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.
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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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Integrity signals
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Cites
Statistics
Claims the paper makes
0 of 47 cited sources checked · 0 supported · 0 flagged
- Findingown data
Two-branch and branch-site models identified 467, 331, and 281 genes putatively shaped by positive selection in the carnivore, felid, and domestic cat ancestral lineages, respectively.
“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).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [17] source
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- Findingown data
Elevated dN/dS values were identified for 20 carnivoran genes that, when mutated in humans, have well-described roles in a spectrum of visual pathologies.
“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).”
Quote in the paperSubstantial claim - Findingown data
The majority of identified positively selected genes possess substitutions with significant predicted structural or biochemical effects based on one or both tests.
“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).”
Quote in the paperNot a substantial claim - Findingcitation
The first chromosome B3 region contains three genes, including ARID3B.
“The first contains three genes, including ARID3B (AT rich interactive domain 3B), which plays a critical role in neural crest cell survival (48).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [48] source
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- Findingown data
130 regions along cat autosomes were identified with either pooled heterozygosity (Hp) 4 SDs below the mean or divergence (FST) greater than 4 SDs from the mean.
“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).”
Quote in the paperSubstantial claim
- Findingown data
After stringent filtering, 8,676,486 and 5,190,430 high-quality SNVs were identified among domestic breeds and wildcats, respectively, at a total of 10,975,197 sites.
“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).”
Quote in the paperSubstantial claim - Findingown data
The complete Or gene repertoires for cat, tiger, and dog show smaller functional repertoires in felids relative to dogs (∼700 genes versus >800, respectively).
“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).”
Quote in the paperSubstantial claim - Findingown data
A second region on chrA1 overlaps with a glutamate receptor gene, GRIA1.
“A second region, also on chrA1 (Fig. 3), overlaps with a glutamate receptor gene, GRIA1.”
Quote in the paperNot a substantial claim - Findingown data
A third region on chromosome D3 encompasses a single gene, DCC, encoding the netrin receptor.
“A third region on chromosome D3 (Fig. 3) encompasses a single gene, DCC, encoding the netrin receptor.”
Quote in the paperNot a substantial claim - Findingown data
PCDHB4 was also identified in the dN/dS analyses.
“PCDHB4 was also identified in the d N /d S analyses.”
Quote in the paperNot a substantial claim - Findingcitation
One putative region of selection along chromosome A1 is denoted by a pair of protocadherin genes (PCDHA1 and PCDHB4).
“One putative region of selection along chromosome A1 (chrA1) (Fig. 3) is denoted by a pair of protocadherin genes (PCDHA1 and PCDHB4), which establish and maintain specific neuronal connections and have implications for synaptic specificity, serotonergic innervation of the brain, and fear conditioning (43).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [43] source
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- Findingown data
Regions of high genetic differentiation between domestic cats and wildcats are enriched in several Wiki and KEGG pathways, including homologous recombination and axon guidance.
“We also examined regions of high genetic differentiation between domestic cats and wildcats and observed enrichment in several Wiki and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways (S2.5 in Dataset S2), including homologous recombination and axon guidance.”
Quote in the paperSubstantial claim - Findingown data
Two additional glutamate receptor genes, GRIA2 and NPFFR2, have elevated dN/dS rates within the domestic cat branch of the felid tree.
“Two additional glutamate receptor genes, GRIA2 and NPFFR2, have elevated d N /d S rates within the domestic cat branch of the felid tree (Fig. 1).”
Quote in the paperNot a substantial claim - Findingown data
Two additional regions on chromosome B3 harbor strong signatures of selection.
“Two additional regions on chromosome B3 harbor strong signatures of selection (Fig. S7).”
Quote in the paperNot a substantial claim - Findingown data
The notable classes of genes overrepresented in the Felinae positively selected list are related to lipid metabolism.
“These aspects of feline biology are reflected in our positive selection results, where the notable classes of genes overrepresented in the Felinae list are related to lipid metabolism (S1.5 in Dataset S1).”
Quote in the paperSubstantial claim - Findingown data
After parsing regions of high confidence displaying both low domestic Hp and high FST, 13 genes underlying five chromosomal regions were found.
“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).”
Quote in the paperSubstantial claim - Findingown data
Whole-genome resequencing data from a pooled sample of Birman cats identified the genomic region containing KIT as an outlier exhibiting unusually low genetic diversity.
