(B) Manhattan plot of the Z|ΔPi| scores between two RJF and four commercial populations. Like birds, it had feat… Other signals overlapped with HNF4G, TBXAS1, GLP1R and GJD2. Writing – original draft, Affiliations Variants in the up- and down-stream regions and in the 3' UTR, 5' UTR regions were merged into the single categories. The black line represents the total number of SNPs in each ΔAF bin and colored lines represent log2 fold changes of the observed SNP count for each category in each bin against the expected SNP count. Meet the birds: These are the citizens of Birdville, and the chorus of The Birds. Modern broilers rapidly reach a body weight of 4–5 kg compared to the ~1 kg weight of an adult RJF male [3]. During the last century, the domestic chicken has been developed into a major food source by adapting the genome to specialized egg laying (layers) and fast-growing meat birds (broilers) whose productivity far exceeds their wild ancestor as well as the domestic chicken present only 100 years ago. In panel A, two regions of high homozygosity are centered over ALX1 and KITLG on GGA1. In modern birds, feathers are also important for insulation, mating displays, and as aerodynamic aids when running. The number of detected variants was 26,290,203 which included 3,442,027 INDELs and 1,024,944 multi-allelic sites. Data Availability: Data is deposited in the European Nucleotide Archive (ENA) with the accession number (PRJEB30270). No, Is the Subject Area "Domestic animals" applicable to this article? A good proportion of these loci are probably dragged to higher frequencies due to linkage with the target loci under selection [9]. SNP by SNP comparison of allele frequency between groups of wild and domestic chicken showed a highly significant deficiency of the proportion of amino acid altering mutations. Also in 1963, Alfred Hitchcock released his movie adaptation of "The Birds." Órnithes) is a comedy by the Ancient Greek playwright Aristophanes.It was performed in 414 BC at the City Dionysia where it won second place. Because of low coverage, we treated the population RJFi as a pool in this analysis. Flight is used by birds as a means of locomotion in order to find food and mates and to avoid predators. Human driven selection during domestication and subsequent specialization into meat type (broilers) and egg layer (layers) birds has left detectable signatures of selection within the genome of modern chicken. (B) Average FST for different categories of SNPs. Yes Many birds can hide in the tall grass and weeds and insects can change their colour to blend into the surroundings. Formal analysis, RJFi, WL and BL along with the three DNA pools (RWp, BRpB and BRpD) were sequenced with 2x101 bp paired-end reads (see Table 1). We observed a marked decline in relative abundance of missense substitutions showing a steady decrease above ΔAF = 0.2 in all contrasts (Fig 4). The average FST values varied both among chromosomes and between autosomes and chromosome Z. Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, United States of America. Maximizing yield however, has been at the price of reduced immunity and accompanied by a number of undesirable traits [5]. First, we explored differentiation of loci between the following combinations of populations. Chair of Animal Breeding, Technical University Munich, Freising, Germany, Affiliation JPT2 (also known as HN1L) shows high sequence conservation among vertebrates and are proposed to be involved in embryo development [15]. Further genetic and functional studies of these allelic variants are necessary to verify their possible contribution to chicken domestication. The R packages SNPRelate and gdsfmt [41] were used for principal component analysis of relatedness using identity-by-descent measures estimated from all SNPs. Each dot represents a 40 kb window in steps of 20 kb along the genome. All these may have been factors in the evolution of feathers in the dinosaur ancestors of birds; it is a matter of some debate among paleontologists as to which factors were most important. Understanding the nature of adaptive forces acting on the genome of commercial chicken provides insight into the complex relationship between production, disease and genes while opening up new directions for further improvement of this important farm animal, that is essential for global food security. The fact that different broiler lines have a high frequency of the variant allele at this locus is consistent with this