DOCSLIB.ORG

A High-Quality Assembly Reveals Genomic Characteristics, 1

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
A High-Quality Assembly Reveals Genomic Characteristics, 1 A High-Quality Assembly Reveals Genomic Characteristics, 1 Phylogenetic Status and Causal Genes for White Feather of 2 Indian Peafowl shaojuan Liu South China Agricultural University College of Animal Science hao Chen Jiangxi Science and Technology Normal University School of Life Science jing Ouyang Jiangxi Science and Technology Normal University School of Life Science min Huang South China Agricultural University College of Animal Science hui Zhang South China Agricultural University College of Animal Science sumei Zheng South China Agricultural University College of Animal Science suwang Xi Jiangxi Agricultural University College of Animal Science and Technology hongbo Tang Jiangxi Science and Technology Normal University School of Life Science yuren Gao Jiangxi Science and Technology Normal University School of Life Science yanpeng Xiong Jiangxi Science and Technology Normal University School of Life Science di Cheng Jiangxi Agricultural University College of Animal Science and Technology kaifeng Chen Jiangxi Agricultural University College of Animal Science and Technology bingbing Liu South China Agricultural University College of Animal Science wanbo Li Jimei University xueming Yan Jiangxi Science and Technology Normal University School of Life Science huirong Mao ( [email protected] ) Jiangxi Agricultural University https://orcid.org/0000-0003-2588-1521 jun Ren South China Agricultural University College of Animal Science Research Keywords: Indian peafowl, Genome assembly, Phylogeny, PMEL, White feather Posted Date: July 1st, 2021 DOI: https://doi.org/10.21203/rs.3.rs-650113/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License 1 A high-quality assembly reveals genomic characteristics, 2 phylogenetic status and causal genes for white feather of 3 Indian peafowl 4 Shaojuan Liu1#, Hao Chen3#, Jing Ouyang3, Min Huang1, Hui Zhang1, Sumei Zheng1, 5 Suwang Xi2, Hongbo Tang3, Yuren Gao3, Yanpeng Xiong3, Di Cheng2, Kaifeng Chen2, 6 Bingbing Liu1,Wanbo Li4, Xueming Yan3*, Huirong Mao2*, Jun Ren 1* 7 1 College of Animal Science, South China Agricultural University, Guangzhou 510642, 8 China 9 2 School of Animal Science and Technology, Jiangxi Agricultural University, 10 Nanchang 330045, China 11 3 College of Life Science, Jiangxi Science & Technology Normal University, Nanchang 12 330013, China 13 4 Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of 14 Agriculture and Rural Affairs, Jimei University, Xiamen 361021, China 15 # Both authors contribute equally to this paper. 16 * Corresponding author. 17 E-mail address: [email protected] (H. M); [email protected] (X. 18 Y) 19 20 21 22 23 24 25 26 27 28 1 29 Abstract 30 Background: Indian peafowl (Pavo cristatus) attracts people's attention because of the 31 exclusively dazzling phenotypic characteristics. However, little is known about the 32 phenotypic evolution and phylogeny of Indian peafowl at the whole-genome level. So 33 far, there has been no report on the genetic mechanism of the formation of white feather 34 in white feather peafowl. 35 Results: This study assembled a draft genome of Indian peafowl with a genome size of 36 1.05 Gb (the sequencing depth is 362×), and N50 of the contig and scaffold was up to 37 6.2 Mb and 11.4 Mb, respectively. Compared with other birds, Indian peafowl changed 38 in terms of metabolism, immunity, skeletal development and feather development, 39 which provided a novel insight into the phenotypic evolution of peafowl, such as the 40 large body size and feather morphologies. It was confirmed that the phylogeny of Indian 41 peafowl was closer to that of turkey than that of chicken. Specially, it was identified 42 that PMEL was a causal gene leading to the formation of white plumage in blue and 43 white feather peafowl. 