“At the same time, whole-genome resequencing data from a pooled sample of Birman cats (n = 4; SI Materials and Methods and S2.6 in Dataset S2) identified the genomic region containing KIT as an outlier exhibiting unusually low genetic diversity (Fig. 4).”
Quote in the paperSubstantial claim - Findingown data
Two adjacent missense mutations were identified that were concordant with the gloving pattern in Birman cats.
“We identified just two adjacent missense mutations that were concordant with the gloving pattern in Birman cats (Fig. 4 and S2.7 in Dataset S2).”
Quote in the paperSubstantial claim - Findingown data
The average nucleotide diversity adjacent to KIT was low.
“The average nucleotide diversity adjacent to KIT was low (Top Right).”
Quote in the paperSubstantial claim - Findingown data
Direct PCR and sequencing excluded the published dominant allele as being associated with the white coloration pattern in Birman.
“Surprisingly, direct PCR and sequencing excluded the published dominant allele as being associated with the white coloration pattern in Birman (SI Materials and Methods).”
Quote in the paperSubstantial claim - Findingown data
The frequency of the Birman gloving haplotype in the Ragdoll breed was 12.3%.
“Interestingly, the frequency of the Birman gloving haplotype in the Ragdoll breed, which shares an extremely similar white-spotting phenotype, was only 12.3%.”
Quote in the paperSubstantial claim - Findingown data
The five regions of putative selection across cat autosomes A1, B3, and D3 contain 12 known genes.
“These regions, across cat autosomes A1, B3, and D3, contain 12 known genes.”
Quote in the paperNot a substantial claim - Findingown data
The study describes a previously unidentified allele for the gloving pigmentation pattern found in the Birman breed.
“Our description of a previously unidentified allele for the gloving pigmentation pattern found in the Birman breed supports the hypothesis that cat breeds experienced strong selection on specific mutations drawn from random bred populations.”
Quote in the paperSubstantial claim - Findingnone given
The study presents the first complete domestic cat reference genome, to the authors' knowledge.
“We present highlights of the first complete domestic cat reference genome, to our knowledge.”
Quote in the paperSubstantial claim - Findingown data
Sequencing experiments identified two adjacent missense mutations within exon 6 of KIT that were concordant with the gloving pattern in Birman cats.
“Sequencing experiments identified two adjacent missense mutations within exon 6 of KIT that were concordant with the gloving pattern in Birman cats (Bottom).”
Quote in the paperSubstantial claim- Rests on an assumption: Birman cats have a white gloving pattern on their paws.
- Findingown data
Sliding window analyses identify five regions of putative selection in the domestic cat genome.
“Sliding window analyses identify five regions of putative selection in the domestic cat genome.”
Quote in the paperSubstantial claim - Findingown data
The study provides a resource of domestic cat genetic variants.
“We provide evolutionary assessments of the feline protein-coding genome, population genetic discoveries surrounding domestication, and a resource of domestic cat genetic variants.”
Quote in the paperSubstantial claim - Interpretationreasoning
The acquisition of selectively advantageous amino acid substitutions within several genes increased visual acuity under low-light conditions in carnivores.
“Many carnivores have excellent night vision (20,25), and we postulate that the acquisition of selectively advantageous amino acid substitutions within several genes increased visual acuity under low-light conditions.”
Quote in the paperSubstantial claim0 of 2 sources checked- cites [20]
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- cites [25]
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- Rests on an assumption: Visual acuity is adaptive for hunting and catching prey, especially for crepuscular predators such as the cat and other carnivores.
- Interpretationcitation
Six positively selected genes were identified that conceivably evolved to increase auditory acuity over a wider range of frequencies in the carnivore ancestor and within Felidae.
“We identified six positively selected genes (Fig. 1) that conceivably evolved to increase auditory acuity over a wider range of frequencies in the carnivore ancestor and within Felidae, as mutations within each gene have been associated with autosomal, nonsyndromic deafness or hearing loss (22,23).”
Quote in the paperSubstantial claim0 of 2 sources checked - Interpretationreasoning
The genetic signals from this analysis fall in line with the predictions of the domestication syndrome hypothesis.
“The genetic signals from this analysis fall in line with the predictions of the domestication syndrome hypothesis (50), which posits that the morphological and physiological traits modified by mammalian domestication are explained by direct and indirect consequences of mild neural crest cell deficits during embryonic development.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [50] source
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- Premisecitation
Cats fed a diet rich in saturated and polyunsaturated fatty acids showed no effects on plasma lipid concentrations that in humans are risk factors for coronary heart disease and atherosclerosis.
