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Cited by 13Genetic and phenotypic traits in livestockLivestock and Poultry ManagementGenetic Mapping and Diversity in Plants and Animals

Genomic Analyses Unveil Helmeted Guinea Fowl (Numida meleagris) Domestication in West Africa

Open access
Shen, Quan-Kuan, Peng, Min-Sheng, Adeola, Adeniyi C, Kui, Ling, Duan, Shengchang, Miao, Yong-Wang, Eltayeb, Nada M, Lichoti, Jacqueline K +23 more·2021·Genome Biology and Evolution
DOI 10.1093/gbe/evab090PMC PMC8214406
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Abstract

Domestication of the helmeted guinea fowl (HGF; Numida meleagris) in Africa remains elusive. Here we report a high-quality de novo genome assembly for domestic HGF generated by long- and short-reads sequencing together with optical and chromatin interaction mapping. Using this assembly as the reference, we performed population genomic analyses for newly sequenced whole-genomes for 129 birds from Africa, Asia, and Europe, including domestic animals (n = 89), wild progenitors (n = 34), and their closely related wild species (n = 6). Our results reveal domestication of HGF in West Africa around 1,300–5,500 years ago. Scanning for selective signals characterized the functional genes in behavior and locomotion changes involved in domestication of HGF. The pleiotropy and linkage in genes affecting plumage color and fertility were revealed in the recent breeding of Italian domestic HGF. In addition to presenting a missing piece to the jigsaw puzzle of domestication in poultry, our study provides valuable genetic resources for researchers and breeders to improve production in this species.

AI snapshot

Written from the paper’s full text.

TL;DR

The study reports a near-chromosome de novo genome assembly for helmeted guinea fowl and whole-genome resequencing of 129 birds, supporting a single domestication origin in West Africa around 1,300–5,500 years ago rather than East Africa. It also identifies selection signals for behavior/locomotion during domestication and a TYR p.Trp218Gly variant associated with white plumage in Italian Camosciata breeding.

Key findings

  • HGFv1 assembly: 1,127 scaffolds, 1,049.9 Mb total; first 16 scaffolds accounted for 90% (949.6 Mb); contig N50 14.17 Mb vs. 0.23 Mb for NumMel1.0; gaps 5.38 vs. 20.12 Mb; BUSCO complete 94.5%; LAI 10.29.
  • Domestication: wild Nigerian HGF was closer to domestic HGF than wild HGF from Kenya/Sudan; momi2 split wild and domestic HGF at 5,452 YBP (95% bootstrap 9,916–2,548), with Nigerian/Sudanese domestic divergence at 1,261 YBP (95% 5,180–162); gene flow from wild Sudanese to wild Nigerian HGF was 9.3% and to domestic Sudanese HGF 5.4%, dated ~1,448 and ~154 YBP.
  • Selection: PCAdapt top 0.1% identified 4,393 SNPs, 1,941 annotated to 453 genes; 78 genes shared with PBS were enriched for nervous system and muscle GO terms (e.g., GRIA4, ACTN1, PIEZO2). In Italian Camosciata, TYR p.Trp218Gly was fixed and predicted probably damaging (PolyPhen-2 0.998), within a 9.5 Mb LD block also containing PGR and MMP13.
  • Diversity: wild HGF had greater nucleotide diversity and lower ROHs than domestic HGF; among domestic populations, Nigerian had the highest diversity and lowest ROHs, while Italian had the lowest diversity and highest LD/ROHs.

Methods

  • De novo assembly used PacBio long-read sequencing, BioNano optical mapping, and Hi-C scaffolding; annotation used the NCBI Eukaryotic Genome Annotation Pipeline, with quality assessed by BUSCO, LAI, RNA-seq mapping, and synteny to chicken GRCg6a.
  • Whole-genome resequencing of 129 guinea fowl: 89 domestic HGF, 34 wild HGF, 5 vulturine guinea fowl, and 1 crested guinea fowl; Illumina paired-end 150 sequencing gave average depth 18× (10.4–42.2), and joint variant calling produced 44,035,924 SNPs and 4,214,076 InDels.
  • Population analyses included FastTree/RAxML phylogeny, PCA, ADMIXTURE, diversity/LD/ROH estimation, f3/D statistics, TreeMix/qpGraph, SMC++/PopSizeABC/momi2 demographic inference, and PCAdapt/PBS/Pi-ratio selection scans with GO enrichment.

