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Liu S, Chen H, Ouyang J, Huang M, Zhang H, Zheng S, Xi S, Tang H, Gao Y, Xiong Y, Cheng D, Chen K, Liu B, Li W, Ren J, Yan X, Mao H. A high-quality assembly reveals genomic characteristics, phylogenetic status, and causal genes for leucism plumage of Indian peafowl. Gigascience 2022; 11:6564124. [PMID: 35383847 PMCID: PMC8985102 DOI: 10.1093/gigascience/giac018] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 11/15/2021] [Accepted: 02/09/2022] [Indexed: 12/28/2022] Open
Abstract
Background The dazzling phenotypic characteristics of male Indian peafowl (Pavo cristatus) are attractive both to the female of the species and to humans. However, little is known about the evolution of the phenotype and phylogeny of these birds at the whole-genome level. So far, there are no reports regarding the genetic mechanism of the formation of leucism plumage in this variant of Indian peafowl. Results A draft genome of Indian peafowl was assembled, with a genome size of 1.05 Gb (the sequencing depth is 362×), and contig and scaffold N50 were up to 6.2 and 11.4 Mb, respectively. Compared with other birds, Indian peafowl showed changes in terms of metabolism, immunity, and skeletal and feather development, which provided a novel insight into the phenotypic evolution of peafowl, such as the large body size and feather morphologies. Moreover, we determined that the phylogeny of Indian peafowl was more closely linked to turkey than chicken. Specifically, we first identified that PMEL was a potential causal gene leading to the formation of the leucism plumage variant in Indian peafowl. Conclusions This study provides an Indian peafowl genome of high quality, as well as a novel understanding of phenotypic evolution and phylogeny of Indian peafowl. These results provide a valuable reference for the study of avian genome evolution. Furthermore, the discovery of the genetic mechanism for the development of leucism plumage is both a breakthrough in the exploration of peafowl plumage and also offers clues and directions for further investigations of the avian plumage coloration and artificial breeding in peafowl.
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Affiliation(s)
- Shaojuan Liu
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Hao Chen
- College of Life Science, Jiangxi Science & Technology Normal University, Nanchang 330013, China
| | - Jing Ouyang
- College of Life Science, Jiangxi Science & Technology Normal University, Nanchang 330013, China
| | - Min Huang
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Hui Zhang
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Sumei Zheng
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Suwang Xi
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Hongbo Tang
- College of Life Science, Jiangxi Science & Technology Normal University, Nanchang 330013, China
| | - Yuren Gao
- College of Life Science, Jiangxi Science & Technology Normal University, Nanchang 330013, China
| | - Yanpeng Xiong
- College of Life Science, Jiangxi Science & Technology Normal University, Nanchang 330013, China
| | - Di Cheng
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Kaifeng Chen
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Bingbing Liu
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Wanbo Li
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Jimei University, Xiamen 361021, China
| | - Jun Ren
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Xueming Yan
- College of Life Science, Jiangxi Science & Technology Normal University, Nanchang 330013, China
| | - Huirong Mao
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China
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2
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Ghimire P, Dahal N, Karna AK, Karki S, Lamichhaney S. Exploring potentialities of avian genomic research in Nepalese Himalayas. AVIAN RESEARCH 2021; 12:57. [PMID: 34745641 PMCID: PMC8556808 DOI: 10.1186/s40657-021-00290-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
UNLABELLED Nepal, a small landlocked country in South Asia, holds about 800 km of Himalayan Mountain range including the Earth's highest mountain. Within such a mountain range in the north and plain lowlands in the south, Nepal provides a habitat for about 9% of global avian fauna. However, this diversity is underrated because of the lack of enough studies, especially using molecular tools to quantify and understand the distribution patterns of diversity. In this study, we reviewed the studies in the last two decades (2000‒2019) that used molecular methods to study the biodiversity in Nepal to examine the ongoing research trend and focus. Although Nepalese Himalaya has many opportunities for cutting-edge molecular research, our results indicated that the rate of genetic/genomic studies is much slower compared to the regional trends. We found that genetic research in Nepal heavily relies on resources from international institutes and that too is mostly limited to research on species monitoring, distribution, and taxonomic validations. Local infrastructures to carry out cutting-edge genomic research in Nepal are still in their infancy and there is a strong need for support from national/international scientists, universities, and governmental agencies to expand such genomic infrastructures in Nepal. We particularly highlight avian fauna as a potential future study system in this region that can be an excellent resource to explore key biological questions such as understanding eco-physiology and molecular basis of organismal persistence to changing environment, evolutionary processes underlying divergence and speciation, or mechanisms of endemism and restrictive distribution of species. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1186/s40657-021-00290-5.
