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An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication
Open accessPublished version of a preprint
Abstract
Teleost fishes are ancient tetraploids descended from an ancestral whole-genome duplication that may have contributed to the impressive diversification of this clade. Whole-genome duplications can occur via self-doubling (autopolyploidy) or via hybridization between different species (allopolyploidy). The mode of tetraploidization conditions evolutionary processes by which duplicated genomes return to diploid meiotic pairing, and subsequent genetic divergence of duplicated genes (cytological and genetic rediploidization). How teleosts became tetraploid remains unresolved, leaving a fundamental gap in the interpretation of their functional evolution. As a result of the whole-genome duplication, identifying orthologous and paralogous genomic regions across teleosts is challenging, hindering genome-wide investigations into their polyploid history. Here, we combine tailored gene phylogeny methodology together with a state-of-the-art ancestral karyotype reconstruction to establish the first high-resolution comparative atlas of paleopolyploid regions across 74 teleost genomes. We then leverage this atlas to investigate how rediploidization occurred in teleosts at the genome-wide level. We uncover that some duplicated regions maintained tetraploidy for more than 60 million years, with three chromosome pairs diverging genetically only after the separation of major teleost families. This evidence suggests that the teleost ancestor was an autopolyploid. Further, we find evidence for biased gene retention along several duplicated chromosomes, contradicting current paradigms that asymmetrical evolution is specific to allopolyploids. Altogether, our results offer novel insights into genome evolutionary dynamics following ancient polyploidizations in vertebrates.
Overview
AI snapshot
Written from the paper’s full text.
TL;DR
The paper builds a comparative atlas of teleost-specific whole-genome duplication (TGD) regions across 74 teleost genomes using WGD-aware gene trees and ancestral karyotype reconstruction. It finds delayed rediploidization of entire chromosomes and biased gene retention, suggesting the teleost ancestor was an autopolyploid.
Key findings
- The atlas integrates 70%–90% of each genome into 24,938 postduplication gene families across 74 teleosts; TGD ohnolog retention varies from 33% in arowana to 19% in cod.
- Ancestral chromosome pairs 3, 10, and 11 show significantly enriched sequence-synteny conflicts, and entire chromosomes continued exchanging genetic material for at least 60 million years after the TGD; among 5557 tested gene trees, 638 favored early ohnolog resolution (AORe), 1361 favored late resolution (LORe), and 3558 were not significantly different.
- Biased gene retention was found on ancestral chromosome pairs 3, 4, 7, 11, and 13, with weaker evidence for pairs 2, 5, 6, 8, and 9, but not for pairs 1, 10, and 12; this bias was not explained by differences in selective pressure or gene expression.
- Zebrafish “a”/“b” gene suffixes are inconsistent with TGD history: 43% would need reassignment, and only 26% of zebrafish genes have such suffixes in ZFIN, whereas the atlas annotates retained paralogs for 84% of zebrafish genes.
Methods
- Data and tree reconstruction: 101 vertebrate genomes including 74 teleosts; 26,692 gene families analyzed with TreeBeST, ProfileNJ, and SCORPiOs using bowfin and spotted gar as outgroups; ancestral karyotype from Nakatani and McLysaght (2017) combined with the FishComparativeAtlas pipeline.
- Rediploidization analysis: a reduced 33-genome set with three Osteoglossiformes and three Clupeocephala plus outgroups; SCORPiOs LORelEi used diagnostic sequence-synteny conflicts and likelihood AU-tests comparing AORe and LORe topologies on 5557 gene families.
- Supporting analyses: gene retention in 10-gene windows using gar/bowfin gene order as ancestral proxy; dN/dS RELAX tests on 1263 ohnolog pairs; expression from PhyloFish across 11 tissues; ZFIN suffix comparison.
Limitations
- Stated: ancestral chromosome assignments depend on the state-of-the-art pre-TGD reconstruction, and precise gene delineations may change; the atlas is based on gene family tree models that are sometimes inaccurate or incomplete, with 2832 gene trees flagged as sequence-synteny inconsistent and potentially less reliable.
- Evident: gene retention analysis assumes outgroup gene order approximates ancestral teleost gene order, and the “a”/“b” chromosome labels are arbitrary and should not be interpreted as distinct parental subgenomes.
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Claims the paper makes
7 of 55 cited sources checked · 6 supported · 0 flagged · accuracy not yet measured
- Premisecitation
Ancestral gene order is particularly difficult to reconstruct in teleosts because of an elevated rate of microsyntenic rearrangements and gene copy losses.
“Because ancestral gene order is particularly difficult to reconstruct in teleosts because of an elevated rate of microsyntenic rearrangements and gene copy losses (Inoue et al. 2015; Nakatani and McLysaght 2017)”
Quote in the paperSubstantial claim2 of 2 sources checked- cites Inoue et al. 2015 source
The Discussion reports rapid gene-copy loss and extensive rearrangements in the ancestral teleost genome after whole-genome duplication. It does not establish an elevated rate of specifically microsyntenic rearrangements or state that these changes make ancestral gene order particularly difficult to reconstruct. (LLM, conf=0.85)
Experimental — accuracy not yet measured - cites Nakatani and McLysaght 2017 source
- Interpretationown data
Our results provide the first genome-wide support for delayed rediploidization in teleosts following the TGD.
“Our results provide the first genome-wide support for delayed rediploidization in teleosts following the TGD, previously suggested as one potential explanation for the enigmatic evolutionary history of the Hox and rhodopsin genes in teleosts, and of several gene families in eels (Martin and Holland 2014; Nakamura et al. 2017; Rozenfeld et al. 2019).”
Quote in the paperSubstantial claim3 of 3 sources checked - Findingown data
The other homeologs appear as a mix of localized AORe and LORe regions, suggesting that rediploidization was ongoing.
“The other homeologs appear as a mix of localized AORe and LORe regions, suggesting that rediploidization was ongoing.”
Quote in the paperSubstantial claim - Findingown data
Zebrafish genes reassigned to a different ancestral chromosome in the comparative map are not overrepresented in synteny-inconsistent trees (7% vs. 14% for all zebrafish genes).
“Zebrafish genes reassigned to a different ancestral chromosome in our comparative map are not overrepresented in synteny-inconsistent trees (7% vs. 14% for all zebrafish genes)”
Quote in the paperSubstantial claim - Findingown data
The 26,692 WGD-aware teleost gene trees predict that the ancestral genome of teleost fish contained 46,206 genes after the duplication event.
“These 26,692 WGD-aware teleost gene trees predict that the ancestral genome of teleost fish contained 46,206 genes after the duplication event, in line with the latest estimates from the Ensembl database (49,255 ancestral teleost genes in release v100; Methods).”