Limitations

  • Stated: the HGF mutation rate was unavailable, so the chicken rate (1.91 × 10−9 per site per year) was used for demographic inference; the long 9.5 Mb LD block made it difficult to refine the causal locus for white plumage.
  • Evident: the paper has no dedicated limitations section; some demographic estimates have wide bootstrap intervals (e.g., wild/domestic split 9,916–2,548 YBP; Nigerian/Sudanese domestic divergence 5,180–162 YBP), and 10 outlier individuals were removed/reclassified before population analyses.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1093/gbe/evab090

Cites

70 of 70 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

26 of 44 cited sources checked · 14 supported · 0 flagged · accuracy not yet measured

  • Findingown data

    Domestic helmeted guinea fowl from Sudan had significantly positive D values (Z > 3), suggesting gene flow between domestic helmeted guinea fowl from Sudan and wild helmeted guinea fowl from Kenya/Sudan.

    “D statistics (Durand et al. 2011) were calculated and showed that the domestic HGF from Sudan had significantly positive D values (Z > 3), suggesting gene flow between domestic HGF from Sudan and wild HGF from Kenya/Sudan (supplementary fig. S5, Supplementary Material online).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites Durand et al. 2011 source
  • Findingown data

    Gene flow from helmeted guinea fowl to domestic helmeted guinea fowl in Sudan was indicated in TreeMix when m = 1 in 99.9% of the bootstrap replicates.

    “Gene flow from the HGF to domestic HGF in Sudan was indicated in the TreeMix (Pickrell and Pritchard 2012) when m = 1 (supplementary fig. S6, Supplementary Material online) in 99.9% of the bootstrap replicates.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites Pickrell and Pritchard 2012 source
  • Findingcitation

    The pattern of domestic populations undergoing sharper decreases than wild populations was also observed in the analysis of PopSizeABC.

    “This pattern was also observed in the analysis of PopSizeABC (Boitard et al. 2016) (supplementary fig. S8, Supplementary Material online).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Boitard et al. 2016 source

      The Results (Application to NGS samples in cattle; page unavailable) report population declines in four domestic cattle breeds and a sharper decrease in their shared ancestral history. That sharper decrease began before domestication, however, and the paper does not compare the declines of domestic populations with those of wild populations. (LLM, conf=0.86)

      Experimental — accuracy not yet measured
  • Findingcitation

    The HGFv1 assembly is compatible with current poultry reference genomes.

    “The HGFv1 assembly is compatible with current poultry reference genomes (Dalloul et al. 2010; Shapiro et al. 2013; Lu et al. 2015; ZhOu et al. 2018; Morris et al. 2020).”
    Quote in the paperSubstantial claim3 of 3 sources checked
    • cites Dalloul et al. 2010 source

      The Introduction identifies the paper’s draft turkey genome as a domestic avian genome, supporting its use as an example of a poultry reference genome. The Methods describe alignment with chicken and zebra finch genomes, but the paper does not mention HGFv1 or establish that HGFv1 is compatible with those genomes. (LLM, conf=0.85)

      Experimental — accuracy not yet measured
    • cites Shapiro et al. 2013 source

      The paper’s Abstract describes sequencing a rock-pigeon reference genome, and its References list turkey and chicken genome studies. Searches for HGFv1 and for assembly comparisons found no passage assessing whether the HGFv1 assembly is compatible with poultry reference genomes. (LLM, conf=0.75)

      Experimental — accuracy not yet measured
    • cites Lu et al. 2015 source

      The Results and discussion sections on genome assembly and comparative genomic analysis describe a goose assembly and its comparisons with duck and chicken genomes; they do not assess HGFv1. Searches for HGFv1 and compatibility with poultry reference genomes found no passage addressing that assembly. (LLM, conf=0.76)

      Experimental — accuracy not yet measured
  • Premisecitation

    GRIA4 belongs to glutamate receptor genes that downregulate excitatory signaling and stress response in domesticated animals.