suggestion. https://doi.org/10.1371/journal.pgen.1007989.s001, https://doi.org/10.1371/journal.pgen.1007989.s002, https://doi.org/10.1371/journal.pgen.1007989.s003, https://doi.org/10.1371/journal.pgen.1007989.s004, https://doi.org/10.1371/journal.pgen.1007989.s005, https://doi.org/10.1371/journal.pgen.1007989.s006, https://doi.org/10.1371/journal.pgen.1007989.s007, https://doi.org/10.1371/journal.pgen.1007989.s008, https://doi.org/10.1371/journal.pgen.1007989.s009, https://doi.org/10.1371/journal.pgen.1007989.s010, https://doi.org/10.1371/journal.pgen.1007989.s011, https://doi.org/10.1371/journal.pgen.1007989.s012, https://doi.org/10.1371/journal.pgen.1007989.s013, https://doi.org/10.1371/journal.pgen.1007989.s014, https://doi.org/10.1371/journal.pgen.1007989.s015, https://doi.org/10.1371/journal.pgen.1007989.s016, https://doi.org/10.1371/journal.pgen.1007989.s017, https://doi.org/10.1371/journal.pgen.1007989.s018. Yes Mutations in MEGF10 have previously been shown to cause an unusual combination of dystrophic and myopathic features leading to the weak muscles in humans [30, 31], suggesting that the mutation reported here may affect muscle growth in broilers. EPOPS, KING OF THE BIRDS: Once a man, Tereus. S1 Fig presents a summary of SNPs called based on different sequencing parameters. Welcome to your online resource for everything you've ever wanted to know about THE BIRDS. Each triangle represents the number (103) of variants exclusively segregating or detected in the corresponding population and overlapping sections denote group-specific variants. Birds and mammals are warm-blooded animals www.reflectivelearn.com 5. The absolute allele frequency difference (ΔAF) was calculated for different categories of SNPs in four contrasts (1) RJFs vs. Coms, (2) BRs vs. LRs, (3) RJFs vs. BRs and (4) RJFs vs. LRs and these ΔAF-values were sorted into 10 bins of allele frequency (ΔAF 0–0.1, etc.) We argue that this sharp decline in the proportion of differentiated missense substitutions represents purifying selection that reduces the frequency of slightly deleterious mutations affecting production and/or health. Another particularly interesting substitution in this contrast overlaps the multiple epidermal growth factor 10 gene (MEGF10, AFBRs = 0.82 and AFLRs = 0.00) on GGA8, known to function as a myogenic regulator of satellite cells in skeletal muscle [30]. Panel C provides a schematic representation of the genome-wide nucleotide diversity (ZPi-scores). This scenario allows us to explore if the same alleles are responsible for the selection response in these parallel populations. There are two basic hypotheses that explain how flight may have evolved in birds: the arboreal (“tree”) hypothesis and the terrestrial (“land”) hypothesis.The arboreal hypothesis posits that tree-dwelling precursors to modern birds jumped from branch to branch using their feathers for gliding before becoming fully capable of flapping flight. The profile of FST also varied among comparisons and chromosomes (S4 Fig), which complicates defining a threshold to distinguish true selective sweeps from regions showing genetic differentiation due to genetic drift. In the second step, we searched the genome for regions with high degrees of fixation. The Birds is a 1952 novelette by Daphne du Maurier first published in her short story collection, The Apple Tree. Contrasting wild and domestic chicken we confirmed selection at the BCO2 and TSHR loci and identified 34 putative sweeps co-localized with ALX1, KITLG, EPGR, IGF1, DLK1, JPT2, CRAMP1, and GLI3, among others. e1007989. Window-based FST values were then normalized and windows in the outlier tail ZFST > 6 were identified as selection candidates for domestication and genetic improvement in commercial populations. Cluster Size and ClusterWindowSize were set to 4 and 10, respectively. Analysis of selection provided a comprehensive list of several tens of independent loci that are likely to have contributed to domestication or improving production. For further information on the behaviour and morphology of these birds we refer to the AVIANDIV project webpage. (A) Comparison of the minor allele frequency spectrum of coding sequences in RJFt and commercial populations. The results revealed a subtle differentiation between wild and modern chicken at most loci, whereas a small percentage of loci showed strong differentiation. This signal was further supported by analysis of the differences in nucleotide diversity between wild and domestic chicken (ΔPi) that revealed a high degree of fixation in domestic chicken in this window on GGA14 (see section ‘Analysis of fixation’ and Fig 2B), therefore we decided to further evaluate this signal. Formal analysis, The size of a selective sweep depends on multiple factors such as the local recombination rate, selection intensity, and the number of generations that passed from the time when a favourable mutation arose and it became fixed. Writing – review & editing, Affiliations BRB was another sire line originally from France, developed in 1970 with a breeding population size varying between 10,000 to 70,000. The RJFi population involved 10 individuals of the Richardson line, originating from RJF caught in India in the 1960´s. Since only windows with >10 SNPs were analysed, the number of windows available for analysis varied from 46,146 to 46,150 per comparison (S5–S8 Tables). The commercial broiler and layer suppliers produce more than 70 billion birds annually to meet current worldwide consumer demands of more than 120 … We further report a highly significant (P<2.5×10−6) deficiency of amino-acid altering mutations among those showing strong genetic differentiation between RJF and commercial birds. Out of the >18 million variants detected in RJFt, as many as 4.4 million were unique to this population (Fig 1B). Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden, Writing – original draft, Data curation, The story follows Pisthetaerus, a middle-aged Athenian who persuades the world’s birds to create a new city in the sky (thereby gaining control over all communications between men and gods), and is himself eventually miraculously transformed into a bird-like god figure himself, and replaces Zeus as the pre-eminent power in the cosmos. And the earth has several natural environments that are spread across large geographic areas. The quality parameters shown from left to right and top to bottom are: Phred Quality Score; Allele Frequency; Depth of Coverage; Base Quality Rank Sum; Clipping Rank Sum; Excess of Heterozygosity; Fisher Strand; Inbreeding Coefficient; Maximum Likelihood Expectation for the Allele counts; Maximum Likelihood Expectation for the Allele Frequency; Mapping Quality; Mapping Quality Rank Sum; Quality by Depth; Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias; Strand Odds Ratio and Allelic Number in called genotypes. EPOPS, KING OF THE BIRDS: Once a man, Tereus. The results contribute to the understanding of major genetic changes that took place during the evolution of modern chickens and in poultry breeding. https://doi.org/10.1371/journal.pgen.1007989.t001. Signals marked by a star represent regions lacking annotated genes. A family tree of birds shows their evolutionary connections. Coding SNPs with ΔAF≥0.7 in the contrast between BRs vs. LRs also included interesting candidate mutations. The SNPs were then sorted into different bins of ΔAF (e.g., 0–0.1, >0.1–0.2, etc.) SNPs called according to the best practices workflow using GATK (McKenna et al., 2010). Birds are categorized as a biological class, Aves. We estimated FST [45] for each of these four contrasts. Nucleotide diversity are estimated only for the six individually sequenced populations. https://doi.org/10.1371/journal.pgen.1007989.g001. Panel A and B represent the contrasts ‘RJFs vs. LRs’ and ‘RJFs vs. BRs’, respectively. The distribution of window-ZFST values are plotted in S4C Fig for all comparisons. The retained variants were distributed in the genome with an average density of 1 SNP every ~50 bases. Friedrich-Loeffler-Institut, Neustadt, Germany, Roles In a further step we estimated nucleotide diversity for groups of birds as well as all six populations of RJFs and commercials (S5A and S5B Fig). Supervision, These negative effects may either be the result of pleiotropy of genes under selection for increased productivity, hitch-hiking of unfavourable alleles with the alleles under selection, or genetic drift. show a substantially smaller proportion of rare alleles that can be attributed to the smaller effective population size caused by recent selective breeding leading to loss of rare alleles. Analysis of selection provided a comprehensive list of several tens of independent loci that are likely to have contributed to domestication or improving production. We identified 34 putative selective sweeps co-localized with, among others, KITLG, ALX1, IGF1, DLK1, JPT2 and CRAMP1. It was adapted into the famous Alfred Hitchcock film of the same name. A study in Drosophila melanogaster showed that a CRAMP1 homolog is involved in epigenetic regulation of gene expression [16]. We observed an FST value of 0.65 (ZFST = 7.0) over BCO2 (Fig 2A) and the localization perfectly overlapped the previously defined sweeps. We carried out enrichment analyses to identify categories of SNPs showing differentiation between groups of birds. The birds suffer the same plights as humanity: the corrupting influence of power, marital issues, discrimination, denial, objectification, etc. Across the genome we observed the largest FST values in contrasts between populations with the lowest nucleotide diversities reflecting genetic drift (Tables 1 and 2). Adaptation is, first of all, a process, rather than a physical part of a body. The window harbouring the TSHR locus showed an FST value of 0.34 (ZFST = 3.4) in the ‘RJFs vs. Coms’ contrast residing within 9% of top differentiated windows (S6 Table). https://doi.org/10.1371/journal.pgen.1007989.s020, https://doi.org/10.1371/journal.pgen.1007989.s021.

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