44 Conclusions: This study provides a peafowl genome with high-quality as well as a 45 novel understanding in the phenotypic evolution and phylogeny of peafowl among 46 other birds. The results contribute a valuable reference genome to the study of the avian 47 genome evolution. In addition, the discovery of the genetic mechanism of white 48 plumage not only is a breakthrough in the exploration of peafowl plumage, but also 49 provides clues and new ideas for further investigations of the avian plumage coloration 50 and artificial breeding in peafowl. 51 Keywords: Indian peafowl; Genome assembly; Phylogeny; PMEL; White feather 52 53 54 55 56 57 58 59 2 60 Introduction 61 Pavo cristatus, commonly called Indian peafowl or blue peafowl, is the king of birds, 62 representing elegance, honour, beauty, luck, and romance in many Asian cultures 63 (Figure 1a) (Gadagkar, 2003; Kushwaha & Kumar, 2016). Peafowl, belonging to the 64 Aves, Galliformes, Phasianidae, and Pavo, has two species: green peafowl and blue 65 peafowl. Indian peafowl, as the national bird of India, has been widely distributed in 66 Bangladesh, Bhutan, India, Nepal, Pakistan, and Sri Lankan (Kushwaha & Kumar, 67 2016; Ramesh & McGowan, 2009). Commonly, the male Indian peafowl is more 68 attractive than female because of its larger body size and more glittering plumage. 69 Indian peafowl is one of the largest and most beautiful birds in pheasant as a valuable 70 ornamental display with their fan-shaped crests, brightly blue plumage, and glaring tails. 71 Moreover, Indian peafowl is well known as a protein resource, because their meat, 72 internal organs, and bones have high nutritional values, even with medicinal values 73 (Mushtaq-ul-Hassan, Ali, Arshad, Mahmood, & Research, 2012; Paranjpe & Dange, 74 2019; Talha, Mia, & Momu, 2018). 75 With the improvement of whole genome sequencing technology, more and more 76 avian genomes were assembled, such as chicken (Gallus gallus) ("Sequence and 77 comparative analysis of the chicken genome provide unique perspectives on vertebrate 78 evolution," 2004), turkey (Meleagris gallopavo) (Dalloul et al., 2010), duck (Anas 79 platyrhynchos) (Z. Zhang et al., 2018), and other birds (Jarvis et al., 2014), which 80 provided basic references for the study of phenotypic characteristics, evolution, 81 economic traits, and environmental adaptation of birds. As for peafowl, the first draft 82 genome of peafowl was released in 2018. However, the length of scaffold and contig 83 N50 of the assembling were only 25.6 kb and 19.3 kb, respectively (Shubham K. 84 Jaiswal et al., 2018). Subsequently, Dhar, et al. improved peafowl genome by using 85 Illumina and Oxford Nanopore technology (ONT), and the length of scaffold N50 was 86 up to 0.23 Mb (Dhar et al., 2019). The previous studies of peafowl focused on courtship 87 behaviour (Dakin, McCrossan, Hare, Montgomerie, & Amador Kane, 2016), immunity 88 (Wang, Zhao, Liu, Shao, & Xing, 2019), and productivity (Samour, Naldo, Rahman, & 89 Sakkir, 2010). Additionally, most researches on the phylogenetic relationship of 90 peafowl and the Phasianidae were based on the mitochondrial genomes, DNA 91 transposable factors, and partial DNA nucleotide sequences, and the conclusions of 3 92 these researches are still controversial (J. Naseer et al., 2018; Shen et al., 2014; Zhou, 93 Sha, Irwin, & Zhang, 2015). Therefore, a better quality assembly of peafowl genome is 94 needed to provide baseline data for further studies on peafowl. It has been suggested 95 that the grey peafowl pheasant (Polyplectron bicalcaratum) could be the ancestor of 96 peafowl (Bush & Strobeck, 2003). However, the phylogenetic relationships of peafowl 97 with other pheasants are still unclear, though there have been several recent attempts to 98 investigate it. Study on Hainan peafowl pheasant provided evidences to argue whether 99 it is a subspecies of the grey peafowl pheasant (Chang et al., 2008). Zhou et al. (2015) 100 analysed the phylogenetic status of Indian peafowl in Phasianidae by using a complete 101 mitochondrial genome, and found out its closest genetic affinity with green peafowl 102 (Zhou et al., 2015). Sun et al. (2014) revealed the close relationships among Pavo, 103 Polyplectron and Argusianus within the Phasianidae (Sun et al., 2014). It is expected 104 that a more clarified taxonomic status of the peafowl in Phasianidae can be investigated 105 via the high-throughput sequencing technology. 