    “GRIA4 (also known as GluR4 in mice) belongs to glutamate receptor genes which downregulate excitatory signaling and stress response in domesticated animals (O’Rourke and Boeckx 2020).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites O’Rourke and Boeckx 2020 source

      The Conclusion (page not given) hypothesizes that certain glutamate receptor genes downregulate excitatory signaling and help regulate the stress response, particularly kainate and Group II/III metabotropic receptors. It does not extend that proposed role to GRIA4; it identifies GRIA2 as the only AMPA receptor gene with potentially convergent selection. (LLM, conf=0.86)

      Experimental — accuracy not yet measured
  • Classified as probably not a substantial claim. 16
  • May combine two claims. 35

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Only two animals were domesticated in Africa: donkey and helmeted guinea fowl (Numida meleagris).

    “In contrast to many plants, only two animals were domesticated in Africa: donkey and HGF (Numida meleagris) (Gifford-Gonzalez and Hanotte 2011).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Gifford-Gonzalez and Hanotte 2011 source

      The Donkeys section says the Nubian donkey lineage was domesticated in Africa, and the Guinea Fowl section calls Numida meleagris an African domesticate. But the paper does not establish that these were the only two animals domesticated there: the Cattle section says independent domestication of African cattle remains unresolved. (LLM, conf=0.86)

      Experimental — accuracy not yet measured

  • May combine two claims.

    Findingown data

    Comparing HGFv1 with NumMel1.0, the contig N50 increases approximately 62 times (14.17 vs. 0.23 Mb) whereas gaps reduce approximately 15 Mb (5.38 vs. 20.12 Mb).

    “Comparing the HGFv1 assembly with the reference NumMel1.0 (Vignal et al. 2019), the contig N50 increases ∼ 62 times (14.17 vs. 0.23 Mb) whereas the gaps reduce ∼15 Mb (5.38 vs. 20.12 Mb) (table 1).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites Vignal et al. 2019 source

  • May combine two claims.

    Findingcitation

    Of 2.05 Gb of RNA-seq data, 92.28% and 88.48% could be mapped to the HGFv1 and NumMel1.0 assemblies, respectively.

    “In addition, 2.05 Gb of RNA-seq data obtained from pancreas, hypothalamus, bone marrow, and bursa (Darris et al. 2015) were mapped onto the assemblies of HGFv1 and NumMel1.0, respectively. Overall, 92.28% and 88.48% of the RNA-seq reads could be mapped to the two assemblies, respectively.”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Darris et al. 2015 source

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    The genes ACTN1 and PIEZO2 play important roles in muscle development and function.

    “The genes of ACTN1 (Blondelle et al. 2019) and PIEZO2 (Delle Vedove et al. 2016) play important roles in muscle development and function.”
    Quote in the paperNot a substantial claim2 of 2 sources checked
    • cites Blondelle et al. 2019 source
    • cites Delle Vedove et al. 2016 source

  • May combine two claims.

    Findingown data

    Among the selected genes, tyrosinase gene (TYR) located in a 9.5 Mb LD block and the pattern of genotype distribution around this TYR gene distinguished breed Camosciata from other helmeted guinea fowl populations.

    “Among the selected genes, tyrosinase gene (TYR) accounting for white plumage in chickens (Chen et al. 2015) located in a 9.5 Mb LD block (fig. 5C) and the pattern of genotype distribution around this TYR gene distinguished breed Camosciata from other HGF populations (supplementary fig. S11, Supplementary Material online).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites Chen et al. 2015 source
    • Rests on an assumption: The Italian breed Camosciata and Selvatica are representative of recent breeding, and their plumage phenotypes are correctly classified.

  • Classified as probably not a substantial claim. May combine two claims.

    Premisecitation

    Previous genetic diversity studies based on mitochondrial DNA and microsatellite markers revealed an absence of genetic structuring in populations of African domestic helmeted guinea fowl, implying a recent domestication accompanied with rapid subsequent dispersal in Africa.

    “Previous genetic diversity studies based on mitochondrial DNA (Adeola et al. 2015; Murunga et al. 2018) and microsatellite markers (Kayang et al. 2010; Botchway et al. 2013) revealed an absence of genetic structuring in populations of African domestic HGF, implying a recent domestication accompanied with rapid subsequent dispersal in Africa.”
    Quote in the paperSubstantial claim2 of 3 sources checked
    • cites Adeola et al. 2015 source
    • cites Murunga et al. 2018 source

      Split into 2 atoms — 1 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.

      Experimental — accuracy not yet measured
    • cites Kayang et al. 2010 source

      Split into 2 atoms — 0 confirmed, 2 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.

      Experimental — accuracy not yet measured

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationcitation

    GRIA4's role implies additional roles in visual deterioration involved in domestication.

