GEPHE SUMMARY
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Gephebase Gene
Entry Status
Published
GepheID
GP00002384
Main curator
Santos
PHENOTYPIC CHANGE
Trait Category
Trait
Trait State in Taxon A
nestling pink beak
Trait State in Taxon B
nestling yellow beak
Ancestral State
Taxon A
Taxonomic Status
Taxon A #1
Latin Name
Common Name
-
Synonyms
Cactornis scandens; Cactornis scandens Gould, 1837; Geospiza scadens
Rank
species
Lineage
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rygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Passeriformes; Thraupidae; Geospiza
Parent
NCBI Taxonomy ID
is Taxon A an Infraspecies?
No
Taxon A #2
Latin Name
Common Name
medium ground-finch
Synonyms
medium ground-finch; Geospiza fortis Gould, 1837
Rank
species
Lineage
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rygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Passeriformes; Thraupidae; Geospiza
Parent
NCBI Taxonomy ID
is Taxon A an Infraspecies?
No
Taxon A #3
Latin Name
Common Name
-
Synonyms
Geospiza conirostris Ridgway, 1890; Geospiza cornirostris
Rank
species
Lineage
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rygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Passeriformes; Thraupidae; Geospiza
Parent
NCBI Taxonomy ID
is Taxon A an Infraspecies?
No
Taxon A #4
Latin Name
Common Name
-
Synonyms
Geospiza magnirostris Gould, 1837
Rank
species
Lineage
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rygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Passeriformes; Thraupidae; Geospiza
Parent
NCBI Taxonomy ID
is Taxon A an Infraspecies?
No
Taxon A #5
Latin Name
Common Name
-
Synonyms
Geospiza fuliginosa Gould, 1837; Geospiza fulingosa
Rank
species
Lineage
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rygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Passeriformes; Thraupidae; Geospiza
Parent
NCBI Taxonomy ID
is Taxon A an Infraspecies?
No
Taxon A #6
Latin Name
Common Name
-
Synonyms
Geospiza parvula; Geospiza parvula Gould, 1837
Rank
species
Lineage
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i; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Passeriformes; Thraupidae; Camarhynchus
NCBI Taxonomy ID
is Taxon A an Infraspecies?
No
Taxon A #7
Latin Name
Common Name
-
Synonyms
-
Rank
species
Lineage
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i; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Passeriformes; Thraupidae; Camarhynchus
NCBI Taxonomy ID
is Taxon A an Infraspecies?
No
Taxon A #8
Latin Name
Common Name
woodpecker finch
Synonyms
Cactornis pallida; Cactospiza pallida; woodpecker finch; Cactornis pallida Sclater & Salvin, 1870; Camarhynchus pallidus (Sclater & Salvin, 1870)
Rank
species
Lineage
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i; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Passeriformes; Thraupidae; Camarhynchus
NCBI Taxonomy ID
is Taxon A an Infraspecies?
No
Taxon A #9
Latin Name
Common Name
-
Synonyms
Geospiza difficilis Sharpe, 1888
Rank
species
Lineage
Show more ...
rygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Passeriformes; Thraupidae; Geospiza
Parent
NCBI Taxonomy ID
is Taxon A an Infraspecies?
No
Taxon B #1
Latin Name
Common Name
-
Synonyms
Cactornis scandens; Cactornis scandens Gould, 1837; Geospiza scadens
Rank
species
Lineage
Show more ...
rygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Passeriformes; Thraupidae; Geospiza
Parent
NCBI Taxonomy ID
is Taxon B an Infraspecies?
No
Taxon B #2
Latin Name
Common Name
medium ground-finch
Synonyms
medium ground-finch; Geospiza fortis Gould, 1837
Rank
species
Lineage
Show more ...
rygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Passeriformes; Thraupidae; Geospiza
Parent
NCBI Taxonomy ID
is Taxon B an Infraspecies?
No
Taxon B #3
Latin Name
Common Name
-
Synonyms
Geospiza conirostris Ridgway, 1890; Geospiza cornirostris
Rank
species
Lineage
Show more ...
rygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Passeriformes; Thraupidae; Geospiza
Parent
NCBI Taxonomy ID
is Taxon B an Infraspecies?
No
Taxon B #4
Latin Name
Common Name
-
Synonyms
Geospiza magnirostris Gould, 1837
Rank
species
Lineage
Show more ...
rygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Passeriformes; Thraupidae; Geospiza
Parent
NCBI Taxonomy ID
is Taxon B an Infraspecies?
No
Taxon B #5
Latin Name
Common Name
-
Synonyms
Geospiza fuliginosa Gould, 1837; Geospiza fulingosa
Rank
species
Lineage
Show more ...
rygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Passeriformes; Thraupidae; Geospiza
Parent
NCBI Taxonomy ID
is Taxon B an Infraspecies?
No
Taxon B #6
Latin Name
Common Name
-
Synonyms
Geospiza parvula; Geospiza parvula Gould, 1837
Rank
species
Lineage
Show more ...
i; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Passeriformes; Thraupidae; Camarhynchus
NCBI Taxonomy ID
is Taxon B an Infraspecies?
No
Taxon B #7
Latin Name
Common Name
-
Synonyms
-
Rank
species
Lineage
Show more ...
i; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Passeriformes; Thraupidae; Camarhynchus
NCBI Taxonomy ID
is Taxon B an Infraspecies?
