Evidence map›Paper›PMID 24125953›Full record

ArticleGene2014

Extraordinarily low evolutionary rates of short wavelength-sensitive opsin pseudogenes.

Shozo Yokoyama, William T Starmer, Yang Liu, Takashi Tada, Lyle Britt

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Gene, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
0.4field-weighted citation impact, top 41% of its field
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

3 citing papers in PubMed, 4 citations in OpenAlex.

  1. Article
  2. Article
  3. 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

5 authors at 3 institutions in 1 country.

Shozo YokoyamaDepartment of Biology, Emory University, Atlanta, GA 30322, USA. Electronic address: syokoya@emory.edu.
William T Starmer
Yang Liu
Takashi Tada
Lyle Britt
Emory University · USNOAA National Marine Fisheries Service Alaska Fisheries Science Center · USSyracuse University · US

Funding

Adaptive Evolution of Color VisionR01EY016400 · NEI · EMORY UNIVERSITY · PI YOKOYAMA, SHOZO · 2006 to 2015
$3.8M
NEI NIH HHS EY016400NEI NIH HHS R01 EY016400
6 · The paper itself

Abstract

Aquatic organisms such as cichlids, coelacanths, seals, and cetaceans are active in UV-blue color environments, but many of them mysteriously lost their abilities to detect these colors. The loss of these functions is a consequence of the pseudogenization of their short wavelength-sensitive (SWS1) opsin genes without gene duplication. We show that the SWS1 gene (BdenS1ψ) of the deep-sea fish, pearleye (Benthalbella dentata), became a pseudogene in a similar fashion about 130 million years ago (Mya) yet it is still transcribed. The rates of nucleotide substitution (~1.4 × 10(-9)/site/year) of the pseudogenes of these aquatic species as well as some prosimian and bat species are much smaller than the previous estimates for the globin and immunoglobulin pseudogenes.

Indexed as

Evolution, MolecularPseudogenesAmino Acid SequenceAnimalsBase SequenceCichlidsFish ProteinsPhylogenyRetinal PigmentsRod OpsinsSequence AnalysisFish ProteinsRetinal PigmentsRod Opsinsshort-wavelength opsinAquatic animalsBayes empirical BayesBEBENCODEmaximum likelihoodmiddle and long wavelength-sensitivemillion years agoMLM/LWSMolecular evolutionMyanaive empirical BayesNEBneighbor-joiningNJRH1RH1-likeRH2rhodopsinshort wavelength-sensitive type 1SWS1SWS1 pseudogenesthe encyclopedia of DNA elements

Identifiers

PMID24125953
PMCPMC3852691
OpenAlexW2081493516

What OpenQuestion holds

Textmetadata
LicenceTDM
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.