Quote in the paperNot a substantial claim
- Findingown data
The comparative atlas integrates 70%-90% of each genome into 24,938 postduplication gene families.
“This comparative atlas integrates 70%–90% of each genome into 24,938 postduplication gene families (Fig. 1A,B), and greatly improves upon the state-of-the-art both in terms of species and genomic coverage.”
Quote in the paperSubstantial claim - Findingown data
Interspersed LORe genes on other homeologs are functionally enriched for different pathways, including TGF-beta signaling pathway, regulation of transferase activity, and regulation of intracellular signal transduction (corrected P-values < 0.05).
“Interspersed LORe genes on other homeologs were functionally enriched for different pathways, including “TGF-beta signaling pathway,” “regulation of transferase activity,” and “regulation of intracellular signal transduction” (corrected P-values < 0.05; Supplemental Tables S3, S4; Methods).”
Quote in the paperNot a substantial claim - Findingown data
Rediploidization was not uniform across the ancestral teleost genome.
“This snapshot of the rediploidization status at the time of the Osteoglossiformes/Clupeocephala lineage split shows that rediploidization was not uniform across the ancestral teleost genome, consistent with results in salmonids (Robertson et al. 2017; Gundappa et al. 2022).”
Quote in the paperSubstantial claim0 of 2 sources checked- cites Robertson et al. 2017 source
Checked before — its earlier verdict is held back until a new check runs.
- cites Gundappa et al. 2022
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Findingown data
In general, Osteoglossiformes, Otomorpha, and Salmoniformes species have retained more ohnologs from the TGD than other Euteleosteomorpha clades that diverged later.
“In general, Osteoglossiformes, Otomorpha, and Salmoniformes species have retained more ohnologs from the TGD than other Euteleosteomorpha clades that diverged later.”
Quote in the paperSubstantial claim - Findingown data
Even large errors in region boundaries did not majorly affect the final atlas, with only 11% of genes changing ancestral chromosome assignations at the highest noise settings.
“We found that even large errors in region boundaries did not majorly affect the final atlas, with only 11% of genes changing ancestral chromosome assignations at the highest noise settings (Supplemental Fig. S3).”
Quote in the paperSubstantial claim - Findingown data
In teleosts, there is no evidence of functional enrichments in either the AORe genes or the LORe genes carried by late-rediploidized ancestral Chromosomes 3, 10, and 11.
“In teleosts, we found no evidence of functional enrichments in either the AORe genes, which rediploidized early, or the LORe genes carried by late-rediploidized ancestral Chromosomes 3, 10, and 11.”
Quote in the paperSubstantial claim - Findingown data
There is no evidence of retention bias between ancestrally duplicated copies for chromosome pairs 1, 10, and 12.
“We however do not find evidence of retention bias between ancestrally duplicated copies for chromosome pairs 1, 10, and 12.”
Quote in the paperNot a substantial claim - Findingown data
Using the comparative atlas, we annotated which paralogs were retained for 84% of all zebrafish genes.
“Using the comparative atlas, we annotated which paralogs were retained for 84% of all zebrafish genes, providing a complementary resource that significantly extends the evolutionary annotation of gene histories in this species (Fig. 4B).”
Quote in the paperSubstantial claim - Findingown data
The comparative atlas includes similar annotations for all 74 studied teleosts.
“The comparative atlas also includes similar annotations for all 74 studied teleosts, as shown for medaka, stickleback, and tetraodon (Supplemental Fig. S11).”
Quote in the paperSubstantial claim - Findingreasoning
Only 26% of zebrafish genes are annotated with an "a" or "b" suffix in ZFIN.
“As a result, only 26% of zebrafish genes are annotated with an “a” or “b” suffix in ZFIN.”
Quote in the paperSubstantial claim - Findingown data
We find evidence for prolonged recombination between entire duplicated chromosomes after the TGD.
“We find evidence for prolonged recombination between entire duplicated chromosomes after the TGD, thus strongly suggesting that the ancestor of teleosts was an autopolyploid.”
Quote in the paperSubstantial claim - Findingown data
The no-bias result is consistent whether looking at average gene expression across 11 tissues in medaka, zebrafish, or tissue by tissue in either medaka or zebrafish.
“This result is consistent whether looking at average gene expression across 11 tissues in medaka (Fig. 3D), zebrafish (Supplemental Fig. S8), or tissue by tissue in either medaka or zebrafish (Supplemental Figs. S9, S10).”
Quote in the paperSubstantial claim - Findingown data
We find no clear correlation linking together differences in gene retention, expression level, and selective pressure.
“Here, we find no clear correlation linking together differences in gene retention, expression level, and selective pressure.”
Quote in the paperSubstantial claim - Findingown data
On ancestral chromosome pairs 8 and 13, genes of one chromosome copy experienced a significant relaxation of selection compared with their ohnologous counterparts.
“On ancestral chromosome pairs 8 and 13, genes of one chromosome copy experienced a significant relaxation of selection compared with their ohnologous counterparts (Fig. 3C).”
Quote in the paperSubstantial claim - Findingown data
Genes under relaxed selection were located on the homeolog with lower retention.
“Genes under relaxed selection were located on the homeolog with lower retention, as predicted if low-selective pressure promotes gene loss.”
Quote in the paperNot a substantial claim - Findingown data
There is additional but weaker evidence for biased gene retention on ancestral chromosome pairs 2, 5, 6, 8, and 9 in some combinations of genome comparisons.
“We find additional but weaker evidence for biased gene retention on ancestral chromosome pairs 2, 5, 6, 8, and 9 in some combinations of genome comparisons.”
Quote in the paperNot a substantial claim - Findingown data
The comparative atlas is the first high-resolution comparative atlas of paleopolyploid regions across 74 teleost genomes.
“Here, we combine tailored gene phylogeny methodology together with a state-of-the-art ancestral karyotype reconstruction to establish the first high-resolution comparative atlas of paleopolyploid regions across 74 teleost genomes.”
Quote in the paperSubstantial claim - Findingown data
There is no bias in ohnolog gene expression between ancestral chromosomes from each pair.
“We find no bias in ohnolog gene expression between ancestral chromosomes from each pair.”
Quote in the paperSubstantial claim - Findingown data
SCORPiOs flagged 2832 gene trees in which sequence identity relationships are inconsistent with their local syntenic context.
“However, we note that SCORPiOs flagged 2832 gene trees in which sequence identity relationships are inconsistent with their local syntenic context, which may represent areas in which the comparative atlas is either less reliable or biologically less informative.”
Quote in the paperNot a substantial claim - Findingown data
There is a consistent, significant bias in gene retention on ancestral chromosome pairs 3, 4, 7, 11, and 13, in which genes were preferentially retained on one homeolog over the other, regardless of study species.
