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Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication
Open accessAbstract
Significance: We present highlights of the first complete domestic cat reference genome, to our knowledge. We provide evolutionary assessments of the feline protein-coding genome, population genetic discoveries surrounding domestication, and a resource of domestic cat genetic variants. These analyses span broadly, from carnivore adaptations for hunting behavior to comparative odorant and chemical detection abilities between cats and dogs. We describe how segregating genetic variation in pigmentation phenotypes has reached fixation within a single breed, and also highlight the genomic differences between domestic cats and wildcats. Specifically, the signatures of selection in the domestic cat genome are linked to genes associated with gene knockout models affecting memory, fear-conditioning behavior, and stimulus-reward learning, and potentially point to the processes by which cats became domesticated.
Overview
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Written from the paper’s full text.
TL;DR
This paper presents a high-quality domestic cat reference genome (FelCat5) and comparative genomic analyses identifying signatures of selection related to carnivory, sensory biology, and domestication. It also reports two recessive KIT missense mutations associated with the Birman gloving pigmentation pattern.
Key findings
- The FelCat5 assembly comprises 2.35 Gb assigned to all 18 autosomes and the X chromosome, plus 11 Mb in unplaced scaffolds, with an N50 contig of 20.6 kb and scaffold N50 of 4.7 Mb; the cat genome is predicted to contain 19,493 protein-coding genes and 1,855 noncoding RNAs.
- Genome-wide dN/dS analyses identified 467, 331, and 281 genes putatively under positive selection in the carnivore, felid, and domestic cat (Felinae) ancestral lineages, respectively; Felinae positively selected genes were enriched for lipid metabolism, and sensory genes included vision and hearing candidates.
- Cats and dogs show an evolutionary tradeoff in chemosensory repertoires: felids have smaller functional olfactory receptor repertoires (~700 genes) than dogs (>800), while the vomeronasal V1r repertoire is reduced in dogs (8 functional genes) but expanded in the cat ancestor (21 functional genes).
- Domestication analyses found 130 autosomal regions with pooled heterozygosity 4 SDs below the mean or FST greater than 4 SDs from the mean; five high-confidence regions contained neural/neural-crest-related genes (reported as 13 genes in Results and 12 known genes in Fig. 3/conclusion). For Birman gloving, two adjacent KIT exon 6 missense mutations were concordant with the phenotype; all 150 Birman cats genotyped were homozygous for both SNPs, and the Birman gloving haplotype frequency was 12.3% in Ragdoll and 10% in the random nonbreed population.
Methods
- A female Abyssinian cat (“Cinnamon”) provided DNA for ~14× whole-genome shotgun coverage using Sanger and 454 technology; a BAC library was constructed and end-sequenced, and sequences were assembled with CABOG.
- Selection analyses used 10,317 sets of 1:1:1:1:1 orthologs from human, cow, dog, tiger, and domestic cat, with PAML 4.0 branch and branch-site models, TreeSAAP and PROVEAN for amino acid impact, and WebGestalt for functional enrichment.
- Domestication scans used pooled resequencing of 22 domestic cats from six breeds (~58× coverage) and a wildcat pool of two European and two Near Eastern wildcats (~7× coverage); SNVs were called with SAMtools, VarScan 2, and PoPoolation2, and 100-kb windows with 50-kb step were tested for low Hp and high FST. KIT exons were resequenced/genotyped in 409 cats from 21 breeds, 5 Birman outcrosses, and 315 random bred cats, with a larger sample of 150 Birman cats and 729 additional cats.
Limitations
- The paper states that the selection inferences “call for additional functional analyses,” so most positively selected genes are computational candidates rather than experimentally validated.
- The paper notes cats are considered only semidomesticated, with ongoing admixture with wildcats, a relatively short cohabitation history, and limited isolation from wild populations, which may explain the modest number of strong domestication signals.
- Evident from the text: domestication scans rely on pooled sequencing and pooled breed samples, the wildcat comparison uses only four individuals at ~7× coverage, and the reported gene count in the five high-confidence regions differs between the Results (13 genes) and Fig. 3/conclusion (12 known genes).
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Claims the paper makes
33 Not checked yet · 26 Own result · 9 Own interpretation · 3 Own method · 2 Partly supported · 2 No basis given · accuracy not yet measured
In the paper
“Two-branch and branch-site models (17) collectively identified 467, 331, and 281 genes that were putatively shaped by positive selection in the carnivore, felid, and domestic cat (subfamily Felinae) ancestral lineages, respectively (S1.1-S1.3 in Dataset S1).”
§ Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication > Results and Discussion
What the sources say
- Not checked yetcites [17] source
hedgeddirectn = 10,317- Asserted: passes — The authors put it forward as true.
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A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Accordingly, we identified elevated d N /d S values for 20 carnivoran genes that, when mutated in humans, have well-described roles in a spectrum of visual pathologies (Fig. 1).”
§ Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication > Results and Discussion
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In the paper
“The majority of identified genes possess substitutions with significant predicted structural or biochemical effects based on one or both tests (Fig. S1 and S1.4 in Dataset S1).”
§ Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication > Results and Discussion
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“The first contains three genes, including ARID3B (AT rich interactive domain 3B), which plays a critical role in neural crest cell survival (48).”
§ Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication > Results and Discussion
What the sources say
- Not checked yetcites [48] source
plain- Asserted: passes — The authors put it forward as true.
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A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We next identified 130 regions along cat autosomes with either pooled heterozygosity (H p ) 4 SDs below the mean or divergence (F ST ) greater than 4 SDs from the mean (Figs.S4 and S6, SI Materials and Methods, and S2.2 and S2.3 in Dataset S2).”
§ Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication > Results and Discussion
plain- Asserted: passes — The authors put it forward as true.
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A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“After stringent filtering of resequencing data, we aligned sequences to the cat reference genome and identified 8,676,486 and 5,190,430 high-quality single-nucleotide variants (SNVs) among domestic breeds and wildcats, respectively, at a total of 10,975,197 sites (Fig. S3).”
§ Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication > Results and Discussion
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“These observations are confirmed by our analysis of the complete Or gene repertoires for cat, tiger, and dog (Fig. 1), illustrating smaller functional repertoires in felids relative to dogs (∼700 genes versus >800, respectively).”
§ Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication > Results and Discussion
boostedcorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“A second region, also on chrA1 (Fig. 3), overlaps with a glutamate receptor gene, GRIA1.”
§ Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication > Results and Discussion
plaincorrelational- Asserted: passes — The authors put it forward as true.
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A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“A third region on chromosome D3 (Fig. 3) encompasses a single gene, DCC, encoding the netrin receptor.”
§ Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication > Results and Discussion
plain- Asserted: passes — The authors put it forward as true.
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A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“PCDHB4 was also identified in the d N /d S analyses.”
§ Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication > Results and Discussion
plain- Asserted: passes — The authors put it forward as true.
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- It may state two separate claims as one. 21
- Probably not a substantial claim. 17
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“The assembly (FelCat5) comprises 2.35 gigabases (Gb) assigned to all 18 autosomes and the X chromosome relying on physical and linkage maps (11) with a further 11 megabases (Mb) in unplaced scaffolds.”
§ Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication > Results and Discussion
What the sources say
- Partly supportedcites [11] sourceExperimental — accuracy not yet measured
The Discussion (page unavailable) says a cat radiation-hybrid map supported the earlier 1.9× and 3× genome assemblies, supporting the cited point that mapping can aid assembly. It does not establish that the specific FelCat5 assembly relied on physical and linkage maps. The citation is attached to that mapping point, not to the assembly-size figures elsewhere in the sentence. (LLM, conf=0.83)
plain- Asserted: passes — The authors put it forward as true.
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- Partly supported
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In the paper
“This gene shows abundant expression in dopaminergic neurons, and behavioral studies of DCC-deficient mice show altered dopaminergic system organization, culminating in impaired memory, behavior, and reward responses (46,47).”
§ Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication > Results and Discussion
What the sources say
- Partly supportedcites [46] sourceExperimental — accuracy not yet measured
The Summary (p. 1) reports impaired spatial and recognition memory after DCC deletion from adult forebrain neurons, supporting the memory portion of the claim. The Conditional Deletion section (p. 3) says the deletion did not target ventral midbrain dopaminergic neurons; the cited passages do not establish abundant DCC expression in those neurons, altered dopaminergic-system organization, or impaired reward responses. (LLM, conf=0.89)
- Not checked yetcites [47] source
plaindirect- Asserted: passes — The authors put it forward as true.
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- Partly supported
In the paper
“The Felis catus genome is predicted to contain 19,493 protein-coding genes and 1,855 noncoding RNAs, similar to dog (14).”
§ Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication > Results and Discussion
What the sources say
- Not checked yetcites [14] source
plain- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“The assembly is represented by an N50 contig length of 20.6 kb and a scaffold N50 of 4.7 Mb, both of which show substantial improvement over previous light-coverage genome survey sequences that included only 60% of the genome (12,13).”
§ Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication > Results and Discussion
plain- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“By contrast, the V1r gene repertoire is markedly reduced in dogs but expanded in the ancestor of the cat family (8 versus 21 functional genes, respectively), with evidence for species-specific gene loss in different felids (Fig. 1 and Figs.S2 and S3).”
§ Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication > Results and Discussion
plaincorrelational- Asserted: passes — The authors put it forward as true.
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The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“The second region contains a single gene, PLEKHH1, which encodes a plekstrin homology domain expressed predominantly in human brain.”
§ Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication > Results and Discussion
plain- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Several genes encode members of the myosin gene family of mechanochemical proteins, with MYO15A notably under selection in all three branches tested.”
§ Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication > Materials and Methods
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
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It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Genotyping these SNPs in a larger sample including 150 Birman cats and 729 additional cats confirmed that all Birman cats were homozygous for both SNPs and that all first-generation outcrossed Birman cats with no gloving were carriers of the poly- morphisms (S2.8 in Dataset S2).”
§ Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication > Results and Discussion
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“GRIA1 knockout mice exhibit defects in stimulus-reward learning, notably those related to food rewards (45).”
§ Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication > Results and Discussion
What the sources say
- Not checked yetcites [45] source
plaindirect- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“Specifically, selection for a recombination driver allele may be favored when it is tightly linked to two or more genes with alleles under selection (61).”
§ Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication > Results and Discussion
What the sources say
- Not checked yetcites [61] source
hedgedconditional- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim.
In the paper
“Human genome-wide association studies link variants in PLEKHH1 with sphingolipid concentrations that, when altered, lead to neurological and psychiatric disease (49).”
§ Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication > Results and Discussion
What the sources say
- Not checked yetcites [49] source
plaindirect- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“A recent study in several white-spotted cats localized the mutation responsible for the spotting pigmentation phenotype within KIT intron 1 (65).”
§ Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication > Results and Discussion
What the sources say
- Not checked yetcites [65]
plaindirect- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“These results add further evidence supporting cats' extensive reliance on pheromones for sociochemical communication (38), which is consistent with a genomic tradeoff between functional Or and V1r repertoires in response to uniquely evolved ecological strategies in the canid and felid lineages (4).”
§ Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication > Results and Discussion
plaincorrelational- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
- Rests on an assumption: Two extensive chemosensory gene families, coding for olfactory (Or) and vomeronasal (V1r) receptors, are responsible for small-molecule detection of odorants and other chemicals for mediating pheromone perception, respectively.
In the paper
“We hypothesize that the close proximity (<350 kb) of two adjacent genes that regulate homologous recombination (ZFYVE26 and RAD51B, which directly interact with BRCA2), two visual genes (RDH11 and RDH12) related to retinol metabolism and dark adaptation (62), and one of our candidate domestication genes, PLEKHH1 (S2.4 in Dataset S2), represents such a case of adaptive linkage.”
§ Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication > Results and Discussion
What the sources say
- Not checked yetcites [62] source
hedgedcorrelational- Asserted: fails — The authors may not put it forward as true.
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Probably not a substantial claim. The authors may not put it forward as true.
None of the sources cited for this claim have been checked yet.
In the paper
“The KIT gene, located on cat chromosome B1 (66), is primarily involved in melanocyte migration, proliferation, and survival (67).”
§ Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication > Results and Discussion
plaindirect- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. It may state two separate claims as one.
In the paper
“Previous studies have suggested that domestication may select for an increase in recombination as a mechanism to generate diversity (60).”
§ Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication > Results and Discussion
What the sources say
- Not checked yetcites [60] source
hedgedconditional- Asserted: passes — The authors put it forward as true.
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- Load-bearing: fails — The paper’s conclusions may not depend on it.
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Probably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“The first contains three genes, including ARID3B (AT rich interactive domain 3B), which plays a critical role in neural crest cell survival (48).”
§ Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication > Results and Discussion
What the sources say
- Not checked yetcites [48] source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“Cats are considered only a semidomesticated species, because many populations are not isolated from wildcats and humans do not control their food supply or breeding (39,40).”
§ Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication > Results and Discussion
plaindirect- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“ARID3B, DCC, PLEKHH1, and protocadherins are all implicated in neural crest cell migration.”
§ Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication > Results and Discussion
plaincorrelational- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“We applied a threshold of Z(H p ) ≤ -4 and Z(F ST ) ≥ 4 for putative selective sweeps, because windows below or above these thresholds represent the extreme lower and extreme upper ends of the respective distributions (Fig. S4).”
§ Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication > Materials and Methods
plain- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. It may state two separate claims as one.
In the paper
“We implemented the Benjamini and Hochberg multiple test adjustment (77) to control for false discovery.”
§ Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication > Materials and Methods
What the sources say
- Not checked yetcites [77] source
plain- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim.
In the paper
“Variants were finally filtered using PoPoolation2 (80) to yield a high-confidence set of SNVs (n = 6,534,957; filtering steps included a minimum coverage of 8, a minimum variant count of 6, a maximum coverage of 500 for the domestic cat pool, and a maximum coverage of 200 for the wildcat pool).”
§ Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication > Materials and Methods
What the sources say
- Not checked yetcites [80] source
plaindirectn = 22- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim.
None of the sources cited for this claim have been checked yet.
In the paper
“The earliest archaeological evidence for human coexistence with cats dates to ∼9.5 kya in Cyprus and ∼5 kya in central China (5,6), during periods when human populations adopted more agricultural lifestyles.”
§ Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication > Abstract
plain- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“All windows containing less than 10 variant sites were removed from the analysis, resulting in n = 46,906 100-kb windows along cat autosomes, as represented in the FelCat5 assembly.”
§ Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication > Materials and Methods
plaindirectn = 46,906- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. It may state two separate claims as one.
In the paper
“The cat family Felidae includes ∼38 species that are widely distributed across the world, inhabiting diverse ecological niches that have resulted in divergent morphological and behavioral adaptations (4).”
§ Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication > Abstract
What the sources say
- Not checked yetcites [4] source
plaindirect- Asserted: passes — The authors put it forward as true.
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- Load-bearing: fails — The paper’s conclusions may not depend on it.
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Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
In the paper
“Both mutations affect the fourth Ig domain of KIT, and mutations in this motif near the dimerization site have been shown to result in accelerated ligand dissociation and reduced downstream signal transduction events (68).”
§ Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication > Results and Discussion
What the sources say
- Not checked yetcites [68] source
boosteddirect- Asserted: passes — The authors put it forward as true.
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What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“The domestic cat pool (n = 22) was sequenced to a genome coverage depth of ∼58fold, whereas the wildcat pool was sequenced to a depth of ∼7-fold (S2.1 in Dataset S2).”
§ Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication > Materials and Methods
plainn = 22- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The frequency of the Birman gloving haplotype is just 10% in the random nonbreed population, thus illustrating a case where segregating genetic variation in ancestral nonbred populations has reached fixation within Birman cats through strong artificial selection in a remarkably short time frame.”
§ Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication > Results and Discussion
boosteddirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“Within carnivores, cats have the broadest hearing range, allowing them to detect both ultrasonic communication by prey as well as their movement (21).”
§ Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication > Results and Discussion
What the sources say
- Not checked yetcites [21] source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“Cats and other members of Carnivora last shared a common ancestor with humans ∼92 million years ago (2,3).”
§ Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication > Abstract
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Given their sustained beneficial role surrounding vermin control since the human transition to agriculture, any selective forces acting on cats may have been minimal subsequent to their domestication.”
§ Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication > Abstract
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Specifically, the signatures of selection in the domestic cat genome are linked to genes associated with gene knockout models affecting memory, fearconditioning behavior, and stimulus-reward learning, and potentially point to the processes by which cats became domesticated.”
§ Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication > Abstract
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper relies on this without support.
Most of the 30-40 cat breeds originated recently, within the past 150 y, largely due to selection for aesthetic rather than functional traits.
“Unlike many other domesticated mammals bred for food, herding, hunting, or security, most of the 30-40 cat breeds originated recently, within the past 150 y, largely due to selection for aesthetic rather than functional traits.”
The paper relies on this without support.
Visual acuity is adaptive for hunting and catching prey, especially for crepuscular predators such as the cat and other carnivores.
“Visual acuity is adaptive for hunting and catching prey, especially for crepuscular predators such as the cat and other carnivores.”
The paper relies on this without support.