106 Previous studies reported that there were many plumage colour mutants, including 107 white, black, variegated, cameo, and oaten (Ouyang et al., 2009; R. G Somes & Burger, 108 1993; R. G. Somes & Burger, 1991), among which, the most ornamental colour was 109 the white plumage, belonging to leucism rather than albinism since the feather was 110 white but the eyes had melanin pigmentation (Figure 1b). The inherited basis of 111 plumage colour has attracted researchers for a long time. The first report on it suggested 112 that the plumage phenotype of peafowl was determined by autosomal genes in a 113 recessive model (R. G. Somes & Burger, 1991). Another study verified that a single 114 autosomal locus was in control of all plumage phenotypes in peacock, where the pied 115 colour appeared in two heterozygous mutant alleles, with the black on recessive mutant 116 allele, and the all-white plumage in homozygous mutant allele as the most dominant (R. 117 G Somes & Burger, 1993). Nevertheless, further studies on the genetic mechanism of 118 the white plumage in peafowl are needed, i.e., to clarify the causative mutations of this 119 phenotype. 120 Therefore, a high-quality (near-chromosomal) reference genome of Indian peafowl 121 was constructed by using the third-generation de novo assembly technology. Based on 122 the assembly, it was devoted to investigate the molecular evolution and phylogenetic 123 classification of peafowl in the Phasianidae at the genome-wide level. Subsequently, 4 124 comparative genomics analysis was performed to investigate the biological 125 characteristics of evolution through comparing the genome of Indian peafowl with the 126 high-quality genomes of other birds, human and mouse. Furthermore, the 127 transcriptomic and pooled resequencing data were analysed to identify the genetic 128 mechanism of the white plumage in Indian peafowl.
Load more

Recommended publications
  • 1471-2148-10-132.Pdf
    Shen et al. BMC Evolutionary Biology 2010, 10:132 http://www.biomedcentral.com/1471-2148/10/132 RESEARCH ARTICLE Open Access AResearch mitogenomic article perspective on the ancient, rapid radiation in the Galliformes with an emphasis on the Phasianidae Yong-Yi Shen1,2,3, Lu Liang1,2,3, Yan-Bo Sun1,2,3, Bi-Song Yue4, Xiao-Jun Yang1, Robert W Murphy1,5 and Ya- Ping Zhang*1,2 Abstract Background: The Galliformes is a well-known and widely distributed Order in Aves. The phylogenetic relationships of galliform birds, especially the turkeys, grouse, chickens, quails, and pheasants, have been studied intensively, likely because of their close association with humans. Despite extensive studies, convergent morphological evolution and rapid radiation have resulted in conflicting hypotheses of phylogenetic relationships. Many internal nodes have remained ambiguous. Results: We analyzed the complete mitochondrial (mt) genomes from 34 galliform species, including 14 new mt genomes and 20 published mt genomes, and obtained a single, robust tree. Most of the internal branches were relatively short and the terminal branches long suggesting an ancient, rapid radiation. The Megapodiidae formed the sister group to all other galliforms, followed in sequence by the Cracidae, Odontophoridae and Numididae. The remaining clade included the Phasianidae, Tetraonidae and Meleagrididae. The genus Arborophila was the sister group of the remaining taxa followed by Polyplectron. This was followed by two major clades: ((((Gallus, Bambusicola) Francolinus) (Coturnix, Alectoris)) Pavo) and (((((((Chrysolophus, Phasianus) Lophura) Syrmaticus) Perdix) Pucrasia) (Meleagris, Bonasa)) ((Lophophorus, Tetraophasis) Tragopan))). Conclusions: The traditional hypothesis of monophyletic lineages of pheasants, partridges, peafowls and tragopans was not supported in this study.