    “implying additional roles in visual deterioration involved in domestication (Wang et al. 2016).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Wang et al. 2016 source

      The Introduction (page not provided) describes reduced visual ability in domestic chickens, and the Results link several vision-related genes to domestication. But our copy does not identify GRIA4 or establish a role for it in that visual deterioration; a search for GRIA4 found no matching passage. (LLM, conf=0.83)

      Experimental — accuracy not yet measured

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    PGR and MMP13 function in poultry fertility.

    “which function in poultry fertility (Shen et al. 2016; Yuan et al. 2016)”
    Quote in the paperNot a substantial claim1 of 2 sources checked
    • cites Shen et al. 2016 source
    • cites Yuan et al. 2016 source

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductcitation

    The assembly quality of HGFv1 was evaluated with BUSCO v3, LAI, and RNA-seq reads mapping.

    “The assembly quality of HGFv1 was evaluated with BUSCO v3 (Waterhouse et al. 2018), LAI (LTR assembly index) (Ou et al. 2018), and RNA-seq reads mapping (Darris et al. 2015).”
    Quote in the paperNot a substantial claim2 of 3 sources checked
    • cites Waterhouse et al. 2018 source
    • cites Ou et al. 2018

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

    • cites Darris et al. 2015 source

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductcitation

    An unbiased estimator for linkage disequilibrium that was not sensitive to small population size was used.

    “We applied a recently developed unbiased estimator for linkage disequilibrium (LD) (Ragsdale and Gravel 2020) that was not sensitive to small population size.”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Ragsdale and Gravel 2020 source

      The Abstract and Introduction describe unbiased estimators of LD statistics and say they are particularly well suited to estimating effective population size in small populations. They do not establish that the estimator is insensitive to population size; the paper also notes limitations at extremely small population sizes (Additional information, Figure S4). (LLM, conf=0.85)

      Experimental — accuracy not yet measured

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    GRIA4 was identified as a susceptibility locus for refractive error and myopia.

    “GRIA4 was also identified as a susceptibility locus for refractive error and myopia (Verhoeven et al. 2013)”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Verhoeven et al. 2013 source

  • May combine two claims.

    Findingown data

    Compared with wild helmeted guinea fowl from Kenya and Sudan, wild helmeted guinea fowl from Nigeria had more positive f3 values, suggesting a closer relationship with domestic helmeted guinea fowl.

    “Compared with wild HGF from Kenya and Sudan, wild HGF from Nigeria had more positive f3 values, suggesting having a closer relationship with domestic HGF (supplementary fig. S4, Supplementary Material online).”
    Quote in the paperSubstantial claim
    • Rests on an assumption: The sampled wild helmeted guinea fowl individuals, after removing outliers, represent the ancestral wild progenitor populations and are not substantially admixed or feral.

  • May combine two claims.

    Findingown data

    When K = 5, which had the lowest cross-validation error value, a dominant component in the Iranian domestic helmeted guinea fowl was detected.

    “When K = 5, which had the lowest cross-validation error value (supplementary fig. S3, Supplementary Material online), a dominant component in the Iranian domestic HGF was detected.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Domestic helmeted guinea fowl populations underwent much sharper decreases than wild populations, and the Italian population had the smallest effective population size estimation.

    “Domestic HGF populations underwent much shaper decreases than wild populations, and the Italian population had the smallest Ne estimation.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Phylogenetic trees constructed with FastTree and RAxML showed that the clade of wild helmeted guinea fowl from East Africa (Sudan and Kenya) diverged first, followed by the split of the wild helmeted guinea fowl from Nigeria and all the domestic helmeted guinea fowl.

    “When using vulturine guinea fowl and crested guinea fowl as outgroup taxa, phylogenetic trees constructed with FastTree and RAxML showed that the clade of wild HGF from East Africa (Sudan and Kenya) diverged first, followed by the split of the wild HGF from Nigeria and all the domestic HGF (fig. 2A and supplementary fig. S2, Supplementary Material online).”
    Quote in the paperSubstantial claim
    • Rests on an assumption: The sampled wild helmeted guinea fowl individuals, after removing outliers, represent the ancestral wild progenitor populations and are not substantially admixed or feral.
    • Rests on an assumption: The outgroup species vulturine guinea fowl and crested guinea fowl are appropriate outgroups for rooting the phylogeny and inferring derived alleles.