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Affiliation(s)
- Prashant Ghimire
- Department of Biological Sciences, Kent State University, Kent, OH USA
| | - Nishma Dahal
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, HP India
| | - Ajit K. Karna
- Center for Health and Disease Studies-Nepal, Kathmandu, Nepal
- Institute of Agriculture and Animal Sciences, Tribhuvan University, Kathmandu, Nepal
| | - Surendra Karki
- Emergency Centre for Transboundary Animal Diseases, Food & Agricultural Organization of the UN, Kathmandu, Nepal
| | - Sangeet Lamichhaney
- Department of Biological Sciences, Kent State University, Kent, OH USA
- School of Biomedical Sciences, Kent State University, Kent, OH USA
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3
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When good mitochondria go bad: Cyto-nuclear discordance in landfowl (Aves: Galliformes). Gene 2021; 801:145841. [PMID: 34274481 DOI: 10.1016/j.gene.2021.145841] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 06/10/2021] [Accepted: 07/13/2021] [Indexed: 11/22/2022]
Abstract
Mitochondrial sequences were among the first molecular data collected for phylogenetic studies and they are plentiful in DNA sequence archives. However, the future value of mitogenomic data in phylogenetics is uncertain, because its phylogenetic signal sometimes conflicts with that of the nuclear genome. A thorough understanding of the causes and prevalence of cyto-nuclear discordance would aid in reconciling different results owing to sequence data type, and provide a framework for interpreting megaphylogenies when taxa which lack substantial nuclear data are placed using mitochondrial data. Here, we examine the prevalence and possible causes of cyto-nuclear discordance in the landfowl (Aves: Galliformes), leveraging 47 new mitogenomes assembled from off-target reads recovered as part of a target-capture study. We evaluated two hypotheses, that cyto-nuclear discordance is "genuine" and a result of biological processes such as incomplete lineage sorting or introgression, and that cyto-nuclear discordance is an artifact of inaccurate mitochondrial tree estimation (the "inaccurate estimation" hypothesis). We identified seven well-supported topological differences between the mitogenomic tree and trees based on nuclear data. These well-supported topological differences were robust to model selection. An examination of sites suggests these differences were driven by small number of sites, particularly from third-codon positions, suggesting that they were not confounded by convergent directional selection. Hence, the hypothesis of genuine discordance was supported.
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4
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Zhou C, Liu Y, Qiao L, Liu Y, Yang N, Meng Y, Yue B. The draft genome of the blood pheasant ( Ithaginis cruentus): Phylogeny and high-altitude adaptation. Ecol Evol 2020; 10:11440-11452. [PMID: 33144976 PMCID: PMC7593199 DOI: 10.1002/ece3.6782] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 06/30/2020] [Accepted: 08/20/2020] [Indexed: 11/10/2022] Open
Abstract
The blood pheasant (Ithaginis cruentus), the only species in the genus Ithaginis, lives in an extremely inhospitable high-altitude environment, coping with hypoxia and ultraviolet (UV) radiation. To further investigate the phylogeny of Phasianidae species based on complete genomes and understand the molecular genetic mechanisms of the high-altitude adaptation of the blood pheasant, we de novo assembled and annotated the complete genome of the blood pheasant. The blood pheasant genome size is 1.04 Gb with scaffold N50 of 10.88 Mb. We identified 109.92 Mb (10.62%) repetitive elements, 279,037 perfect microsatellites, and 17,209 protein-coding genes. The phylogenetic tree of Phasianidae based on whole genomes revealed three highly supported major clades with the blood pheasant included in the "erectile clade." Comparative genomics analysis showed that many genes were positively selected in the blood pheasant, which was associated with response to hypoxia and/or UV radiation. More importantly, among these positively selected genes (PSGs) which were related to high-altitude adaptation, sixteen PSGs had blood pheasant-specific missense mutations. Our data and analysis lay solid foundation to the study of Phasianidae phylogeny and provided new insights into the potential adaptation mechanisms to the high altitude employed by the blood pheasant.