“We uncover a consistent, significant bias in gene retention on ancestral chromosome pairs 3, 4, 7, 11, and 13, in which genes were preferentially retained on one homeolog over the other, regardless of study species.”
Quote in the paperSubstantial claim - Findingown data
We found only few discrepancies between megabase-scale regions predicted to descend from the same ancestral chromosome from Nakatani and McLysaght (2017) and paralogy relationships predicted at gene-to-gene resolution by our gene trees.
“We have previously shown that SCORPiOs significantly improves gene tree accuracy after a WGD event (Parey et al. 2020), and we found only few discrepancies between megabase-scale regions predicted to descend from the same ancestral chromosome from Nakatani and McLysaght (2017) and paralogy relationships predicted at gene-to-gene resolution by our gene trees.”
Quote in the paperNot a substantial claim - Findingown data
The preferential gene retention is not an artifact of the atlas construction because conservatively assigning genes unassigned to either duplicated chromosome to the homeolog with the lowest retention did not offset the retention imbalance.
“This preferential gene retention is not an artifact of the atlas construction because of genes unassigned to either duplicated chromosome: indeed, conservatively assigning such genes to the homeolog with the lowest retention did not offset the retention imbalance (Supplemental Table S6).”
Quote in the paperSubstantial claim - Interpretationown data
The enrichment of sequence-synteny conflicts in chromosome pairs 3, 10, and 11 hints toward prolonged recombination between these homeologs after the TGD.
“thus hinting toward prolonged recombination between these homeologs after the TGD”
Quote in the paperSubstantial claim - Interpretationown data
The comparative atlas greatly improves upon the state of the art in both species and genomic coverage.
“and greatly improves upon the state-of-the-art both in terms of species and genomic coverage.”
Quote in the paperNot a substantial claim - Study design and conductown data
Random noise simulations show that the comparative atlas is robust to potential uncertainty or errors in the original ancestral genome reconstruction.
“Additionally, we used random noise simulations to show that the comparative atlas is robust to potential uncertainty or errors in the original ancestral genome reconstruction.”
Quote in the paperSubstantial claim - Premisecitation
Nakatani and McLysaght delineated between 353 and 690 megabase-scale genomic regions that descend from the 13 ancestral chromosomes in zebrafish, tetraodon, stickleback, and medaka.
“Nakatani and McLysaght delineated between 353 and 690 megabase-scale genomic regions that descend from these 13 ancestral chromosomes in zebrafish, tetraodon, stickleback, and medaka.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Nakatani and McLysaght 2017 source
- Interpretationown data
The higher discrepancy in zebrafish likely reflects small-scale rearrangements in zebrafish captured by individual gene trees but missed by the macrosyntenic approach of Nakatani and McLysaght.
“This likely reflects small-scale rearrangements in zebrafish captured by our individual gene trees but missed by the macrosyntenic approach of Nakatani and McLysaght (2017).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Nakatani and McLysaght 2017 source
- Premisereasoning
Auto- and allopolyploidization differentially shape the rediploidization process.
“In particular, auto- and allopolyploidization differentially shape the rediploidization process, that is, how the polyploid genome returns to a largely diploid state over time.”
Quote in the paperSubstantial claim - Study design and conductown data
Correcting gene trees with SCORPiOs had a decisive impact on the establishment of the comparative atlas, enabling the inclusion of a significantly larger fraction of teleost genes (83% vs. 61%).
“Finally, we report that correcting gene trees with SCORPiOs had a decisive impact on the establishment of the comparative atlas, enabling the inclusion of a significantly larger fraction of teleost genes (83% vs. 61%; Supplemental Fig. S4).”
Quote in the paperSubstantial claim - Interpretationown data
The prolonged exchange of genetic material between duplicated chromosomes after the TGD strongly suggests that the teleost ancestor was an autotetraploid.
“This prolonged exchange of genetic material between duplicated chromosomes after the TGD strongly suggests that the teleost ancestor was an autotetraploid.”
Quote in the paperSubstantial claim - Premisecitation
After allotetraploidization, one of the two subgenomes often loses more genes than the other.
“After allotetraploidization, one of the two subgenomes often loses more genes than the other (Garsmeur et al. 2014; Session et al. 2016; Cheng et al. 2018), although not always (Sun et al. 2017).”
Quote in the paperNot a substantial claim0 of 3 sources checked - Interpretationown data
The orthology relationships and chromosomal reassignations of reassigned zebrafish genes are overall well-supported by their sequences and syntenic gene neighborhoods.
“suggesting that their orthology relationships and chromosomal reassignations are overall well-supported by their sequences and syntenic gene neighborhoods.”
Quote in the paperSubstantial claim - Interpretationown data
Biased gene retention cannot be considered as reliable evidence in favor of allopolyploidization in vertebrates.
“We highlight that biased gene retention cannot be considered as reliable evidence in favor of allopolyploidization in vertebrates, as we provide formal evidence that the same chromosomes can initially recombine and then experience biased gene retention, suggesting that this bias is unrelated to initial sequence divergence in teleosts.”
Quote in the paperSubstantial claim - Interpretationreasoning
Gene annotations are unhelpful to study large-scale processes such as chromosome evolution or genome-wide rediploidization.
“Gene annotations are therefore unhelpful to study large-scale processes such as chromosome evolution or genome-wide rediploidization.”
Quote in the paperNot a substantial claim - Interpretationreasoning
"a" and "b" gene assignments are not informative of the underlying sequence information contained in genomic regions that showed delayed rediploidization.
“As such, “a” and “b” gene assignments are not informative of the underlying sequence information contained in genomic regions that showed delayed rediploidization, and these genes should be considered as tetralogs rather than paralogs and orthologs (Martin and Holland 2014; Robertson et al. 2017).”
Quote in the paperSubstantial claim0 of 2 sources checked - Interpretationreasoning
The bias in gene retention is unrelated to initial sequence divergence in teleosts.
“We highlight that biased gene retention cannot be considered as reliable evidence in favor of allopolyploidization in vertebrates, as we provide formal evidence that the same chromosomes can initially recombine and then experience biased gene retention, suggesting that this bias is unrelated to initial sequence divergence in teleosts.”
Quote in the paperSubstantial claim - Interpretationreasoning
Delayed rediploidization has profound consequences on the dynamics of gene evolution.
“Second, delayed rediploidization has profound consequences on the dynamics of gene evolution.”
Quote in the paperSubstantial claim - Study design and conductreasoning
This ancestral gene number is an indirect but accurate approximation of the quality of inferred gene trees.
“This ancestral gene number is an indirect but accurate approximation of the quality of inferred gene trees, because the major challenge is to accurately position duplications at this ancestral node.”