  • May combine two claims.

    Findingown data

    The assembled HGFv1 genome consists of 1,127 scaffolds with total length of 1049.9 Mb.

    “Using the strategy based on PacBio long-reads sequencing, BioNano optical mapping, and Hi-C scaffolding, we assembled 1,127 scaffolds with total length of 1049.9 Mb to generate assembly HGFv1 (supplementary fig. S1, Supplementary Material online), in which the first 16 scaffolds accounted for 90% (949.6 Mb) of the total assembly, approaching near-chromosome level (fig. 1A).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Among the domestic helmeted guinea fowl samples, LD decay rates were highest in the Nigerian population and lowest in the Italian population followed by the Sudanese population.

    “Among the domestic HGF samples, LD decay rates were highest in the Nigerian population and lowest in the Italian population followed by the Sudanese population.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Joint variant calling produced 44,035,924 SNPs and 4,214,076 InDels.

    “Joint variant calling produced 44,035,924 SNPs and 4,214,076 InDels (details in Materials and Methods).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The Italian and Sudanese populations presented the highest mean number and sum length of ROHs, respectively.

    “The Italian and Sudanese populations presented the highest mean number and sum length of ROHs, respectively.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The locus of p.Trp218Gly was conserved across species and located closely to the highly conserved histidine residues which were essential in catalytic activity of tyrosinase via binding to copper ions.

    “This locus was conserved across species and located closely to the highly conserved histidine residues which were essential in catalytic activity of tyrosinase via binding to copper ions (fig. 5E).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Iranian gfIR09 and gfIR10 and Hungarian HUNG12 and HUNG13 grouped with the samples from Hungary and China, respectively.

    “In addition, Iranian gfIR09 and gfIR10 and Hungarian HUNG12 and HUNG13 grouped with the samples from Hungary and China, respectively.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Among the domestic helmeted guinea fowl samples, the genetic diversity was highest in the Nigerian population and lowest in the Italian population.

    “Among the domestic HGF samples, the genetic diversity was highest in the Nigerian population and lowest in the Italian population.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Using the threshold of top > 0.1% SNPs (P < 0.001), the authors identified 4,393 SNPs as potentially having selective signals, among which 1,941 were annotated into 453 genes.

    “Using the threshold of top > 0.1% SNPs (P < 0.001), we identified 4,393 SNPs as potentially having selective signals, among which 1,941 were annotated into 453 genes (supplementary table S3 and fig. S10, Supplementary Material online).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The K = 6 and K = 7 divisions distinguished the ancestry-component for wild helmeted guinea fowl from Nigeria and Sudan, respectively.

    “The K = 6 and K = 7 divisions distinguished the ancestry-component for wild HGF from Nigeria and Sudan, respectively (supplementary fig. S3, Supplementary Material online).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Analyses identified 15,173 protein-coding genes, in which 14,373 were functionally annotated.

    “Analyses identified 15,173 protein-coding genes, in which 14,373 were functionally annotated.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Synteny analysis showed HGFv1 scaffold 5 corresponding to chicken GRCg6a chromosome Z; scaffold 4 to chromosomes 4q and 9; scaffold 6 to chromosomes 6 and 7.

    “We further computed synteny between the HGFv1 assembly and the chicken reference GRCg6a to show HGFv1 scaffold 5 corresponding to GRCg6a chromosome Z; scaffold 4 to chromosomes 4q and 9; scaffold 6 to chromosomes 6 and 7 (fig. 1B).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    2,887 out of 4,393 SNPs were fixed with derived alleles in all domestic helmeted guinea fowl populations except for domestic helmeted guinea fowl from Sudan since gene flow from wild helmeted guinea fowl was detected in the population.

    “We found that 2,887 out of 4,393 SNPs were fixed with derived alleles in all domestic HGF populations except for domestic HGF from Sudan since gene flow from wild HGF was detected in the population (supplementary fig. S6, Supplementary Material online).”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    Noncoding RNA was classified into rRNA (~45 kb), snRNA (~32 kb), tRNA (~22 kb), and miRNA (~15 kb).

    “We classified noncoding RNA into rRNA (∼45 kb), snRNA (∼32 kb), tRNA (∼22 kb), and miRNA (∼15 kb).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    Around 13.64% of the HGFv1 assembly were characterized as repeats.