“Furthermore, cats fed a diet rich in saturated and polyunsaturated fatty acids showed no effects on plasma lipid concentrations that in humans are risk factors for coronary heart disease and atherosclerosis (28).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [28] source
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- Interpretationreasoning
Changes in neural crest-related genes underlie the evolution of tameness during cat domestication.
“Taken together, we propose that changes in these neural crest-related genes underlie the evolution of tameness during cat domestication, in agreement with analyses of other domesticated genomes (56)(57)(58).”
Quote in the paperSubstantial claim0 of 3 sources checked - Interpretationnone given
Genes within each of these five regions play important roles in neural processes, notably pathways related to synaptic circuitry that influence behavior and contextual clues related to reward.
“Genes within each of these regions play important roles in neural processes, notably pathways related to synaptic circuitry that influence behavior and contextual clues related to reward.”
Quote in the paperNot a substantial claim - Interpretationcitation
The enrichment of genes related to lipid metabolism is likely a signature of adaptation for accommodating the hypercarnivorous diet of felids.
“The enrichment of genes related to lipid metabolism is likely a signature of adaptation for accommodating the hypercarnivorous diet of felids (31), and mirrors similar signs of selection on lipid metabolic pathways in the genomes of polar bears (32).”
Quote in the paperSubstantial claim0 of 2 sources checked - Premisecitation
Cats rely less on smell to hunt and locate prey in comparison with dogs.
“Cats rely less on smell to hunt and locate prey in comparison with dogs, which are wellknown for their olfactory prowess (35).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [35]
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- Premisecitation
Cats are unable to synthesize arachidonic acid due to low Delta-6-desaturase activity.
“One outcome of this adaptive process is that cats are unable to synthesize certain essential fatty acids, specifically arachidonic acid, due to low Delta-6-desaturase activity (27).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [27] source
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- Interpretationcitation
Divergence in regions harboring homologous recombination genes (RAD51B, ZFYVE26, BRCA2) may contribute to the high recombination rate reported for domestic cats relative to other mammals.
“Divergence in regions harboring homologous recombination genes (RAD51B, ZFYVE26, BRCA2) may contribute to the high recombination rate reported for domestic cats relative to other mammals (59).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [59] source
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- Study design and conductown data
The study mitigated genetic drift effects by combining sequence data from 22 cats from six phylogenetically and geographically dispersed domestic breeds before variant detection and performing selection analyses relative to variants detected within a pool of European and Near Eastern wildcats.
“We mitigated this effect by combining sequence data from a collection of 22 cats (∼58× coverage) from six phylogenetically and geographically dispersed domestic breeds (42) before variant detection and performed selection analyses relative to variants detected within a pool of European (F.silvestris silvestris) and Near Eastern (F.silvestris lybica) wildcats (∼7× coverage; Figs. S4 and S5 and S2.1”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [42] source
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- Interpretationown data
Cat breeds experienced strong selection on specific mutations drawn from random bred populations.
“Our description of a previously unidentified allele for the gloving pigmentation pattern found in the Birman breed supports the hypothesis that cat breeds experienced strong selection on specific mutations drawn from random bred populations.”
Quote in the paperSubstantial claim- Rests on an assumption: Most of the 30-40 cat breeds originated recently, within the past 150 y, largely due to selection for aesthetic rather than functional traits.
- Interpretationown data
The gloving phenotype in the Birman breed is the result of two recessive mutations in KIT.
“Several lines of evidence indicate that the gloving phenotype in the Birman breed is the result of these two recessive mutations in KIT.”
Quote in the paperSubstantial claim - Interpretationreasoning
Other genetic variants, including the endogenous retrovirus insertion in KIT intron 1, likely contribute to the white-spotting phenotype in the Ragdoll breed.
“We suggest that other genetic variants, including the endogenous retrovirus insertion in KIT intron 1 (65), likely contribute to the white-spotting phenotype in the Ragdoll breed.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [65]
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- Interpretationown data
The study's analyses identified genetic signatures within feline genomes that match their unique biology and sensory skills.
“In conclusion, our analyses have identified genetic signatures within feline genomes that match their unique biology and sensory skills.”