Quote in the paperSubstantial claim - Premisecitation
The atlas is ultimately based on gene family tree models, which are sometimes inaccurate or incomplete.
“Second, although we show that the comparative atlas is resilient to species-specific errors in ancestral chromosome or gene orthology group assignations owing to the redundant information provided by multiple species, the atlas is ultimately based on gene family tree models, which are sometimes inaccurate or incomplete (Hahn 2007; Som 2015).”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites Hahn 2007 source
Checked before — its earlier verdict is held back until a new check runs.
- cites Som 2015
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Interpretationown data
The biased gene retention along several duplicated chromosomes contradicts current paradigms that asymmetrical evolution is specific to allopolyploids.
“contradicting current paradigms that asymmetrical evolution is specific to allopolyploids.”
Quote in the paperSubstantial claim - Interpretationown data
Differences in selective pressures do not explain the observed bias in gene retention.
“Thus, differences in selective pressures do not explain the observed bias in gene retention.”
Quote in the paperSubstantial claim - Interpretationreasoning
There are no strict 1:1 orthology relationships between duplicated genes across species that separated before meiosis resolution.
“However, in this evolutionary scenario, ohnolog sequences only start diverging once recombination is suppressed, which implies that there are no strict 1:1 orthology relationships between duplicated genes across species that separated before meiosis resolution.”
Quote in the paperSubstantial claim - Interpretationreasoning
"a" and "b" chromosomes should not be interpreted as distinct parental subgenomes of allopolyploidization.
“As the TGD is likely an autopolyploidization event, “a” and “b” correspond to different chromosome copies and are interchangeable for each chromosome pair—“a” and “b” chromosomes should not be interpreted as distinct parental subgenomes of allopolyploidization.”
Quote in the paperSubstantial claim - Interpretationown data
The ancestor of teleosts was an autopolyploid.
“We find evidence for prolonged recombination between entire duplicated chromosomes after the TGD, thus strongly suggesting that the ancestor of teleosts was an autopolyploid.”
Quote in the paperSubstantial claim - Interpretationreasoning
The genetic and functional divergence of these genes has occurred independently in each subsequent lineage.
“The genetic and functional divergence of these genes has occurred independently in each subsequent lineage, and further inquiry will reveal whether these specific evolutionary dynamics have contributed to lineage-specific evolution in the major teleost clades, as described in salmonids (Robertson et al. 2017; Gundappa et al. 2022).”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites Robertson et al. 2017 source
Checked before — its earlier verdict is held back until a new check runs.
- cites Gundappa et al. 2022
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Premisecitation
Biased gene retention is a character more frequently observed in allopolyploids.
“In summary, we find that genes were preferentially retained on one duplicated chromosome in a subset of ancestral chromosomes, a character more frequently observed in allopolyploids (Garsmeur et al. 2014; Cheng et al. 2018).”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites Garsmeur et al. 2014
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- cites Cheng et al. 2018 source
- Interpretationnone given
AORe and LORe tree topologies can be distinguished when at least one teleost group (Osteoglossiformes or Clupeocephala) retained both ohnologs, although not necessarily in the same species.
“In practice, these topologies can be distinguished when at least one teleost group (Osteoglossiformes or Clupeocephala) retained both ohnologs, although not necessarily in the same species.”
Quote in the paperSubstantial claim - Interpretationreasoning
In this evolutionary scenario, ohnolog sequences only start diverging once recombination is suppressed.
“However, in this evolutionary scenario, ohnolog sequences only start diverging once recombination is suppressed, which implies that there are no strict 1:1 orthology relationships between duplicated genes across species that separated before meiosis resolution.”
Quote in the paperSubstantial claim - Interpretationreasoning
Inaccurate trees may result in local misspecifications of gene paralogs or ancestral assignations in the comparative atlas.
“Inaccurate trees may result in local misspecifications of gene paralogs or ancestral assignations in the comparative atlas.”
Quote in the paperNot a substantial claim - Interpretationown data
Biased gene retention following autopolyploidization may be driven by distinct and underappreciated factors.
“However, we find that biased gene retention in teleosts is not correlated with other features classically observed in allopolyploids, and our results suggest that biased gene retention can occur following autopolyploidization, possibly driven by distinct and underappreciated factors.”
Quote in the paperSubstantial claim - Study design and conductreasoning
The comparative atlas is resilient to species-specific errors in ancestral chromosome or gene orthology group assignations owing to the redundant information provided by multiple species.
“Second, although we show that the comparative atlas is resilient to species-specific errors in ancestral chromosome or gene orthology group assignations owing to the redundant information provided by multiple species, the atlas is ultimately based on gene family tree models, which are sometimes inaccurate or incomplete (Hahn 2007; Som 2015).”
Quote in the paperNot a substantial claim - Interpretationreasoning
Biased gene retention can occur following autopolyploidization.
“However, we find that biased gene retention in teleosts is not correlated with other features classically observed in allopolyploids, and our results suggest that biased gene retention can occur following autopolyploidization, possibly driven by distinct and underappreciated factors.”
Quote in the paperSubstantial claim - Interpretationown data
Biased gene retention in teleosts is not correlated with other features classically observed in allopolyploids.
“However, we find that biased gene retention in teleosts is not correlated with other features classically observed in allopolyploids, and our results suggest that biased gene retention can occur following autopolyploidization, possibly driven by distinct and underappreciated factors.”
Quote in the paperSubstantial claim
- Probably not a substantial claim. 36
- It may state two separate claims as one. 25
- The quote only partly states this claim. 2
Probably not a substantial claim. The paper’s conclusions may not depend on it.
Premisecitation26% of all zebrafish genes are still retained as duplicated ohnologs.
“For instance, 26% of all zebrafish genes are still retained as duplicated ohnologs (Howe et al. 2013).”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites Howe et al. 2013 source
Probably not a substantial claim. The paper’s conclusions may not depend on it.
PremisecitationSCORPiOs significantly improves gene tree accuracy after a WGD event.
“We have previously shown that SCORPiOs significantly improves gene tree accuracy after a WGD event (Parey et al. 2020), and we found only few discrepancies between megabase-scale regions predicted to descend from the same ancestral chromosome from Nakatani and McLysaght (2017) and paralogy relationships predicted at gene-to-gene resolution by our gene trees.”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites Parey et al. 2020 source
It may state two separate claims as one.
Findingown dataThe col12a1a-col12a1b ohnologs had stopped recombining and accumulated independent substitutions by the time Osteoglossiformes and Clupeocephala diverged.
“For example, the col12a1a - col12a1b ohnologs had stopped recombining and accumulated independent substitutions by the time Osteoglossiformes and Clupeocephala diverged (Fig. 2C).”
Quote in the paperNot a substantial claimIt may state two separate claims as one.