    “Around 13.64% of the HGFv1 assembly were characterized as repeats (details in Materials and Methods).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Among the domestic HGF populations in this study, the domestic HGF from Nigeria has the highest level of genetic diversity and LD decay rate, but the lowest level of ROHs.

    “Among the domestic HGF populations in our study, the domestic HGF from Nigeria has the highest level of genetic diversity and LD decay rate, but the lowest level of ROHs (fig. 3).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    During domestication, genetic diversity decreased but levels of LD and ROHs increased.

    “The genetic diversity was decreased but the levels of LD and ROHs were increased (fig. 3).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The Italian population, consisting of two breeds (Camosciata and Selvatica), shows the lowest levels of genetic diversity but the highest levels of LD and ROHs compared with other domestic HGF populations.

    “As compared with other domestic HGF populations, Italian population, consisting of two breeds (Camosciata and Selvatica), shows the lowest levels of genetic diversity but the highest levels of LD and ROHs (fig. 3).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    After domestication from wild helmeted guinea fowl, the domestic helmeted guinea fowl spread widely across sub-Saharan Africa, and then underwent a global expansion due to human translocations and its ability to adapt to a wide range of habitats.

    “After domestication from wild HGF, the domestic HGF spread widely across sub-Saharan Africa, and then underwent a global expansion due to human translocations and its ability to adapt to a wide range of habitats (Blench and MacDonald 2000; Roberts 2002).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Blench and MacDonald 2000

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

    • cites Roberts 2002

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • May combine two claims.

    Interpretationown data

    Sudanese "domestic" individuals DSU02 and DSU08 clustered with the wild samples, likely reflecting wild-caught individuals.

    “Sudanese “domestic” individuals DSU02 and DSU08 clustered with the wild samples, likely reflecting wild-caught individuals.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    GRIA4 encodes an AMPA-sensitive glutamate receptor that functions as a ligand-gated ion channel and mediates synaptic transmission and neuroplasticity.

    “For instance, GRIA4 encodes an AMPA-sensitive glutamate receptor that functions as a ligand-gated ion channel and mediates synaptic transmission and neuroplasticity (Zhu et al. 2000).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Zhu et al. 2000 source

  • May combine two claims.

    Interpretationown data

    The mutation p.Trp218Gly was predicted to be probably damaging with a score of 0.998 in PolyPhen-2, suggesting it likely affected tyrosinase function and caused white plumage in the Camosciata breed.

    “The mutation p.Trp218Gly was predicted to be probably damaging with a score of 0.998 (sensitivity: 0.27; specificity: 0.99) in the PolyPhen-2 prediction, suggesting it likely affected tyrosinase function and caused white plumage in the Camosciata breed.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: The Italian breed Camosciata and Selvatica are representative of recent breeding, and their plumage phenotypes are correctly classified.

  • May combine two claims.

    Interpretationown data

    Three Nigerian (Y10, Y4, and Y27) and one Sudanese (WSU15) "wild" helmeted guinea fowl individuals clustered with domestic samples, which potentially indicated feral domesticated helmeted guinea fowl.

    “Three Nigerian (Y10, Y4, and Y27) and one Sudanese (WSU15) “wild” HGF individuals clustered with domestic samples, which potentially indicated feral domesticated HGF.”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim.

    Study design and conductcitation

    To reduce the effects of population structure and cryptic relatedness, the authors removed ten outliers and re-grouped the remaining 119 samples into 12 populations in subsequent population genomic analyses.

    “To reduce the effects of population structure and cryptic relatedness (Lawson and Falush 2012), we removed these 10 outliers and re-grouped the remaining 119 samples into 12 populations in subsequent population genomic analyses.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Lawson and Falush 2012 source

  • Probably not a substantial claim: may not pass S1 (asserted).

    Interpretationreasoning

    A single domestication event occurred in West Africa.

    “we hypothesize a single domestication event in West Africa (fig. 4B)”
    Quote in the paperNot a substantial claim
    • Rests on an assumption: Wild HGF sampled from Nigeria are truly wild and represent the ancestral wild population.

  • May combine two claims.

    Premisecitation

    Domestic HGFs are generally less skittish and locomotive than their wild counterparts.

    “Domestic HGFs are generally less skittish and locomotive than their wild counterparts (Roberts 2002).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Roberts 2002

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • May combine two claims.

    Interpretationcitation

    All patterns are consistent with bottlenecking in extensive breeding practices, as known from evidence on selection starting in the first half of the 1900s.