Quote in the paperSubstantial claim - Interpretationreasoning
Selection for docility, as a result of becoming accustomed to humans for food rewards, was most likely the major force that altered the first domesticated cat genomes.
“Our results suggest that selection for docility, as a result of becoming accustomed to humans for food rewards, was most likely the major force that altered the first domesticated cat genomes.”
Quote in the paperSubstantial claim
- May combine two claims. 21
- Classified as probably not a substantial claim. 17
May combine two claims.
FindingcitationThe Felis catus genome is predicted to contain 19,493 protein-coding genes and 1,855 noncoding RNAs, similar to dog.
“The Felis catus genome is predicted to contain 19,493 protein-coding genes and 1,855 noncoding RNAs, similar to dog (14).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [14] source
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FindingcitationThe FelCat5 assembly has an N50 contig length of 20.6 kb and a scaffold N50 of 4.7 Mb, both substantially improved over previous light-coverage genome survey sequences that included only 60% of the genome.
“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).”
Quote in the paperSubstantial claim0 of 2 sources checkedMay combine two claims.
FindingcitationThe domestic cat reference genome assembly (FelCat5) comprises 2.35 Gb assigned to all 18 autosomes and the X chromosome, with a further 11 Mb in unplaced scaffolds.
“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.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [11] source
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Findingown dataThe 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.
“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).”
Quote in the paperSubstantial claimMay combine two claims.
Findingnone givenThe second chromosome B3 region contains a single gene, PLEKHH1, which encodes a plekstrin homology domain expressed predominantly in human brain.
“The second region contains a single gene, PLEKHH1, which encodes a plekstrin homology domain expressed predominantly in human brain.”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataSeveral genes encode members of the myosin gene family of mechanochemical proteins, with MYO15A notably under selection in all three branches tested.
“Several genes encode members of the myosin gene family of mechanochemical proteins, with MYO15A notably under selection in all three branches tested.”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataGenotyping 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 polymorphisms.
“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).”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationGRIA1 knockout mice exhibit defects in stimulus-reward learning, notably those related to food rewards.
“GRIA1 knockout mice exhibit defects in stimulus-reward learning, notably those related to food rewards (45).”
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PremisecitationSelection for a recombination driver allele may be favored when it is tightly linked to two or more genes with alleles under selection.
“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).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [61] source
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PremisecitationHuman genome-wide association studies link variants in PLEKHH1 with sphingolipid concentrations that, when altered, lead to neurological and psychiatric disease.
“Human genome-wide association studies link variants in PLEKHH1 with sphingolipid concentrations that, when altered, lead to neurological and psychiatric disease (49).”
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PremisecitationA recent study localized the mutation responsible for the spotting pigmentation phenotype within KIT intron 1.
“A recent study in several white-spotted cats localized the mutation responsible for the spotting pigmentation phenotype within KIT intron 1 (65).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [65]
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Interpretationown dataThese results support cats' extensive reliance on pheromones for sociochemical communication and are consistent with a genomic tradeoff between functional Or and V1r repertoires in response to uniquely evolved ecological strategies in the canid and felid lineages.
“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).”
Quote in the paperSubstantial claim0 of 2 sources checked- 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.
Probably not a substantial claim: may not pass S1 (asserted).
InterpretationreasoningThe close proximity (<350 kb) of two adjacent genes that regulate homologous recombination (ZFYVE26 and RAD51B), two visual genes (RDH11 and RDH12), and PLEKHH1 represents a case of adaptive linkage.
“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.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [62] source
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PremisecitationThe KIT gene is located on cat chromosome B1 and is primarily involved in melanocyte migration, proliferation, and survival.
“The KIT gene, located on cat chromosome B1 (66), is primarily involved in melanocyte migration, proliferation, and survival (67).”
Quote in the paperSubstantial claim0 of 2 sources checkedProbably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationPrevious studies have suggested that domestication may select for an increase in recombination as a mechanism to generate diversity.
“Previous studies have suggested that domestication may select for an increase in recombination as a mechanism to generate diversity (60).”
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PremisecitationARID3B plays a critical role in neural crest cell survival.
“The first contains three genes, including ARID3B (AT rich interactive domain 3B), which plays a critical role in neural crest cell survival (48).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [48] source
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PremisecitationCats are considered only a semidomesticated species because many populations are not isolated from wildcats and humans do not control their food supply or breeding.