Findingown dataAncestral chromosome pairs 3, 10, and 11 had not yet rediploidized when teleosts started diversifying, with large runs of LORe ohnologous families spanning the entire length of their descendant chromosomes in medaka (Chromosomes 2, 3, 6, 21, and 23).
“This visualization revealed that ancestral chromosome pairs 3, 10, and 11 had not yet rediploidized when teleosts started diversifying, with large runs of LORe ohnologous families spanning the entire length of their descendant chromosomes in medaka (Chromosomes 2, 3, 6, 21, and 23).”
Quote in the paperSubstantial claimThe quote only partly states this claim.
Findingown dataBiased gene retention occurred along several duplicated chromosomes after the TGD.
“Further, we find evidence for biased gene retention along several duplicated chromosomes”
Quote in the paperSubstantial claimIt may state two separate claims as one.
Findingown dataSome duplicated regions, including entire chromosomes, maintained tetraploidy and continued exchanging genetic material for at least 60 million years after the TGD, with three chromosome pairs diverging only after the separation of major teleost families.
“We uncover that some duplicated regions maintained tetraploidy for more than 60 million years, with three chromosome pairs diverging genetically only after the separation of major teleost families.”
- Also stated in: § The teleost duplication was followed by delayed rediploidization · boosted
“Altogether, we provide the first evidence that entire chromosomes experienced delayed rediploidization in teleosts and continued to exchange genetic material between homeologs for at least 60 million years after the teleost whole genome duplication.”
Quote in the paperSubstantial claim- Also stated in: § The teleost duplication was followed by delayed rediploidization · boosted
The quote only partly states this claim.
Findingown dataAncestral chromosome pairs 3, 10, and 11 are significantly enriched in sequence-synteny conflicts (P < 0.05, hypergeometric tests corrected for multiple testing).
“Three anciently duplicated chromosome pairs (3, 10, and 11) are significantly enriched in sequence-synteny conflicts”
Quote in the paperSubstantial claimIt may state two separate claims as one.
Findingnone givenThe map1aa-map1ab TGD ohnologs presumably still recombined when the taxa diverged, and both ohnologs diverged independently later on in each lineage.
“On the other hand, the map1aa - map1ab TGD ohnologs presumably still recombined when the taxa diverged, and both ohnologs diverged independently later on in each lineage (Fig. 2D).”
Quote in the paperNot a substantial claimIt may state two separate claims as one.
Findingown dataFor 638 gene trees, the early resolution topology (AORe) was significantly more likely, whereas the late resolution topology (LORe) was favored for 1361 trees; no significant differences were found for the remaining 3558 trees.
“For 638 gene trees, the early resolution topology (AORe) was significantly more likely, whereas the late resolution topology (LORe) was favored for 1361 trees (likelihood AU-tests, alternative topology rejected at α = 0.05; no significant differences for the remaining 3558 trees).”
Quote in the paperSubstantial claimIt may state two separate claims as one.
Findingown data9% of zebrafish genes differ in ancestral chromosome assignation between the comparative map and the pre-TGD karyotype, versus 2%-3% in medaka, tetraodon, or stickleback.
“We found that 9% of zebrafish genes differ in ancestral chromosome assignation between our comparative map and the pre-TGD karyotype, versus 2%–3% in medaka, tetraodon, or stickleback.”
Quote in the paperSubstantial claimIt may state two separate claims as one.
Findingown dataTeleost fishes vary substantially in their retention of duplicated gene copies (ohnologs) since the TGD, which make up 33% of the arowana genome but only 19% of the cod genome.
“The atlas reveals that teleost fishes vary substantially in their retention of duplicated gene copies (ohnologs) since the TGD, which make up 33% of the arowana genome but only 19% of the cod genome (Supplemental Table S2).”
Quote in the paperSubstantial claimIt may state two separate claims as one.
Findingown dataWe identified 8144 teleost gene subtrees out of 17,493 (47%) that were inconsistent with synteny information, of which 5611 could be corrected (32% of all subtrees).
“We identified 8144 teleost gene subtrees out of 17,493 (47%) that were inconsistent with synteny information, of which 5611 could be corrected (32% of all subtrees).”
Quote in the paperSubstantial claimProbably not a substantial claim. The paper’s conclusions may not depend on it.
Findingnone givenThe corrected-to-inconsistent tree ratio (69%) is comparable to our previous application of SCORPiOs to fish data.
“We note that the corrected-to-inconsistent tree ratio (69%) is comparable to our previous application of SCORPiOs to fish data.”
Quote in the paperNot a substantial claimIt may state two separate claims as one.
Findingown dataHomeologs with significant differences in selective pressure correspond only to two out of six chromosomes showing strongly biased gene retention (n = 13; P = 0.1923; Fisher's exact test), with nonsignificant differences in selective pressure in the same direction as the gene retention bias for two chromosome pairs (4 and 11) and in the opposite direction for the two others (3 and 7).
“However, homeologs with significant differences in selective pressure correspond only to two out of six chromosomes showing strongly biased gene retention (n = 13; P = 0.1923; Fisher's exact test), with nonsignificant differences in selective pressure in the same direction as the gene retention bias for two chromosome pairs (4 and 11) and in the opposite direction for the two others (3 and 7).”
Quote in the paperSubstantial claimProbably not a substantial claim. The paper’s conclusions may not depend on it.
FindingcitationThe proportion of errors in initial sequence-based gene trees is in line with our previous application of SCORPiOs to a data set of 47 teleost species.
“Similarly, the proportion of errors in initial sequence-based gene trees is in line with our previous application of SCORPiOs to a data set of 47 teleost species (Parey et al. 2020).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Parey et al. 2020 source
Checked before — its earlier verdict is held back until a new check runs.
Probably not a substantial claim.
Findingnone givenIn the comparative atlas, "a" and "b" labels are arbitrarily assigned to duplicated chromosomes, such that genes descended from Chromosomes 1a and 1b could be swapped to 1b and 1a.
“In the comparative atlas, “a” and “b” labels are arbitrarily assigned to duplicated chromosomes; that is, genes descended from Chromosomes 1a and 1b could be swapped to 1b and 1a.”
Quote in the paperSubstantial claimProbably not a substantial claim.
Findingnone givenThe comparative genomic atlas is the first resource that allows an in-depth, genome-wide analysis of the TGD and the early genome evolution processes that followed it.
“The comparative genomic atlas is the first resource that allows an in-depth, genome-wide analysis of the TGD, and in particular of the early genome evolution processes that followed after the TGD.”
Quote in the paperSubstantial claimIt may state two separate claims as one.
PremisecitationAll teleost fish species are paleopolyploids descended from an ancient whole-genome duplication dated at approximately 320 Mya.