    “All the patterns consistent with bottlenecking in extensive breeding practices, as known by the evidences on selection starting in the first half of 1900s (Ghigi 1936).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Ghigi 1936

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductreasoning

    Eight different samples for each HGF population were randomly selected to avoid bias in sample size.

    “We randomly selected eight different samples for each of HGF populations to avoid bias in sample size.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationreasoning

    HGFv1 provides a robust reference not only for various helmeted guinea fowl researches, but also for Galliformes poultry studies.

    “Thus, HGFv1 provides a robust reference not only for various HGF researches, but also for Galliformes poultry (e.g., chicken, quail, and turkey) studies.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationreasoning

    The single domestication event occurred after the split of wild and domestic HGF around 5,500 YBP but before the divergence of domestic HGF around 1,300 YBP.

    “which appears to have occurred after the split of wild and domestic HGF around 5,500 YBP but before the divergence of domestic HGF around 1,300 YBP.”
    Quote in the paperSubstantial claim
    • The authors state this as an assumption: The mutation rate for HGF is the same as the chicken lineage rate of 1.91 × 10−9 per site per year.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductreasoning

    ROHs were detected using the pruned data set to eliminate the impact of strong LD.

    “We used the R package detectRUNS (Biscarini et al. 2018) to detect ROHs using the pruned data set to eliminate the impact of strong LD.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Biscarini et al. 2018

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • May combine two claims.

    Interpretationcitation

    The long LD block brought a challenge to refining the causal loci of white plumage but provided an opportunity to investigate pleiotropy and linkage involved in breeding.

    “The long LD block in the genomes brought challenge to refining the casual loci of white plumage, but provided an opportunity to investigate the pleiotropy and linkage involved in the breeding (Wright et al. 2010).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Wright et al. 2010 source
46 of 46

  • The paper relies on this without support.

    The sampled wild helmeted guinea fowl individuals, after removing outliers, represent the ancestral wild progenitor populations and are not substantially admixed or feral.

    “To reduce the effects of population structure and cryptic relatedness (Lawson and Falush 2012), we removed these 10 outliers and re-grouped the remaining 119 samples into 12 populations in subsequent population genomic analyses.”

  • The paper relies on this without support.

    The demographic model implemented in momi2 and the selected model structure adequately capture the true history of helmeted guinea fowl domestication, including the number and direction of gene flow events.

    “The selected model, which included 100 additional bootstrap iterations (fig. 4B and supplementary fig. S9, Supplementary Material online), showed that domestic HGF populations split from wild HGF populations at 5,452 YBP (95% bootstrap interval 9,916–2,548).”

  • The paper relies on this without support.

    The Italian breed Camosciata and Selvatica are representative of recent breeding, and their plumage phenotypes are correctly classified.

    “Because plumage color is a classical paradigm in poultry domestication and breeding (Domyan et al. 2014; Chen et al. 2015; Zhou et al. 2018), we screened for selective sweeps on the Italian domestic breed Camosciata showing cream white plumage with defined white spots (mutant type; fig. 5) (Ghigi 1936).”

  • The paper relies on this without support.

    The outgroup species vulturine guinea fowl and crested guinea fowl are appropriate outgroups for rooting the phylogeny and inferring derived alleles.

    “When using vulturine guinea fowl and crested guinea fowl as outgroup taxa, phylogenetic trees constructed with FastTree and RAxML showed that the clade of wild HGF from East Africa (Sudan and Kenya) diverged first, followed by the split of the wild HGF from Nigeria and all the domestic HGF (fig. 2A and supplementary fig. S2, Supplementary Material online).”

  • The paper relies on this without support.

    Wild HGF sampled from Nigeria are truly wild and represent the ancestral wild population.

    “The sampling of wild species was approved by Kenyan Wildlife Service and Nigeria National Park Service under permit numbers KWS/BRM/5001 and NPH/GEN/530/I/33, respectively.”

  • The authors state this as an assumption.

    The mutation rate for HGF is the same as the chicken lineage rate of 1.91 × 10−9 per site per year.

    “Because the mutation rate for HGF was unavailable, we used the rate 1.91 × 10−9 per site per year (Jarvis et al. 2014) for the chicken lineage.”
6 of 6

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.

  • Two thresholds stated for SNP-based PBS

    Major

    The statistical-thresholds section first includes PBS among methods using a top-0.1% threshold, then specifies a top-0.5% threshold for SNP-based PBS.