    [Show full text]
  • 2011, Article ID 423938, 16 Pages Doi:10.4061/2011/423938
    SAGE-Hindawi Access to Research International Journal of Evolutionary Biology Volume 2011, Article ID 423938, 16 pages doi:10.4061/2011/423938 Research Article A Macroevolutionary Perspective on Multiple Sexual Traits in the Phasianidae (Galliformes) Rebecca T. Kimball, Colette M. St. Mary, and Edward L. Braun Department of Biology, University of Florida, P.O. Box 118525, Gainesville, FL 32611, USA Correspondence should be addressed to Rebecca T. Kimball, [email protected]fl.edu Received 2 October 2010; Accepted 26 February 2011 Academic Editor: Rob Kulathinal Copyright © 2011 Rebecca T. Kimball et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Traits involved in sexual signaling are ubiquitous among animals. Although a single trait appears sufficient to convey information, many sexually dimorphic species exhibit multiple sexual signals, which may be costly to signalers and receivers. Given that one signal may be enough, there are many microevolutionary hypotheses to explain the evolution of multiple signals. Here we extend these hypotheses to a macroevolutionary scale and compare those predictions to the patterns of gains and losses of sexual dimorphism in pheasants and partridges. Among nine dimorphic characters, including six intersexual signals and three indicators of competitive ability, all exhibited both gains and losses of dimorphism within the group. Although theories of intersexual selection emphasize gain and elaboration, those six characters exhibited greater rates of loss than gain; in contrast, the competitive traits showed a slight bias towards gains. The available models, when examined in a macroevolutionary framework, did not yield unique predictions, making it difficult to distinguish among them.
    [Show full text]
  • Early Holocene Chicken Domestication in Northern China
    Early Holocene chicken domestication in northern China Hai Xianga, Jianqiang Gaob, Baoquan Yuc, Hui Zhoud, Dawei Caid, Youwen Zhanga, Xiaoyong Chena, Xi Wanga, Michael Hofreitere,1, and Xingbo Zhaoa,1 aNational Engineering Laboratory for Animal Breeding, Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding, and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; bHebei Provincial Institute of Cultural Relic, Shijiazhuang 050031, China; cXushui County Office for Preservation of Ancient Monuments, Xushui 072550, China; dAncient DNA Laboratory, Research Center for Chinese Frontier Archaeology, College of Life Science, Jilin University, Changchun 130023, China; eFaculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany; and Department of Biology, University of York, Heslington, York YO10 5DD, United Kingdom Edited by Elizabeth Matisoo-Smith, Otago School of Medical Sciences, Dunedin, New Zealand, and accepted by the Editorial Board October 23, 2014 (received for review June 24, 2014) Chickens represent by far the most important poultry species, yet of chicken domestication in particular regions over the world the number, locations, and timings of their domestication have have also been worked out using ancient DNA analysis (14–17). remained controversial for more than a century. Here we report However, the oldest chicken sequences analyzed to date are only ancient mitochondrial DNA sequences from the earliest archaeo- around 4,000 y old, substantially postdating the beginning of logical chicken bones from China, dating back to ∼10,000 B.P. The chicken domestication. results clearly show that all investigated bones, including the old- Therefore, we chose 39 ancient chicken bones from three est from the Nanzhuangtou site, are derived from the genus Gal- archaeological sites in the area of the Yellow River (Cishan, lus, rather than any other related genus, such as Phasianus.