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Affiliation(s)
- Chuang Zhou
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education)College of Life SciencesSichuan UniversityChengduChina
| | - Yi Liu
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education)College of Life SciencesSichuan UniversityChengduChina
| | - Lu Qiao
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education)College of Life SciencesSichuan UniversityChengduChina
| | - Yang Liu
- Chengdu Zoo/Chengdu Wildlife Research InstituteChengduChina
| | - Nan Yang
- Institute of Qinghai‐Tibetan PlateauSouthwest Minzu UniversityChengduChina
| | - Yang Meng
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education)College of Life SciencesSichuan UniversityChengduChina
| | - Bisong Yue
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education)College of Life SciencesSichuan UniversityChengduChina
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5
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Tiley GP, Kimball RT, Braun EL, Burleigh JG. Comparison of the Chinese bamboo partridge and red Junglefowl genome sequences highlights the importance of demography in genome evolution. BMC Genomics 2018; 19:336. [PMID: 29739321 PMCID: PMC5941490 DOI: 10.1186/s12864-018-4711-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 04/23/2018] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Recent large-scale whole genome sequencing efforts in birds have elucidated broad patterns of avian phylogeny and genome evolution. However, despite the great interest in economically important phasianids like Gallus gallus (Red Junglefowl, the progenitor of the chicken), we know little about the genomes of closely related species. Gallus gallus is highly sexually dichromatic and polygynous, but its sister genus, Bambusicola, is smaller, sexually monomorphic, and monogamous with biparental care. We sequenced the genome of Bambusicola thoracicus (Chinese Bamboo Partridge) using a single insert library to test hypotheses about genome evolution in galliforms. Selection acting at the phenotypic level could result in more evidence of positive selection in the Gallus genome than in Bambusicola. However, the historical range size of Bambusicola was likely smaller than Gallus, and demographic effects could lead to higher rates of nonsynonymous substitution in Bambusicola than in Gallus. RESULTS We generated a genome assembly suitable for evolutionary analyses. We examined the impact of selection on coding regions by examining shifts in the average nonsynonymous to synonymous rate ratio (dN/dS) and the proportion of sites subject to episodic positive selection. We observed elevated dN/dS in Bambusicola relative to Gallus, which is consistent with our hypothesis that demographic effects may be important drivers of genome evolution in Bambusicola. We also demonstrated that alignment error can greatly inflate estimates of the number of genes that experienced episodic positive selection and heterogeneity in dN/dS. However, overall patterns of molecular evolution were robust to alignment uncertainty. Bambusicola thoracicus has higher estimates of heterozygosity than Gallus gallus, possibly due to migration events over the past 100,000 years. CONCLUSIONS Our results emphasized the importance of demographic processes in generating the patterns of variation between Bambusicola and Gallus. We also demonstrated that genome assemblies generated using a single library can provide valuable insights into avian evolutionary history and found that it is important to account for alignment uncertainty in evolutionary inferences from draft genomes.