“All teleost fish species are paleopolyploids descended from an ancient round of whole-genome duplication (WGD), dated at approximately 320 Mya (Jaillon et al. 2004).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Jaillon et al. 2004 source
Probably not a substantial claim. The paper may give no reason why it holds.
Premisenone givenCytological rediploidization, the return to bivalent meiotic pairing, is necessary to enable diploid inheritance of two distinct duplicated regions in the genome.
“Cytological rediploidization, that is, the return to bivalent meiotic pairing, is necessary to enable the diploid inheritance of two distinct duplicated regions in the genome.”
Quote in the paperNot a substantial claimProbably not a substantial claim. The paper’s conclusions may not depend on it.
PremisecitationMaintenance of tetraploidy for millions of years over entire homeologs has been previously shown following autotetraploidization events in salmonids and Acipenseriformes.
“Maintenance of tetraploidy for millions of years over entire homeologs has been previously shown following autotetraploidization events in salmonids and Acipenseriformes (Robertson et al. 2017; Gundappa et al. 2022; Redmond et al. 2022).”
Quote in the paperNot a substantial claim0 of 3 sources checked- cites Robertson et al. 2017 source
Checked before — its earlier verdict is held back until a new check runs.
- cites Gundappa et al. 2022
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- cites Redmond et al. 2022
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
PremisecitationWhole-genome duplication can arise through autopolyploidization or allopolyploidization, with different consequences on subsequent genome evolution.
“WGD can arise through two mechanisms: autopolyploidization (within or between populations of a single species) or allopolyploidization (after hybridization of related species), with different consequences on subsequent genome evolution (Stebbins 1947; Mason and Wendel 2020).”
Quote in the paperNot a substantial claim0 of 2 sources checkedProbably not a substantial claim. The paper’s conclusions may not depend on it.
PremisecitationIt remains unclear whether the teleost whole-genome duplication corresponds to an ancestral auto- or allotetraploidization event.
“It remains unclear whether the teleost whole-genome duplication corresponds to an ancestral auto- or an allotetraploidization event, a significant gap in our understanding of the early vertebrate evolutionary processes that led to the diversification of teleosts (Martin and Holland 2014; Conant 2020).”
Quote in the paperNot a substantial claim0 of 2 sources checkedProbably not a substantial claim. It may state two separate claims as one.
PremisereasoningYoung autopolyploid genomes are characterized by multivalent meiotic behavior and tetrasomic inheritance, with recombination and gene conversion occurring between homeologous chromosomes.
“Because of the initial sequence similarity between duplicated chromosomes (homeologs), young autopolyploid genomes are characterized by multivalent meiotic behavior and tetrasomic inheritance, with recombination and gene conversion occurring between homeologous chromosomes.”
Quote in the paperSubstantial claimProbably not a substantial claim.
PremisereasoningIn autopolyploidy, gene losses are expected to affect both homeologs equally owing to their high similarity.
“Conversely, in the case of autopolyploidy, gene losses are expected to affect both homeologs equally owing to their high similarity.”
Quote in the paperSubstantial claimProbably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds. It may state two separate claims as one.
Premisenone givenHomeologous exchange events typically concern a minor fraction of allopolyploid genomes (<3%) and have never been shown to be maintained over millions of years.
“These events typically concern a minor fraction of allopolyploid genomes (<3%), and have never been shown to be maintained over millions of years.”
Quote in the paperNot a substantial claimIt may state two separate claims as one.
PremisecitationPrevious characterizations of double-conserved syntenic regions in teleosts were limited to regions of highly conserved gene order or small species sets; the largest multispecies data set comprised eight fish species and included about 29% of all genes in DCS regions.
“Previous characterizations of DCS regions in teleosts were therefore limited to regions of highly conserved gene order or small species sets: the largest multispecies data set comprised eight fish species and included ∼29% of all genes in DCS regions (Conant 2020).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Conant 2020 source
Checked before — its earlier verdict is held back until a new check runs.
It may state two separate claims as one.
Premisenone givenIn salmonids and Acipenseriformes, rediploidization has been an extended process, with some duplicated genomic regions quickly restoring diploid behavior and others maintaining tetraploidy for tens of millions of years.
“In these clades, rediploidization has been an extended process, with some duplicated genomic regions quickly restoring diploid behavior, whereas others have maintained tetraploidy for tens of millions of years.”
Quote in the paperSubstantial claimProbably not a substantial claim. The paper’s conclusions may not depend on it.
PremisecitationLocalized homeologous exchanges have been observed in allopolyploids, including allopolyploid crops and paleopolyploid carps.
“Localized homeologous exchanges, in which sequences from one subgenome are substituted by sequences from the other, have been observed in allopolyploids, including allopolyploid crops and paleopolyploid carps (Lloyd et al. 2018; Li et al. 2021).”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites Lloyd et al. 2018
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- cites Li et al. 2021
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
PremisecitationThe ancestral teleost karyotype comprised 13 chromosomes.
“According to the state-of-the-art reference, this ancestral teleost karyotype comprised 13 chromosomes (Nakatani and McLysaght 2017).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Nakatani and McLysaght 2017 source
Probably not a substantial claim. The paper’s conclusions may not depend on it.
Premisenone givenUnequal gene retention after allotetraploidization has been linked to differences in transposable element repertoires and epigenetic silencing in the two subgenomes.
“This unequal gene retention has been linked to differences in transposable element repertoires and epigenetic silencing in the two subgenomes, and orients further functional evolution.”
Quote in the paperNot a substantial claimProbably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.
Premisenone givenAfter allopolyploidization events, the extent of duplicated chromosome pairing depends on genetic similarity between the parental genomes.
“In contrast, after allopolyploidization events, the extent of duplicated chromosome pairing depends on genetic similarity between the parental genomes.”
Quote in the paperNot a substantial claimIt may state two separate claims as one.
Interpretationown dataThe teleost comparative genomic atlas represents a reliable, comprehensive, and robust resource for fish genomics.
“The teleost comparative genomic atlas represents therefore a reliable, comprehensive, and robust resource for fish genomics.”
Quote in the paperSubstantial claimProbably not a substantial claim. The authors may not put it forward as true. It may state two separate claims as one.
PremisecitationGenes on silenced chromosome copies are expressed at lower levels, and therefore subjected to lower selective pressures and ultimately to pseudogenization.
“Genes on silenced chromosome copies are expressed at lower levels, and therefore subjected to lower selective pressures and ultimately to pseudogenization.”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites Freeling et al. 2012 source
- cites Bird et al. 2021
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
Probably not a substantial claim. The paper may give no reason why it holds.
Interpretationnone givenThe TGD is likely an autopolyploidization event.