    [Show full text]
  • Habitat Preference of the Sole Wild Population of Francolinus Bicalcaratus Ayesha in the Palearctic: Implications for Conservation and Management
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by I-Revues Revue d’Ecologie (Terre et Vie), Vol. 71 (3), 2016 : 288-297 HABITAT PREFERENCE OF THE SOLE WILD POPULATION OF FRANCOLINUS BICALCARATUS AYESHA IN THE PALEARCTIC: IMPLICATIONS FOR CONSERVATION AND MANAGEMENT 1* 2 1 3 Saâd HANANE , Nabil ALAHYANE , Najib MAGRI , Mohamed-Aziz EL AGBANI 3 & Abdeljebbar QNINBA 1 Forest Research Center, High Commission for Water, Forests and Desertification Control, Avenue Omar Ibn El Khattab, BP 763, 10050, Rabat-Agdal, Morocco. 2 Faculté des Sciences de Rabat, 4 Avenue Ibn Battouta, BP 1014 RP, 10090, Agdal-Rabat, Morocco. 3 Université Mohammed V-Agdal, Institut Scientifique de Rabat, Avenue Ibn Battouta, BP 703, 10090, Agdal-Rabat, Morocco. * Corresponding author. E-mail : [email protected] ; phone: +212 660 125799 ; Fax: +212 537 671151 RÉSUMÉ.— Préférence d’habitat de la seule population sauvage de Francolinus bicalcaratus ayesha dans le Paléarctique : implications pour sa conservation et sa gestion.— Le Francolin à double éperon (Francolinus bicalcaratum ayesha) est un oiseau en danger critique d’extinction et endémique du Maroc, où il habite les forêts de chêne-liège. Ses populations ont été réduites principalement en raison de la chasse et de la destruction des habitats. La caractérisation de l’habitat utilisé par ces oiseaux indigènes peut optimiser les programmes futurs de réintroduction. La méthode de détection auditive a été utilisée sur des transects pour localiser les mâles chanteurs. Nous avons analysé les facteurs qui déterminent la présence du Francolin à double éperon dans le Nord-Ouest du Maroc en considérant 13 variables explicatives.
    [Show full text]
  • International Galliformes Symposium 2004
    INTERNATIONAL GALLIFORMES SYMPOSIUM 2007 CHENGDU & WOLONG, CHINA Symposium Programme SUNDAY 14 OCTOBER 2007 1600: REGISTRATION – LOBBY WANG JIANG HOTEL 1900: DINNER – WANG JIANG CLUB RESTAURANT MONDAY 15 OCTOBER 2007 0930: INAUGURAL SESSION 1040: SYMPOSIUM PHOTOGRAPH FOLLOWED BY TEA & COFFEE 1130: TECHNICAL SESSION 1: INTRODUCTION Chair G. R Potts 1130: SCIENTIFIC PROGRAMME COMMITTEE CHAIRMAN’S INTRODUCTION - Stephen J. Browne 1145: CONSERVING ASIA’S GALLIFORMES: PROGRESS AND CHALLENGES - Philip J.K. McGowan 1215: AN INTRODUCTION TO RESEARCH AND CONSERVATION OF CHINA’S GALLIFORMES - Zhang Zhengwang & Zheng Guangmei 1245: LUNCH 1400: TECHNICAL SESSION 2: CHINA 1 Chair Sun Yuehua 1400: CONSERVATION HOTSPOTS AND GAP ANALYSIS OF THE GALLIFORMES IN CHINA – Ding Changqing & Zhang Cheng’an 1420: ROOSTING BEHAVOIUR OF BUFF-THROATED PARTRIDGE TETRAOPHASIS SZECHENYII - Xu Yu, Ran Jianghong, Zhou Xin, Yang Nan, Yue Bisong & Wang Ying 1440: A STUDY OF THE GENETIC STRUCTURE AND MOLECULAR PHYLOGEOGRAPHY OF THE TIBETIAN SNOWCOCK TETRAOGALLUS TIBETANUS IN QINGHAI-TIBETAN PLATEAU - An Bei, Zhang Lixun, Ruan Luzhang, Song Sen & Liu Naifa 1500: AN INTRODUCTION TO RESEARCH ON CABOT’S TRAGOPAN TRAGOPAN CABOT IN CAPTIVITY – Zhang Yanyun & Zheng Guangmei 1 1520: TEA & COFFEE 1550: TECHNICAL SESSION 3 CHINA 2 Chair Ding Ping 1550: OCCURRENCE PATTERN OF ELLIOT’S PHEASANT SYRMATICUS ELLIOTI IN FRAGMENTED HABITATS – Ding Ping, Zheng Jiawen, Jiang Pingping, Xia Guirong & Xu Xiaojiang 1610: ESTIMATION OF HOME RANGE OF THE REEVES’S PHEASANTS SYRMATICUS REEVESII: COMPARING