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Affiliation(s)
- G P Tiley
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA. .,Department of Biology, Duke University, Durham, NC, 27708, USA.
| | - R T Kimball
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - E L Braun
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - J G Burleigh
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
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6
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Hasegawa M, Kuroda S. Phylogeny mandalas of birds using the lithographs of John Gould’s folio bird books. Mol Phylogenet Evol 2017; 117:141-149. [DOI: 10.1016/j.ympev.2016.12.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Revised: 10/12/2016] [Accepted: 12/05/2016] [Indexed: 12/19/2022]
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7
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Yan C, Mou B, Meng Y, Tu F, Fan Z, Price M, Yue B, Zhang X. A novel mitochondrial genome of Arborophila and new insight into Arborophila evolutionary history. PLoS One 2017; 12:e0181649. [PMID: 28742865 PMCID: PMC5526529 DOI: 10.1371/journal.pone.0181649] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Accepted: 07/05/2017] [Indexed: 01/16/2023] Open
Abstract
The lineage of the Bar-backed Partridge (Arborophila brunneopectus) was investigated to determine the phylogenetic relationships within Arborophila as the species is centrally distributed within an area covered by the distributions of 22 South-east Asian hill partridge species. The complete mitochondrial genome (mitogenome) of A. brunneopectus was determined and compared with four other hill partridge species mitogenomes. NADH subunit genes are radical in hill partridge mitogenomes and contain the most potential positive selective sites around where variable sites are abundant. Together with 44 other mitogenomes of closely related species, we reconstructed highly resolved phylogenetic trees using maximum likelihood (ML) and Bayesian inference (BI) analyses and calculated the divergence and dispersal history of Arborophila using combined datasets composed of their 13-protein coding sequences. Arborophila is reportedly be the oldest group in Phasianidae whose ancestors probably originated in Asia. A. rufipectus shares a closer relationship with A. ardens and A. brunneopectus compared to A. gingica and A. rufogularis, and such relationships were supported and profiled by NADH dehydrogenase subunit 5 (ND5). The intragenus divergence of all five Arborophila species occurred in the Miocene (16.84~5.69 Mya) when there were periods of climate cooling. We propose that these cooling events in the Miocene forced hill partridges from higher to lower altitudes, which led to geographic isolation and speciation. We demonstrated that the apparently deleterious +1 frameshift mutation in NADH dehydrogenase subunit 3 (ND3) found in all Arborophila is an ancient trait that has been eliminated in some younger lineages, such as Passeriformes. It is unclear of the biological advantages of this elimination for the relevant taxa and this requires further investigation.
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Affiliation(s)
- Chaochao Yan
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Biqin Mou
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Yang Meng
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Feiyun Tu
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China
- Institute of Wildlife Conservation, Jiangxi Academy of Forestry, Nanchang, P.R. China
| | - Zhenxin Fan
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Megan Price
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Bisong Yue
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Xiuyue Zhang
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China
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8
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Wang N, Hosner PA, Liang B, Braun EL, Kimball RT. Historical relationships of three enigmatic phasianid genera (Aves: Galliformes) inferred using phylogenomic and mitogenomic data. Mol Phylogenet Evol 2017; 109:217-225. [DOI: 10.1016/j.ympev.2017.01.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Revised: 12/24/2016] [Accepted: 01/07/2017] [Indexed: 12/09/2022]
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9
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Li X, Lin L, Cui A, Bai J, Wang X, Xin C, Zhang Z, Yang C, Gao R, Huang Y, Lei F. Taxonomic status and phylogenetic relationship of tits based on mitogenomes and nuclear segments. Mol Phylogenet Evol 2016; 104:14-20. [DOI: 10.1016/j.ympev.2016.07.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 06/20/2016] [Accepted: 07/18/2016] [Indexed: 11/24/2022]
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10
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Li XJ, Lin LL. Complete mitochondrial genome of Francolinus pintadeanus (Galliformes: Phasianidae). MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:579-580. [PMID: 33473561 PMCID: PMC7799774 DOI: 10.1080/23802359.2016.1197059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The complete mitochondrial genome (mitogenome) of Francolinus pintadeanus, consisting of 16,693 bp, was determined and analyzed. It displayed as typical genome organization as other Galliformes mitogenomes: 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and one control region. The phylogenetic relationships of 25 Phasianidae species and three Odontophoridae species as outgroup using maximum likelihood and Bayesian inference methods based on a concatenated dataset from mitogenomes were analyzed. The results reveal that F. pintadeanus had a close relationship with Gallus gallus gallus/Bambusicola thoracica, then this clade formed a sister group with Pavo muticus/Argusianus argus.