  • Conflicting protein-coding gene counts

    Minor

    The Results report 15,173 protein-coding genes, of which 14,373 were functionally annotated, while the Discussion gives a different count of 14,573 protein-coding genes without explaining what it represents.

  • Demographic-model run count changes within one sentence

    Minor

    The Methods say 20 independent runs were fitted, then say the best model was chosen from three runs.

  • Conflicting FastTree resampling counts

    Minor

    The figure caption describes support from 100 bootstraps, but the Methods say FastTree used 1,000 resamples to calculate support values.

4 of 4

Cites

Flagged first, then by citations

2 of the 72 references couldn’t be matched to a known paper.

Research works printed but not linked: 3

  1. Biscarini, 2018, CRAN (The comprehensive R archive network)
  2. Ghigi, 1936, Galline di Faraone e Tacchini
  3. Roberts, 2002, Guineafowl past and present

Cited by

Sorted by citations

Related

Authors
Shen, Q.-K., Peng, M.-S., Adeola, A. C., Kui, L., Duan, S., Miao, Y.-W., Eltayeb, N. M., Lichoti, J. K., Otecko, N. O., Strillacci, M. G., Gorla, E., Bagnato, A., Charles, O. S., Sanke, O. J., Dawuda, P. M., Okeyoyin, A. O., Musina, J., Njoroge, P., Agwanda, B., Kusza, S., Nanaei, H. A., Pedar, R., Xu, M.-M., Du, Y., Nneji, L. M., Murphy, R. W., Wang, M.-S., Esmailizadeh, A., Dong, Y., Ommeh, S. C., & Zhang, Y.-P.
Affiliations
  • Kunming Institute of Zoology (CN)
  • Harvard University (US)
  • Kunming Institute of Physics (CN)
  • Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
  • University of Bahri (SD)
  • Ministry of Agriculture Livestock and Fisheries (KE)
  • University of Milan (IT)
  • University of Ibadan (NG)
  • Taraba State Ministry of Agriculture and Natural Resources, Jalingo, Nigeria
  • Joseph Sarwuan Tarka University Makurdi (NG)
  • National Park Service Headquarter, Federal Capital Territory, Abuja, Nigeria
  • National Museums of Kenya (KE)
  • University of Debrecen (HU)
  • Shahid Bahonar University of Kerman (IR)
  • State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
  • Royal Ontario Museum (CA)
  • Howard Hughes Medical Institute, University of California Santa Cruz, California, USA
  • Yunnan Agricultural University (CN)
  • Jomo Kenyatta University of Agriculture and Technology (KE)
Corresponding author
  • Esmailizadeh, Ali
  • Dong, Yang
  • Ommeh, Sheila C
  • Zhang, Ya-Ping
ORCID
Venue
Genome Biology and Evolution
Publisher
Oxford University Press (OUP)
Published
2021-05-01
Volume
13
Issue
6
ISSN
1759-6653 (ISSN-L)
DOI
10.1093/gbe/evab090
PMC
PMC8214406
OpenAlex
W3160004338
Semantic Scholar
85adc2c3e7559b6ca5d4a5d69f88ca198a5e3411
Cited by
13
References
72
Citations by year
2026: 3 · 2025: 3 · 2024: 4 · 2023: 1 · 2022: 2
FWCI
0.88
Type
journal article
Language
en
Open access
Licence
Locations
  • Genome Biology and Evolution (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • PubMed Central (submittedVersion, cc-by)
  • Archivio Istituzionale della Ricerca (Universita Degli Studi Di Milano) (submittedVersion, other-oa)
Funders
  • Chinese Academy of Sciences (2016VBA050, SAJC201306, SAJC201611)
  • Natural Sciences and Engineering Research Council of Canada (A3148)
  • Sino-Africa Joint Research Center, Chinese Academy of Sciences (SAJC201611)
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 › Livestock and Poultry Management
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
Keywords
helmeted guineafowl, guinea fowl, domestication, de novo genome assembly, population genomics, West Africa, plumage coloration, fertility, pleiotropy, linkage, wild progenitor
MeSH terms
Domestication, Animals, Male, Phylogeny, Selection, Genetic, Genetic Variation, Genome, Galliformes, Phylogeography

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 2026-10-09.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-09.

Cited sources are checked by 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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