    [Show full text]
  • Phasianinae Species Tree
    Phasianinae Blood Pheasant,Ithaginis cruentus Ithaginini ?Western Tragopan, Tragopan melanocephalus Satyr Tragopan, Tragopan satyra Blyth’s Tragopan, Tragopan blythii Temminck’s Tragopan, Tragopan temminckii Cabot’s Tragopan, Tragopan caboti Lophophorini ?Snow Partridge, Lerwa lerwa Verreaux’s Monal-Partridge, Tetraophasis obscurus Szechenyi’s Monal-Partridge, Tetraophasis szechenyii Chinese Monal, Lophophorus lhuysii Himalayan Monal, Lophophorus impejanus Sclater’s Monal, Lophophorus sclateri Koklass Pheasant, Pucrasia macrolopha Wild Turkey, Meleagris gallopavo Ocellated Turkey, Meleagris ocellata Tetraonini Ruffed Grouse, Bonasa umbellus Hazel Grouse, Tetrastes bonasia Chinese Grouse, Tetrastes sewerzowi Greater Sage-Grouse / Sage Grouse, Centrocercus urophasianus Gunnison Sage-Grouse / Gunnison Grouse, Centrocercus minimus Dusky Grouse, Dendragapus obscurus Sooty Grouse, Dendragapus fuliginosus Sharp-tailed Grouse, Tympanuchus phasianellus Greater Prairie-Chicken, Tympanuchus cupido Lesser Prairie-Chicken, Tympanuchus pallidicinctus White-tailed Ptarmigan, Lagopus leucura Rock Ptarmigan, Lagopus muta Willow Ptarmigan / Red Grouse, Lagopus lagopus Siberian Grouse, Falcipennis falcipennis Spruce Grouse, Canachites canadensis Western Capercaillie, Tetrao urogallus Black-billed Capercaillie, Tetrao parvirostris Black Grouse, Lyrurus tetrix Caucasian Grouse, Lyrurus mlokosiewiczi Tibetan Partridge, Perdix hodgsoniae Gray Partridge, Perdix perdix Daurian Partridge, Perdix dauurica Reeves’s Pheasant, Syrmaticus reevesii Copper Pheasant, Syrmaticus
    [Show full text]
  • Management of Galliformes
    38_Galliforms.qxd 8/24/2005 10:02 AM Page 861 CHAPTER 38 Management of Galliformes GARY D. BUTCHER, BS, MS, DVM, P hD, D ipl ACPV Members of the order Galliformes are found on every continent except Antarctica. The red junglefowl, com- mon turkey and helmeted guinea fowl have been domesticated for centuries. Their descendants, through selective breeding, are of considerable economic impor- tance today. Some varieties are very plentiful in the wild, while others like the Japanese quail (Coturnix japonica) and various pheasants are approaching a level of com- plete domestication. Many Galliformes are commonly maintained as game and food (meat and/or eggs) birds. Some are stable in captivity under variable ambient conditions, easy to breed and inexpensive. Other species are from niches with specific environmental requirements and need spe- cialized diets, humidity and temperature ranges to sur- vive. Currently, commercial production of chickens and turkeys in the USA for food has surpassed that of the Greg J. Harrison Greg J. Fig 38.1 | In warm climates, game cocks are housed on “string beef, pork and fish industries. In 1900, per capita con- walks”. A leg leash, just long enough for the bird to reach a sumption of chicken was 1 pound and had risen to 80 shelter but not to fight with other birds, allows group confine- pounds by the year 2000! ment. Fighting of cocks is considered inhumane and illegal in some countries; however, it is a part of the culture in others. In this chapter, “domestic fowl” means Gallus gallus, forma domestica (domestic form of the red junglefowl); “domestic turkey” is Meleagris gallopavo, forma domes- tica (domestic form of the common turkey) and “domes- tic guinea fowl” is Numida meleagris, forma domestica (domestic form of the helmeted guinea fowl) (Table 38.1).