“As the TGD is likely an autopolyploidization event, “a” and “b” correspond to different chromosome copies and are interchangeable for each chromosome pair—“a” and “b” chromosomes should not be interpreted as distinct parental subgenomes of allopolyploidization.”
Quote in the paperNot a substantial claimProbably not a substantial claim. It may be too vague to check against evidence.
Interpretationown dataThe atlas is generally accurate.
“This suggests that the atlas is generally accurate.”
Quote in the paperNot a substantial claimProbably not a substantial claim.
PremisecitationZFIN guidelines recommend that adjacent genes should carry the same suffix when they belong to a continuous syntenic block inherited since the TGD, sometimes called syntelogs.
“ZFIN guidelines recommend that adjacent genes should carry the same suffix when they belong to a continuous syntenic block inherited since the TGD, sometimes called syntelogs (Zhao et al. 2017).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Zhao et al. 2017 source
Probably not a substantial claim. It may be too vague to check against evidence. The paper’s conclusions may not depend on it.
InterpretationreasoningThe precise delineation of genes descending from each of the 13 ancestral groups may be subject to modifications as the field evolves.
“There is a general consensus that the ancestral teleost genome contained 13 chromosomes (Kasahara et al. 2007; Nakatani and McLysaght 2017)—however, the precise delineation of genes descending from each of those 13 groups may be subject to modifications as the field evolves, which may lead to updates in the ancestral assignations of the regions in the comparative atlas.”
Quote in the paperNot a substantial claimProbably not a substantial claim. It may state two separate claims as one.
PremisecitationZFIN provides manually curated, high-quality reference annotations for zebrafish genes and implements rigorous conventions for gene naming.
“The Zebrafish Information Network (ZFIN) provides manually curated, high-quality reference annotations for zebrafish genes and implements rigorous conventions for gene naming (Ruzicka et al. 2019).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Ruzicka et al. 2019
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
It may state two separate claims as one.
PremisecitationTreeBeST systematically infers a number of gene duplication nodes that are overly old and poorly supported.
“Although TreeBeST remains the most efficient method to build gene trees for large data sets (Noutahi et al. 2016), it systematically infers a number of gene duplication nodes that are overly old and poorly supported (Hahn 2007).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Hahn 2007 source
Checked before — its earlier verdict is held back until a new check runs.
It may state two separate claims as one.
Interpretationreasoning"a" and "b" correspond to different chromosome copies and are interchangeable for each chromosome pair.
“As the TGD is likely an autopolyploidization event, “a” and “b” correspond to different chromosome copies and are interchangeable for each chromosome pair—“a” and “b” chromosomes should not be interpreted as distinct parental subgenomes of allopolyploidization.”
Quote in the paperSubstantial claimProbably not a substantial claim. It may be too vague to check against evidence.
InterpretationcitationGenes in genomic regions that showed delayed rediploidization should be considered as tetralogs rather than paralogs and orthologs.
“As such, “a” and “b” gene assignments are not informative of the underlying sequence information contained in genomic regions that showed delayed rediploidization, and these genes should be considered as tetralogs rather than paralogs and orthologs (Martin and Holland 2014; Robertson et al. 2017).”
Quote in the paperNot a substantial claim0 of 2 sources checkedProbably not a substantial claim. The paper’s conclusions may not depend on it.
PremisecitationThere is a general consensus that the ancestral teleost genome contained 13 chromosomes.
“There is a general consensus that the ancestral teleost genome contained 13 chromosomes (Kasahara et al. 2007; Nakatani and McLysaght 2017)—however, the precise delineation of genes descending from each of those 13 groups may be subject to modifications as the field evolves, which may lead to updates in the ancestral assignations of the regions in the comparative atlas.”
Quote in the paperNot a substantial claim0 of 2 sources checkedProbably not a substantial claim. The paper’s conclusions may not depend on it.
PremisecitationBiased gene retention is generally considered a hallmark of allopolyploidization.
“Biased gene retention is generally considered a hallmark of allopolyploidization (Garsmeur et al. 2014), but has mostly been observed in plants, and the mechanisms of gene retention in polyploid vertebrate genomes may differ.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Garsmeur et al. 2014
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
Probably not a substantial claim.
PremisecitationPrevious observations on a limited subset of genes suggested that the ancestral teleost genome experienced biased gene retention after the TGD.
“Previous observations on a limited subset of genes have suggested that the ancestral teleost genome has experienced biased gene retention after the TGD (Conant 2020).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Conant 2020 source
Checked before — its earlier verdict is held back until a new check runs.
Probably not a substantial claim. It may state two separate claims as one.
PremisecitationRELAX estimates dN/dS distributions across sites on the sets of "a" and "b" branches and fits a selection intensity parameter "k", which captures the extent of selection intensification (k > 1) or relaxation (k < 1).
“Briefly, RELAX estimates dN/dS distributions across sites on the sets of “a” and “b” branches and fits a selection intensity parameter “k”, which captures the extent of selection intensification (k > 1) or relaxation (k < 1).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Wertheim et al. 2015 source
Probably not a substantial claim. It may state two separate claims as one.
PremisecitationPrevious studies have highlighted that allopolyploid subgenomes are often subjected to asymmetrical evolution, whereas in autopolyploids all chromosome copies are highly similar and equally affected by rediploidization.
“Previous studies have highlighted the contrasting genomic implications of allopolyploidization and autopolyploidization, in which the two subgenomes of allopolyploids are often—although not systematically—subjected to asymmetrical evolution, whereas in autopolyploids all chromosome copies are highly similar and equally affected by the rediploidization process (Garsmeur et al. 2014; Cheng et al. 2”
Quote in the paperSubstantial claim0 of 2 sources checked- cites Garsmeur et al. 2014
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- cites Cheng et al. 2018 source
Probably not a substantial claim. The paper’s conclusions may not depend on it.
PremisecitationBiased gene retention has mostly been observed in plants.
“Biased gene retention is generally considered a hallmark of allopolyploidization (Garsmeur et al. 2014), but has mostly been observed in plants, and the mechanisms of gene retention in polyploid vertebrate genomes may differ.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Garsmeur et al. 2014
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
PremisecitationAfter whole-genome duplication, duplicated gene copies can diverge and undergo specialized evolution by partitioning ancestral functions (subfunctionalization) or acquiring new expression patterns (neofunctionalization).
“After whole-genome duplication, duplicated gene copies can diverge and undergo specialized evolution by partitioning ancestral functions (subfunctionalization) or acquiring new expression patterns (neofunctionalization) (Ohno et al. 1968; Force et al. 1999; Lynch and Conery 2000).”
Quote in the paperNot a substantial claim0 of 3 sources checkedIt may state two separate claims as one.