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Affiliation(s)
- Xue-Juan Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Li-Liang Lin
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
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11
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Cui Y, Yan C, Sun T, Li J, Yue B, Zhang X, Li J. Identification of CR1 retroposons in Arborophila rufipectus and their application to Phasianidae phylogeny. Mol Ecol Resour 2016; 16:1037-49. [PMID: 26929266 DOI: 10.1111/1755-0998.12514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 01/26/2016] [Accepted: 01/28/2016] [Indexed: 12/22/2022]
Abstract
Chicken repeat 1 (CR1), a member of non-LTR retroposon, is an important phylogenetic marker in avian systematics. In this study, we reported several characteristics of CR1 elements in a draft genome of Arborophila rufipectus (Sichuan partridge). According to the analyses of RepeatMasker, approximately 254 966 CR1 elements were identified in A. rufipectus, covering 6.7% of the genome. Subsequently, we selected eighteen novel CR1 elements by comparing the chicken genome, turkey genome and assembled A. rufipectus scaffolds. Here, a combined data set comprising of 22 CR1 loci, mitochondrial genomes and eight unlinked introns was analysed to infer the evolutionary relationships of twelve Phasianidae species. The applicability of CR1 sequences for inferring avian phylogeny relative to mtDNA and intron sequences was investigated as well. Our results elucidated the position of A. rufipectus in Phasianidae with robust supports that it presented a sister clade to Arborophila ardens/Arborophila brunneopectus, and implied that genus Arborophila was in a basal phylogenetic position within Phasianidae and a phylogenetic affinity between Meleagris gallopavo and Pucrasia macrolopha. Therefore, this work not only resolved some of the confounding relationships among Phasianidae, but also suggested CR1 sequences could provide powerful complementary data for phylogeny reconstruction.
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Affiliation(s)
- Yaoyao Cui
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, China.,Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, China
| | - Chaochao Yan
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, China.,Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, China
| | - Tianlin Sun
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, China.,Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, China
| | - Jing Li
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, China
| | - Bisong Yue
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, China
| | - Xiuyue Zhang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, China
| | - Jing Li
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, China.,Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, China
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12
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Yang N, Moermond TC, Lloyd H, Xu Y, Dou L, Zhang K, Yue B, Ran J. Effects of Supplementary Feeding on the Breeding Ecology of the Buff-Throated Partridge in a Tibetan Sacred Site, China. PLoS One 2016; 11:e0146568. [PMID: 26784961 PMCID: PMC4718519 DOI: 10.1371/journal.pone.0146568] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 12/18/2015] [Indexed: 11/29/2022] Open
Abstract
Our goal was to document effects of year-round supplemental feeding on breeding ecology of the Buff-throated Partridge, Tetraophasis szechenyii, within a Tibetan sacred site. We evaluated effects of supplemental feeding used as religious/cultural practices which could potentially aid conservation of endangered phasianids. We compared fed breeding groups to neighboring nonfed groups. Fed groups initiated first clutches significantly earlier than nonfed groups. Earlier laying groups within fed and nonfed groups showed significantly lower hatching rates than later groups; however, fed groups showed significantly higher hatching rates than nonfed groups laying in the same period. Earlier laying increased opportunities to renest. All six fed groups with clutch failures renested compared to only one of five nonfed groups with clutch failures. Fed female breeders showed significantly greater investment in their young with larger clutches and larger eggs, which likely increased survivability of early hatchlings. We observed no predation on birds at feeding sites and recorded only four cases of predation on incubating females, which showed no detectable difference between fed and nonfed groups. Ground-nesting birds typically face high risks of predation. Ten of the 48 groups nested in trees, which occurs in few phasianid species. Tree nests showed significantly higher hatching rates compared to ground nests; however, we found no significant difference in tree nesting between fed and nonfed groups. This partridge is one of four gallinaceous species with cooperative breeding. Breeding groups with helpers had significantly greater reproductive success than single pairs, and fed female breeders with helpers laid bigger eggs than single pairs. Comparing annual reproductive output per group, fed groups not only produced significantly more independent young (≥150 days post-hatching), their young hatched significantly earlier, which likely have greater reproductive value over later hatched young of nonfed groups. Supplemental feeding year-round is likely what enabled the successes of the fed partridges.