“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).”
Quote in the paperSubstantial claim0 of 2 sources checkedMay combine two claims.
PremisecitationDCC shows abundant expression in dopaminergic neurons, and DCC-deficient mice show altered dopaminergic system organization, culminating in impaired memory, behavior, and reward responses.
“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).”
Quote in the paperSubstantial claim0 of 2 sources checkedMay combine two claims.
InterpretationreasoningARID3B, DCC, PLEKHH1, and protocadherins are all implicated in neural crest cell migration.
“ARID3B, DCC, PLEKHH1, and protocadherins are all implicated in neural crest cell migration.”
Quote in the paperSubstantial claimClassified as probably not a substantial claim. May combine two claims.
Study design and conductown dataA threshold of Z(Hp) ≤ -4 and Z(FST) ≥ 4 was applied for putative selective sweeps because these thresholds represent the extreme lower and upper ends of the respective distributions.
“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).”
Quote in the paperSubstantial claimClassified as probably not a substantial claim.
Study design and conductcitationThe Benjamini and Hochberg multiple test adjustment was implemented to control for false discovery.
“We implemented the Benjamini and Hochberg multiple test adjustment (77) to control for false discovery.”
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Study design and conductown dataVariants were filtered using PoPoolation2 to yield a high-confidence set of 6,534,957 SNVs.
“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).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [80] source
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Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationThe earliest archaeological evidence for human coexistence with cats dates to ∼9.5 kya in Cyprus and ∼5 kya in central China.
“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.”
Quote in the paperNot a substantial claim0 of 2 sources checkedClassified as probably not a substantial claim. May combine two claims.
Study design and conductown dataAll windows containing less than 10 variant sites were removed, resulting in 46,906 100-kb windows along cat autosomes.
“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.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationThe 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.
“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).”
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PremisecitationBoth 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.
“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).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [68] source
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Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
Study design and conductown dataThe domestic cat pool (n = 22) was sequenced to a genome coverage depth of ∼58-fold, whereas the wildcat pool was sequenced to a depth of ∼7-fold.
“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).”
Quote in the paperNot a substantial claimMay combine two claims.
InterpretationreasoningThe frequency of the Birman gloving haplotype is 10% in the random nonbreed population, illustrating that segregating genetic variation in ancestral nonbred populations has reached fixation within Birman cats through strong artificial selection in a remarkably short time frame.
“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.”
Quote in the paperSubstantial claimMay combine two claims.
PremisecitationWithin carnivores, cats have the broadest hearing range, allowing them to detect both ultrasonic communication by prey as well as their movement.
“Within carnivores, cats have the broadest hearing range, allowing them to detect both ultrasonic communication by prey as well as their movement (21).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [21] source
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationCats and other members of Carnivora last shared a common ancestor with humans ∼92 million years ago.
“Cats and other members of Carnivora last shared a common ancestor with humans ∼92 million years ago (2,3).”
Quote in the paperNot a substantial claim0 of 2 sources checkedProbably not a substantial claim: may not pass S3 (load-bearing), S4 (based).
InterpretationreasoningGiven 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.
“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.”
Quote in the paperNot a substantial claimMay combine two claims.
InterpretationreasoningThe 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 processes by which cats became domesticated.
“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.”
Quote in the paperSubstantial claim
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?
KIT is involved in melanocyte differentiation, and evidence points to its importance in selection for coat color, with signals on KIT in Clydesdale horses and Birman cats implicated in their breed-specific coat patterns.
“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.
Five selected regions contain 13 genes in the text but 12 in the figure captions
MinorThe Results report 13 genes in the five regions meeting both selection criteria, whereas the Fig. 3 caption reports 12 genes in those regions. The Fig. 2 caption also gives 12.
“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).”
“A total of 12 genes was found within these regions, many of which are implicated in neural processes;”
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Self-citationBredemeyer, K. R., Hillier, L., Harris, A. J., Hughes, G. M., Foley, N. M., Lawless, C., Carroll, R. A., Storer, J. M., Batzer, M. A., Rice, E. S., et al. (2023) · Nature Genetics · doi:10.1038/s41588-023-01548-y · Cited by 37 · see citing works
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Self-citationAnalysis of the genetic loci of pigment pattern evolution in vertebrates
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- 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 › Biochemistry, Genetics and Molecular Biology › Genetics › 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.
Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-10.
Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-10.
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.
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