No
Taxon B #8
Latin Name
Common Name
woodpecker finch
Synonyms
Cactornis pallida; Cactospiza pallida; woodpecker finch; Cactornis pallida Sclater & Salvin, 1870; Camarhynchus pallidus (Sclater & Salvin, 1870)
Rank
species
Lineage
Show more ...
i; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Passeriformes; Thraupidae; Camarhynchus
NCBI Taxonomy ID
is Taxon B an Infraspecies?
No
Taxon B #9
Latin Name
Common Name
-
Synonyms
Geospiza difficilis Sharpe, 1888
Rank
species
Lineage
Show more ...
rygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Passeriformes; Thraupidae; Geospiza
Parent
NCBI Taxonomy ID
is Taxon B an Infraspecies?
No
GENOTYPIC CHANGE
Generic Gene Name
BCO2
Synonyms
BCDO2; B-DIOX-II
String
Sequence Similarities
Belongs to the carotenoid oxygenase family.
GO - Molecular Function
GO:0046872 : metal ion binding
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GO - Biological Process
GO:0055114 : oxidation-reduction process
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GO - Cellular Component
GO:0005739 : mitochondrion
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UniProtKB
Homo sapiens
Homo sapiens
Presumptive Null
Molecular Type
Aberration Type
Molecular Details of the Mutation
"By closely inspecting this region in a combined sample of all 456 finches of the two species we identified a single exonic SNP with a likelihood ratio test (LRT) statistic exceeding 166 (Figure 1C). It is also the only consistently elevated SNP in an analysis of each species alone (Figure S1), is the best fit variant under a recessive model (STAR Methods), and occurs on multiple haplotypes (Figure S1C). This SNP (chr24:6,166,878; p6166878 hereafter) leads to a synonymous change 32 bp into exon 4 of BCO2. "
"The functional importance of the observed synonymous change is uncertain, and the presence of an unidentified linked causal variant cannot be completely ruled out (see Conclusions). However, a functional explanation is possible because codon usage can be under strong selection30 and may have functional consequences on translation,30 RNA stability,31 and transcription.32 Notably, p6166878 changes the highest frequency valine codon (ƒGTG = 27.3%) to the lowest (ƒGTA = 7.6%) in the reference genome. This is in line with the observed phenotypic effect of the yellow mutation because a lower abundance codon is expected to be associated with lower protein expression.33 In this case, less BCO2 activity results in more carotenoid deposition in the yellow morph. In fact, we found that yellow homozygotes showed significantly lower BCO2 expression compared to pink homozygotes in the upper beak of developing embryos (Figure 1F) that were sourced from a variety of different species and islands (Table S1): small sample sizes prohibit species-specific analysis. Among the six heterozygous individuals, the pink allele was expressed more than the yellow allele in five samples tested using a droplet-digital PCR (Figure S2C). Differences in expression between the two alleles, and in the absence of alternative splice variants (STAR Methods), raise the possibility that the synonymous change alters transcription factor binding affinity in exon 4. Further research into tissue-specific expression and the specific transcription factors that regulate BCO2 is warranted."
"The functional importance of the observed synonymous change is uncertain, and the presence of an unidentified linked causal variant cannot be completely ruled out (see Conclusions). However, a functional explanation is possible because codon usage can be under strong selection30 and may have functional consequences on translation,30 RNA stability,31 and transcription.32 Notably, p6166878 changes the highest frequency valine codon (ƒGTG = 27.3%) to the lowest (ƒGTA = 7.6%) in the reference genome. This is in line with the observed phenotypic effect of the yellow mutation because a lower abundance codon is expected to be associated with lower protein expression.33 In this case, less BCO2 activity results in more carotenoid deposition in the yellow morph. In fact, we found that yellow homozygotes showed significantly lower BCO2 expression compared to pink homozygotes in the upper beak of developing embryos (Figure 1F) that were sourced from a variety of different species and islands (Table S1): small sample sizes prohibit species-specific analysis. Among the six heterozygous individuals, the pink allele was expressed more than the yellow allele in five samples tested using a droplet-digital PCR (Figure S2C). Differences in expression between the two alleles, and in the absence of alternative splice variants (STAR Methods), raise the possibility that the synonymous change alters transcription factor binding affinity in exon 4. Further research into tissue-specific expression and the specific transcription factors that regulate BCO2 is warranted."
Experimental Evidence
Authors
Enbody ED; Sprehn CG; Abzhanov A; Bi H; Dobreva MP; Osborne OG; Rubin CJ; Grant PR; et al.
... show more
Abstract
Carotenoid-based polymorphisms are widespread in populations of birds, fish, and reptiles, but generally little is known about the factors affecting their maintenance in populations. We report a combined field and molecular-genetic investigation of a nestling beak color polymorphism in Darwin's finches. Beaks are pink or yellow, and yellow is recessive. Here we show that the polymorphism arose in the Galápagos half a million years ago through a mutation associated with regulatory change in the BCO2 gene and is shared by 14 descendant species. The polymorphism is probably a balanced polymorphism, maintained by ecological selection associated with survival and diet. In cactus finches, the frequency of the yellow genotype is correlated with cactus fruit abundance and greater hatching success and may be altered by introgressive hybridization. Polymorphisms that are hidden as adults, as here, may be far more common than is currently recognized, and contribute to diversification in ways that are yet to be discovered.
Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.
Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.
Additional References
RELATED GEPHE
Related Genes
No matches found.
Related Haplotypes
No matches found.
EXTERNAL LINKS
COMMENTS
Geospiza propinqua and Geospiza acutirostris should have been included in this entry but they do not have a listed taxonomy ID. Only included species were the phenotype was described.
@parallelism
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