Interpretationown dataThe same chromosomes can initially recombine and then experience biased gene retention.
“We highlight that biased gene retention cannot be considered as reliable evidence in favor of allopolyploidization in vertebrates, as we provide formal evidence that the same chromosomes can initially recombine and then experience biased gene retention, suggesting that this bias is unrelated to initial sequence divergence in teleosts.”
Quote in the paperSubstantial claimProbably not a substantial claim. It may be too vague to check against evidence.
InterpretationreasoningThe annotations of chromosomal copies in the comparative atlas should not be misinterpreted as two distinct parental subsets.
“First, as the ancestral teleost was a probable autotetraploid, the formal distinction between ancestral subgenomes is irrelevant, and the annotations of chromosomal copies in the comparative atlas should not be misinterpreted as two distinct parental subsets, in which all “a” chromosomes (or “b”) descend from a single parental genome.”
Quote in the paperNot a substantial claimProbably not a substantial claim. The paper may give no reason why it holds. It may state two separate claims as one.
Interpretationnone givenAs the ancestral teleost was a probable autotetraploid, the formal distinction between ancestral subgenomes is irrelevant.
“First, as the ancestral teleost was a probable autotetraploid, the formal distinction between ancestral subgenomes is irrelevant, and the annotations of chromosomal copies in the comparative atlas should not be misinterpreted as two distinct parental subsets, in which all “a” chromosomes (or “b”) descend from a single parental genome.”
Quote in the paperNot a substantial claimProbably not a substantial claim. It may be too vague to check against evidence. The paper’s conclusions may not depend on it.
Interpretationown dataThese flagged areas may represent areas in which the comparative atlas is either less reliable or biologically less informative.
“However, we note that SCORPiOs flagged 2832 gene trees in which sequence identity relationships are inconsistent with their local syntenic context, which may represent areas in which the comparative atlas is either less reliable or biologically less informative.”
Quote in the paperNot a substantial claimProbably not a substantial claim. The authors may not put it forward as true.
PremisecitationPrevious observations have suggested that biased gene retention in allopolyploid genomes reflects partial epigenetic silencing of one parental subgenome.
“Previous observations have suggested that biased gene retention in allopolyploid genomes reflects partial epigenetic silencing of one parental subgenome (Freeling et al. 2012; Bird et al. 2021).”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites Freeling et al. 2012 source
- cites Bird et al. 2021
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
Study design and conductnone givenThe assignations to ancestral chromosomes before the TGD are only as good as the state-of-the-art ancestral genome reconstruction.
“First, the assignations to ancestral chromosomes before the TGD are only as good as the state-of-the-art ancestral genome reconstruction.”
Quote in the paperNot a substantial claim
The paper relies on this without support.
The teleost-specific genome duplication doubled all chromosomes and genes present in the teleost ancestor.
“This evolutionary event, referred to as the teleost-specific genome duplication (TGD), doubled all chromosomes and genes present in the teleost ancestor.”
The paper relies on this without support.
After a whole-genome duplication, orthologous genes are expected to be embedded in orthologous neighborhoods.
“After a WGD, orthologous genes are expected to be embedded in orthologous neighborhoods.”
The paper relies on this without support.
ZFIN gene names are propagated to orthologous genes in other teleost genomes, providing the basis of the entire teleost gene nomenclature and functional annotation transfers.
“These gene names are then propagated to orthologous genes in other teleost genomes, providing the basis of the entire teleost gene nomenclature and functional annotation transfers.”
The authors state this as an assumption.
Consecutive genes on the outgroup genome, all assigned to the same preduplication chromosome, represent the ancestral gene order.
“Here, we make the assumption that consecutive genes on the outgroup genome, all assigned to the same preduplication chromosome, represent the ancestral gene order.”
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
Each contradiction between two passages listed here was confirmed by an independent check.
Expression analysis points to the selective-pressure figure panel
MinorThe expression-analysis method cites Figure 3C, but the figure caption assigns selective pressure to panel C and average expression to panel D.
“Average expression across tissue (Fig. 3C; Supplemental Fig. S8) and by-tissue expression (Supplemental Figs. S9, S10) were calculated for ohnologs grouped by their ancestral chromosome of origin.”
“(C) Number of genes experiencing relaxed selection compared with their ohnolog across homeologs (Methods; Fisher's exact tests with Benjamini–Hochberg correction for multiple testing, P-values as in B). (D) Average expression across tissues in medaka.”
Vertebrate genome count includes nonvertebrates
MinorThe listed genomes total 101, but only 96 are vertebrates: 74 teleosts, two other fish, and 20 other vertebrates. The remaining five are explicitly described as nonvertebrates.
Reported 101 · recomputed 96
“We collected a data set of 101 vertebrate genomes, including 74 teleost fish, two nonteleost fish (bowfin and spotted gar, which did not undergo the teleost genome duplication or TGD), 20 other vertebrates of which six are mammals, and five nonvertebrate genomes”
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Metadata
- Authors
- Parey, E., Louis, A., Montfort, J., Guiguen, Y., Crollius, H. R., & Berthelot, C.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR)
- Corresponding author
- Crollius, Hugues Roest
- Berthelot, Camille
- ORCID
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2022-08-12
- Volume
- 32
- Issue
- 9
- Pages
- 1685-1697
- ISSN
- 1088-9051 (ISSN-L)
- 1549-5469
- PMC
- PMC9528989
- OpenAlex
- W4290948790
- Cited by
- 83
- References
- 82
- Citations by year
- 2026: 27 · 2025: 16 · 2024: 21 · 2023: 17 · 2022: 2
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (submittedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- HAL (submittedVersion)
- HAL (submittedVersion, other-oa)
- UCL Discovery (University College London) (submittedVersion)
- Funders
- Agence Nationale de la Recherche (ANR) GenoFish (ANR-16-CE12-0035-02)
- French Government
- ANR (ANR–10–LABX– 54)
- MEMOLIFE (ANR–10–IDEX–0001–02)
- PSL* Research University
- Horizon 2020 (817923)
- AQUA-FAANG
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- teleosts, whole-genome duplication, rediploidization, paleopolyploidy, autopolyploidy, allopolyploidy, ancestral karyotype reconstruction, gene phylogeny, tetraploidy, genome evolution, comparative genomics
- MeSH terms
- Animals, Fishes, Phylogeny, Polyploidy, Genome, Evolution, Molecular, Gene Duplication, Tetraploidy
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
A language model drew the claims from the paper on 2026-11-10, under version 3 of the claim definition (model deepseek-v4.1-flash, prompt extract-v3).
A second model labelled each claim on 2026-11-10 (model jev-1.13-20260917, definition revision gold-guideline-v0.2).
Cited sources are checked with a language model’s help (gpt-6-sol).
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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