    [Show full text]
  • Ecography ECOG-04871
    Ecography ECOG-04871 Rotenberry, J. T. and Balasubramaniam, P. 2020. Connecting species’ geographical distributions to environmental variables: range maps versus observed points of occurrence. – Ecography doi: 10.1111/ecog.04871 Supplementary material Appendix 1 Supplementary Material Appendix Table A1. Data downloaded from Global Biodiversity Information Facility, 16 January – 4 May 2018. Each file can be accessed at https://www.gbif.org/occurrence/download/<GBIF ID as indicated in the first column>. Each file was generated by searching for the taxa indicated. Taxonomy of species downloaded from GBIF was reconciled with IOC 7.3 taxonomy (Gill and Donsker 2017); this principally involved updating recent species’ genera changes that had yet to be incorporated in all data from GBIF. See text for how data were cleaned. GBIF ID Taxon (GBIF search field) 0001404-180412121330197 Acryllium vulturinum 0001407-180412121330197 Afropavo congensis 0001410-180412121330197 Alectoris 0001415-180412121330197 Ammoperdix 0001413-180412121330197 Perdix 0001416-180412121330197 Arborophila 0001417-180412121330197 Argusianus argus 0002656-180412121330197 Argusianus argus 0002659-180412121330197 Bambusicola 0002667-180412121330197 Chrysolophus 0002663-180412121330197 Callipepla 0002665-180412121330197 Bonasa 0002670-180412121330197 Colinus 0002672-180412121330197 Coturnix 0003685-180412121330197 Excalfactoria chinensis 0003686-180412121330197 Excalfactoria adansonii 0003688-180412121330197 Synoicus 0003814-180412121330197 Megapodius 0003818-180412121330197 Megapodiidae
    [Show full text]
  • Galliform Diversity in South-West Yunnan, China, with Notes on Blood Pheasant Ithaginis Cruentus and White Eared Pheasant Crosso
    Galliform diversity in south-west Yunnan, China, with notes on Blood Pheasant Ithaginis cruentus and White Eared Pheasant Crossoptilon crossoptilon biology Authors: Daniel M. Brooks, Paul J. Buzzard, Xueyou Li, and William V. Bleisch Source: Bulletin of the British Ornithologists’ Club, 139(3) : 205-214 Published By: British Ornithologists' Club URL: https://doi.org/10.25226/bboc.v139i3.2019.a3 BioOne Complete (complete.BioOne.org) is a full-text database of 200 subscribed and open-access titles in the biological, ecological, and environmental sciences published by nonprofit societies, associations, museums, institutions, and presses. Your use of this PDF, the BioOne Complete website, and all posted and associated content indicates your acceptance of BioOne’s Terms of Use, available at www.bioone.org/terms-of-use. Usage of BioOne Complete content is strictly limited to personal, educational, and non-commercial use. Commercial inquiries or rights and permissions requests should be directed to the individual publisher as copyright holder. BioOne sees sustainable scholarly publishing as an inherently collaborative enterprise connecting authors, nonprofit publishers, academic institutions, research libraries, and research funders in the common goal of maximizing access to critical research. Downloaded From: https://bioone.org/journals/Bulletin-of-the-British-Ornithologists’-Club on 26 Sep 2019 Terms of Use: https://bioone.org/terms-of-use Daniel M. Brooks et al. 205 Bull. B.O.C. 2019 139(3) Galliform diversity in south-west Yunnan, China,
    [Show full text]
  • Gallus Gallus) and Its Domestic Descendant in East Asia
    Quaternary Science Reviews 142 (2016) 102e119 Contents lists available at ScienceDirect Quaternary Science Reviews journal homepage: www.elsevier.com/locate/quascirev Holocene cultural history of Red jungle fowl (Gallus gallus) and its domestic descendant in East Asia * Joris Peters a, b, , Ophelie Lebrasseur c, Hui Deng d, Greger Larson c a Department of Veterinary Sciences, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, LMU Munich, Kaulbachstr. 37, D-80539 Munich, Germany b SNSB, Bavarian State Collection of Anthropology and Palaeoanatomy, Karolinenplatz 2a, D-80333 Munich, Germany c Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology, Dyson Perrins Building, South Parks Road, Oxford OX1 3QY, UK d Department of History and Culture, Shanxi University, No. 92 Wucheng Road, Taiyuan City, Shanxi Province, PR China article info abstract Article history: Nearly three decades ago, zooarchaeologists postulated that chicken husbandry was practiced in Received 4 November 2015 Northern China by ~8.0 ka calBP. Recently, ancient mitogenome analyses of galliform remains suggested Received in revised form that Red jungle fowl (Gallus gallus) was already present in the Yellow River basin several millennia 26 March 2016 earlier, shortly after the onset of the Holocene. If these conclusions are correct, the origins of chicken Accepted 5 April 2016 domestication and husbandry in the region may have been spurred by agricultural innovations in the lower Yellow River basin including millet cultivation, pig husbandry, and dog breeding. In addition, the dispersal of poultry farming from East Asia to Asia Minor and Europe could therefore date to the Keywords: Red jungle fowl (Gallus gallus) Neolithic along ancient trade routes across Central Asia rather than via South Asia and Mesopotamia.
