Evidence map›Paper›PMID 21993624›Full record

ArticleNature2011

A high-resolution map of human evolutionary constraint using 29 mammals.

Kerstin Lindblad-Toh, Manuel Garber, Or Zuk, Michael F Lin, Brian J Parker, Stefan Washietl, Pouya Kheradpour, Jason Ernst, Gregory Jordan, Evan Mauceli and 79 more

Abstract readComparative Study
In one paragraph

Article in Nature, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 670 papers, 5 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
670citing papers in PubMed, 5 pooled it
–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

670 citing papers in PubMed, 5 syntheses or guidelines pooled it.

  1. Pooled it
  2. Pooled it
  3. Pooled it
  4. Pooled it
  5. Pooled it
  6. Review
  7. Article
  8. Article
  9. Pervasive cryptic selection in the human noncoding genome.bioRxiv : the preprint server for biology · 2026
    Article
  10. Article
  11. Article
  12. Review
  13. Review
  14. Article
  15. Article
  16. Article
  17. Article
  18. Article
  19. Distinguishing causal from tagging enhancers using single-cell multiome data.medRxiv : the preprint server for health sciences · 2026
    Article
  20. Article

610 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

89 authors.

Kerstin Lindblad-TohBroad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA. kersli@broadinstitute.org
Manuel Garber
Or Zuk
Michael F Lin
Brian J Parker
Stefan Washietl
Pouya Kheradpour
Jason Ernst
Gregory Jordan
Evan Mauceli
Lucas D Ward
Craig B Lowe
Alisha K Holloway
Michele Clamp
Sante Gnerre
Jessica Alföldi
Kathryn Beal
Jean Chang
Hiram Clawson
James Cuff
Federica Di Palma
Stephen Fitzgerald
Paul Flicek
Mitchell Guttman
Melissa J Hubisz
David B Jaffe
Irwin Jungreis
W James Kent
Dennis Kostka
Marcia Lara
Andre L Martins
Tim Massingham
Ida Moltke
Brian J Raney
Matthew D Rasmussen
Jim Robinson
Alexander Stark
Albert J Vilella
Jiayu Wen
Xiaohui Xie
Michael C Zody
Broad Institute Sequencing Platform and Whole Genome Assembly Team
Jen Baldwin
Toby Bloom
Chee Whye Chin
Dave Heiman
Robert Nicol
Chad Nusbaum
Sarah Young
Jane Wilkinson
Kim C Worley
Christie L Kovar
Donna M Muzny
Richard A Gibbs
Baylor College of Medicine Human Genome Sequencing Center Sequencing Team
Andrew Cree
Huyen H Dihn
Gerald Fowler
Shalili Jhangiani
Vandita Joshi
Sandra Lee
Lora R Lewis
Lynne V Nazareth
Geoffrey Okwuonu
Jireh Santibanez
Wesley C Warren
Elaine R Mardis
George M Weinstock
Richard K Wilson
Genome Institute at Washington University
Kim Delehaunty
David Dooling
Catrina Fronik
Lucinda Fulton
Bob Fulton
Tina Graves
Patrick Minx
Erica Sodergren
Ewan Birney
Elliott H Margulies
Javier Herrero
Eric D Green
David Haussler
Adam Siepel
Nick Goldman
Katherine S Pollard
Jakob S Pedersen
Eric S Lander
Manolis Kellis

Funding

Large Scale Sequencing and Analysis of GenomesU54HG003067 · NHGRI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI GABRIEL, STACEY, LANDER, ERIC S · 2004 to 2015
$568.6M
The Human Genome Sequencing CenterU54HG003273 · NHGRI · BAYLOR COLLEGE OF MEDICINE · PI GIBBS, RICHARD A · 2004 to 2015
$341.3M
Whole-genome shotgun sequencing strategy and assemblyR01HG003474 · NHGRI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI JAFFE, DAVID B · 2005 to 2013
$6.1M
Regulatory Morif Discovery in the Human Genome Using Comparative GenomicsR01HG004037 · NHGRI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI KELLIS, MANOLIS · 2007 to 2015
$3.9M
What Made Us Human?R01GM082901 · NIGMS · J. DAVID GLADSTONE INSTITUTES · PI POLLARD, KATHERINE S. · 2008 to 2011
$1.4M
Howard Hughes Medical InstituteNHGRI NIH HHS R01 HG003474NHGRI NIH HHS R01 HG004037NHGRI NIH HHS U54 HG003067NHGRI NIH HHS U54 HG003273NIGMS NIH HHS GM82901NIGMS NIH HHS R01 GM082901Wellcome Trust 095908
6 · The paper itself

Abstract

The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering ∼4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for ∼60% of constrained bases. These elements reveal a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons. We find 220 candidate RNA structural families, and nearly a million elements overlapping potential promoter, enhancer and insulator regions. We report specific amino acid residues that have undergone positive selection, 280,000 non-coding elements exapted from mobile elements and more than 1,000 primate- and human-accelerated elements. Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease.

Indexed as

Evolution, MolecularAnimalsDiseaseExonsGenomeGenome, HumanGenomicsHealthHumansMammalsMolecular Sequence AnnotationPhylogenyRNASelection, GeneticSequence AlignmentSequence Analysis, DNARNA

Identifiers

PMID21993624
PMCPMC3207357

What OpenQuestion holds

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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 OpenQuestion graph.