Gene duplication and gene loss events often play substantial roles in phenotypic differences between species.
“Gene duplication and gene loss events often play substantial roles in phenotypic differences between species.”
The paper relies on this without support.
Two extensive chemosensory gene families, coding for olfactory (Or) and vomeronasal (V1r) receptors, are responsible for small-molecule detection of odorants and other chemicals for mediating pheromone perception, respectively.
“Two extensive chemosensory gene families, coding for olfactory (Or) and vomeronasal (V1r) receptors, are responsible for smallmolecule detection of odorants and other chemicals for mediating pheromone perception, respectively.”
The paper relies on this without support.
Birman cats have a white gloving pattern on their paws.
“The paws of the Birman breed (Top Left) are distinguished by white gloving.”
The paper relies on this without support.
MYO7A expression is associated with hearing and vision.
“MYO7A (*) expression is associated with hearing and vision.”
The authors state this as an assumption.
The species tree topology for the selection analysis is (((cat, tiger), dog), cow, human).
“We tested for signatures of natural selection assuming the species tree topology (((cat, tiger), dog), cow, human).”
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“This gene is involved in melanocyte differentiation, and evidence points to its importance in selection for coat color: Signals occurring on KIT in Clydesdale horses and Birman cats have been implicated in their breed-specific coat patterns (Schubert et al., 2014;Montague et al., 2014).”
From Glutamate receptors in domestication and modern human evolution (2020) · cites this paper as Montague et al., 2014
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.
Rated minor: it would not touch a result — a value no result rests on, a p-value that stays on the same side of the significance level, or a conflict that is clerical, resolved elsewhere in the paper, or outside its own findings.
In the paper
§ Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication > Results and Discussion
“After parsing regions of high confidence displaying both low domestic H p and high F ST , we found 13 genes underlying five chromosomal regions (Fig. 2, Fig. S4, and S2.4 in Dataset S2).”
§ Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication > Results and Discussion
“A total of 12 genes was found within these regions, many of which are implicated in neural processes;”
Citations
Cites
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The Sequence Alignment/Map format and SAMtools
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PAML 4: Phylogenetic Analysis by Maximum Likelihood
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Primer3—new capabilities and interfaces
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VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencingPreprint
Koboldt, D. C., Zhang, Q., Larson, D. E., Shen, D., McLellan, M. D., Lin, L., Miller, C. A., Mardis, E. R., Ding, L., & Wilson, R. K. (2012) · Genome Research · doi:10.1101/gr.129684.111 · Cited by 4,954
Self-citationKEGG for integration and interpretation of large-scale molecular data sets
Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., & Tanabe, M. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr988 · Cited by 4,848
Predicting the Functional Effect of Amino Acid Substitutions and Indels
Choi, Y., Sims, G. E., Murphy, S., Miller, J. R., & Chan, A. P. (2012) · PLoS ONE · doi:10.1371/journal.pone.0046688 · Cited by 2,890
Genome sequence, comparative analysis and haplotype structure of the domestic dog
members, B. S. P., Lindblad-Toh, K., Wade, C. M., Mikkelsen, T. S., Karlsson, E. K., Jaffe, D. B., Kamal, M., Clamp, M., Chang, J. L., Kulbokas, E. J., et al. (2005) · Nature · doi:10.1038/nature04338 · Cited by 2,568
Self-citation
Research works printed but not linked: 4
- ; American Pet Product Manufacturing Association National Pet Owner’s Survey (Am Pet Prod Manuf Assoc, Greenwich, CT, 2008).
- RJG Savage, Evolution in carnivorous mammals. Palaeontology 20, 237–271 (1977).
- RF Ewer The Carnivores (Cornell Univ Press, New York, 1973).
- VA David, , Endogenous retrovirus insertion in the KIT oncogene determines white and white spotting in domestic cats. G3 (Bethesda), 2014).