    [Show full text]
  • The Phylogenetic Position and Speciation Dynamics of the Genus Perdix (Phasianidae, Galliformes)
    ARTICLE IN PRESS Molecular Phylogenetics and Evolution xxx (2010) xxx–xxx Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev The phylogenetic position and speciation dynamics of the genus Perdix (Phasianidae, Galliformes) Xin-kang Bao a, Nai-fa Liu a,*, Jiang-yong Qu b, Xiao-li Wang a, Bei An a, Long-ying Wen c, Sen Song a a School of Life Science, Lanzhou University, Lanzhou 730000, China b Department of Biological Science and Technology, Qiongzhou College, Wuzhishan, Hainan 572200, China c Department of Chemistry & Life Sciences, Leshan Teachers College, Leshan, Sichuan 614004, China article info abstract Article history: The nuclear gene (c-mos) and mitochondrial genes (CYT B and ND2) sequences, representing 44 phasia- Received 30 December 2009 nid species and 26 genera (mainly distributed in China), were used to study the phylogeny of the genus Revised 24 March 2010 Perdix, which comprises three partridge species. Maximum parsimony and Bayesian methods were Accepted 29 March 2010 employed, and the analysis of mitochondrial sequence data and the combined dataset showed that Perdix Available online xxxx is specifically related either to typical pheasants or to Ithaginis. Phylogenetic trees also indicated that: (1) Perdix is monophyletic; (2) the Tibetan partridge (Perdix hodgsoniae) has been consistently placed as basal Keywords: to all other Perdix, and the Daurian partridge (Perdix dauuricae) is placed sister to gray partridge (Perdix Phasianidae perdix); (3) the Daurian partridge subspecies przewalskii and Tibetan partridge subspecies hodgsoniae are Perdix c-mos basal to other subspecies in their species clade, respectively. Speciation in Perdix was likely promoted by Cytochrome b the late Pliocene/early Pleistocene intensive uplift of the Tibetan Plateau and by Pleistocene glaciations.
    [Show full text]
  • The Evolution of Iridescent Plumage in the Galliformes: Proximate Mechanisms and Ultimate Functions
    University of Windsor Scholarship at UWindsor Electronic Theses and Dissertations Theses, Dissertations, and Major Papers 2013 The evolution of iridescent plumage in the Galliformes: Proximate mechanisms and ultimate functions Kevyn K. Gammie University of Windsor Follow this and additional works at: https://scholar.uwindsor.ca/etd Recommended Citation Gammie, Kevyn K., "The evolution of iridescent plumage in the Galliformes: Proximate mechanisms and ultimate functions" (2013). Electronic Theses and Dissertations. 4908. https://scholar.uwindsor.ca/etd/4908 This online database contains the full-text of PhD dissertations and Masters’ theses of University of Windsor students from 1954 forward. These documents are made available for personal study and research purposes only, in accordance with the Canadian Copyright Act and the Creative Commons license—CC BY-NC-ND (Attribution, Non-Commercial, No Derivative Works). Under this license, works must always be attributed to the copyright holder (original author), cannot be used for any commercial purposes, and may not be altered. Any other use would require the permission of the copyright holder. Students may inquire about withdrawing their dissertation and/or thesis from this database. For additional inquiries, please contact the repository administrator via email ([email protected]) or by telephone at 519-253-3000ext. 3208. The evolution of iridescent plumage in the Galliformes: proximate mechanisms and ultimate functions by Kevyn Gammie A Thesis Submitted to the Faculty of Graduate Studies
    [Show full text]