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Affiliation(s)
- Nan Yang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Timothy C. Moermond
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Huw Lloyd
- Division of Biology and Conservation Ecology, School of Science and the Environment, Manchester Metropolitan University, Chester Street, Manchester, United Kingdom
| | - Yu Xu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Liang Dou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Kai Zhang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Bisong Yue
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Jianghong Ran
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
- * E-mail:
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13
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Li X, Huang Y, Lei F. Comparative mitochondrial genomics and phylogenetic relationships of the Crossoptilon species (Phasianidae, Galliformes). BMC Genomics 2015; 16:42. [PMID: 25652939 PMCID: PMC4326528 DOI: 10.1186/s12864-015-1234-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 01/12/2015] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Phasianidae is a family of Galliformes containing 38 genera and approximately 138 species, which is grouped into two tribes based on their morphological features, the Pheasants and Partridges. Several studies have attempted to reconstruct the phylogenetic relationships of the Phasianidae, but many questions still remain unaddressed, such as the taxonomic status and phylogenetic relationships among Crossoptilon species. The mitochondrial genome (mitogenome) has been extensively used to infer avian genetic diversification with reasonable resolution. Here, we sequenced the entire mitogenomes of three Crossoptilon species (C. harmani, C. mantchuricum and C. crossoptilon) to investigate their evolutionary relationship among Crossoptilon species. RESULTS The complete mitogenomes of C. harmani, C. mantchuricum and C. crossoptilon are 16682 bp, 16690 bp and 16680 bp in length, respectively, encoding a standard set of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a putative control region. C. auritum and C. mantchuricum are more closely related genetically, whereas C. harmani is more closely related to C. crossoptilon. Crossoptilon has a closer relationship with Lophura, and the following phylogenetic relationship was reconstructed: ((Crossoptilon + Lophura) + (Phasianus + Chrysolophus)). The divergence time between the clades C. harmani-C. crossoptilon and C. mantchuricum-C. auritum is consistent with the uplift of the Tibetan Plateau during the Tertiary Pliocene. The Ka/Ks analysis showed that atp8 gene in the Crossoptilon likely experienced a strong selective pressure in adaptation to the plateau environment. CONCLUSIONS C. auritum with C. mantchuricum and C. harmani with C. crossoptilon form two pairs of sister groups. The genetic distance between C. harmani and C. crossoptilon is far less than the interspecific distance and is close to the intraspecific distance of Crossoptilon, indicating that C. harmani is much more closely related to C. crossoptilon. Our mito-phylogenomic analysis supports the monophyly of Crossoptilon and its closer relationship with Lophura. The uplift of Tibetan Plateau is suggested to impact the divergence between C. harmani-C. crossoptilon clade and C. mantchuricum-C. auritum clade during the Tertiary Pliocene. Atp8 gene in the Crossoptilon species might have experienced a strong selective pressure for adaptation to the plateau environment.
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Affiliation(s)
- Xuejuan Li
- Co-Innovation Center for Qinba Regions' Sustainable Development, School of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China.
| | - Yuan Huang
- Co-Innovation Center for Qinba Regions' Sustainable Development, School of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China.
| | - Fumin Lei
- Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, the Chinese Academy of Sciences, Beijing, 100101, China.
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