Cited by
Sorted by citations
Ancient genomes revisit the ancestry of domestic and Przewalski’s horses
Gaunitz, C., Fages, A., Hanghøj, K., Albrechtsen, A., Khan, N., Schubert, M., Seguin-Orlando, A., Owens, I. J., Felkel, S., Bignon-Lau, O., et al. (2018) · Science · doi:10.1126/science.aao3297 · Cited by 298
Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae)Preprint
Li, G., Davis, B. W., Eizirik, E., & Murphy, W. J. (2015) · Genome Research · doi:10.1101/gr.186668.114 · Cited by 329
Self-citationYak whole-genome resequencing reveals domestication signatures and prehistoric population expansions
Qiu, Q., Wang, L., Wang, K., Yang, Y. P., Ma, T., Wang, Z., Zhang, X., Ni, Z., Hou, F., Long, R., et al. (2015) · Nature Communications · doi:10.1038/ncomms10283 · Cited by 309
A New Chicken Genome Assembly Provides Insight into Avian Genome Structure
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Self-citationA single generation of domestication heritably alters the expression of hundreds of genes
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Metadata
- Authors
- Montague, M. J., Li, G., Gandolfi, B., Khan, R., Aken, B. L., Searle, S. M. J., Minx, P., Hillier, L. W., Koboldt, D. C., Davis, B. W., Driscoll, C. A., Barr, C. S., Blackistone, K., Quilez, J., Lorente-Galdos, B., Marques-Bonet, T., Alkan, C., Thomas, G. W. C., Hahn, M. W., Menotti-Raymond, M., O’Brien, S. J., Wilson, R. K., Lyons, L. A., Murphy, W. J., & Warren, W. C.
- Affiliations
- Washington University in St. Louis (US)
- Texas A&M University (US)
- University of Missouri (US)
- University of California, Davis (US)
- Wellcome Sanger Institute (GB)
- National Institutes of Health (US)
- Institució Catalana de Recerca i Estudis Avançats (ES)
- Catalan Institution for Research and Advanced Studies, Institute of Evolutionary Biology, Pompeu Fabra University, 08003 Barcelona, Spain;
- Bilkent University (TR)
- Indiana University Bloomington (US)
- Frederick National Laboratory for Cancer Research (US)
- St Petersburg University (RU)
- ORCID
- Montague, Michael J.
- Li, Gang
- Aken, Bronwen L.
- Minx, Patrick
- Hillier, LaDeana W.
- Koboldt, Daniel C.
- Davis, Brian W.
- Driscoll, Carlos A.
- Barr, Christina S.
- Blackistone, Kevin
- Quilez, Javier
- Alkan, Can
- Thomas, Gregg W. C.
- Hahn, Matthew W.
- Menotti-Raymond, Marilyn
- O’Brien, Stephen J.
- Wilson, Richard K.
- Lyons, Leslie A.
- Murphy, William J.
- Warren, Wesley C.
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2014-11-10
- Volume
- 111
- Issue
- 48
- Pages
- 17230-17235
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC4260561
- OpenAlex
- W2069681519
- Semantic Scholar
- 389bc19b62fca13184e19f715befa43ea4bee50d
- Cited by
- 340
- References
- 79
- Citations by year
- 2026: 20 · 2025: 12 · 2024: 28 · 2023: 28 · 2022: 49 · 2021: 34 · 2020: 27 · 2019: 46 · 2018: 28 · 2017: 24 · 2016: 24 · 2015: 20
- FWCI
- 14.85
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- NSUWorks (Nova Southeastern University) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- OakTrust (Texas A&M University Libraries) (submittedVersion)
- Bilkent University Institutional Repository (Bilkent University) (submittedVersion)
- Zenodo (CERN European Organization for Nuclear Research)
- Funders
- U.S. Department of Veterans Affairs (CDA 10-014)
- Wellcome Trust (095908)
- National Institutes of Health (R24OD010928)
- Biotechnology and Biological Sciences Research Council (BB/I025506/1, BB/I025360/2)
- National Human Genome Research Institute (U54HG003079)
- National Center for Research Resources (R24RR016094)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Human-Animal Interaction Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Keywords
- positive selection, lipid metabolism, olfactory receptor genes, vomeronasal receptor genes, pheromone detection, domestication syndrome, cat breeds
- MeSH terms
- Adaptation, Physiological, Amino Acid Sequence, Animals, Animals, Domestic, Animals, Wild, Cats, Chromosome Mapping, Dogs, Female, Male, Molecular Sequence Data, Phylogeny, Selection, Genetic, Species Specificity, Genome, Gene Deletion, Sequence Homology, Amino Acid, Sequence Analysis, DNA, Gene Duplication, Genomics, Membrane Transport Proteins, DNA Copy Number Variations, Carnivory
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 2026-10-10, under version 3 of the claim definition (model deepseek-v4.1-flash, prompt extract-v3).
A second model labelled each claim on 2026-10-10 (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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