of subsets of oligos that were curated at each step of the analysis, including subsets of oligos that were removed because they were deemed uninformative (<b>Tables 3-6</b>), or subjected to a name verification and/or reannotation effort (<b>Tables 8-13</b>). The step-by-step curation of these oligos is described in the manuscript associated with this dataset.</div><div><br></div><div>Oligos in various categories are identified by 'oligo IDs' given by Duke University. Those subject to name verification and/or reannotation effort also have recorded the most recent oligo consensus symbols and names applied in two studies referenced in the related paper, Chromosomal and strand information to which the oligo aligns, and related HGNC ID Gene Description and HGNC Symbol Status, where relevant.</div><div><br></div><div><b>Background</b></div><div>Zebra finches are a major model organism for investigating mechanisms of vocal learning, a trait that enables spoken language in humans. The development of EST/cDNA database collections and microarrays has allowed extensive molecular characterizations of the vocal learning and production circuitry. However, poor curation of these databases can lead to errors in transcriptome and bioinformatics analyses, limiting the impact of these resources. Here we used genomic alignments and synteny analysis for orthology verification to curate and reannotate a large set of oligonucleotides and corresponding ESTs/cDNAs that make-up Agilent microarrays for gene expression analysis in finches.<br></div><div><br></div></div