1
|
Increased microbial diversity and decreased prevalence of common pathogens in the gut microbiomes of wild turkeys compared to domestic turkeys. Appl Environ Microbiol 2022; 88:e0142321. [PMID: 35044852 PMCID: PMC8904053 DOI: 10.1128/aem.01423-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Turkeys (Meleagris gallopavo) provide a globally important source of protein and constitute the second most important source of poultry meat in the world. Bacterial diseases are common in commercial poultry production causing significant production losses for farmers. Due to the increasingly recognized problems associated with large-scale/indiscriminant antibiotic use in agricultural settings, poultry producers need alternative methods to control common bacterial pathogens. In this study we compared the cecal microbiota of wild and domestic turkeys, hypothesizing that environmental pressures faced by wild birds may select for a disease-resistant microbial community. Sequence analysis of 16S rRNA genes amplified from cecal samples indicate that free-roaming wild turkeys carry a rich and variable microbiota compared to domestic turkeys raised on large-scale poultry farms. Wild turkeys also had very low levels of Staphylococcus, Salmonella and E. coli when compared to domestic turkeys. E. coli strains isolated from wild or domestic turkey cecal samples also belong to distinct phylogenetic backgrounds and differ in their propensity to carry virulence genes. E. coli strains isolated from factory-raised turkeys were far more likely to carry genes for capsule (kpsII, kpsIII) or siderophore (iroN, fyuA) synthesis than those isolated from wild turkeys. These results suggest that the microbiota of wild turkeys may provide colonization resistance against common poultry pathogens. Importance Due to the increasingly recognized problems associated with antibiotic use in agricultural settings, poultry producers need alternative methods to control common bacterial pathogens. In this study we compare the microbiota of wild and domestic turkeys. Results suggest that free ranging wild turkeys carry a distinct microbiome when compared to farm raised turkeys. The microbiome of wild birds contains very low levels of poultry pathogens compared to farm raised birds. The microbiomes of wild turkeys may be used to guide development of new ways to control disease in large scale poultry production.
Collapse
|
2
|
Pal A, Pal A, Mallick AI, Biswas P, Chatterjee PN. Molecular characterization of Bu-1 and TLR2 gene in Haringhata Black chicken. Genomics 2020; 112:472-483. [PMID: 30902756 DOI: 10.1016/j.ygeno.2019.03.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/17/2019] [Accepted: 03/18/2019] [Indexed: 11/21/2022]
Abstract
Haringhata Black is the only registered indigenous poultry genetic resource of West Bengal till date. Molecular characterization of HB revealed that Bu-1 to be highly glycoylated transmembrane protein unlike mammalian Bu-1, whereas TLR2 of HB chicken was observed to be rich in Leucine rich repeat. HB chicken was observed to be genetically close to chicken of Japan, while distant to chicken breed of UK and Chicago. Avian species wise evolution study indicates genetic closeness of HB chicken with turkey. Differential mRNA expression profile for the immune response genes (TLR2, TLR4 and Bu1 gene) were studied for HB chicken with respect to other chicken breed and poultry birds, which reveals that HB chicken were better in terms of B cell mediated immunity and hence better response to vaccination. Hence HB chicken is one of the best poultry genetic resources to be reared under backyard system where biosecurity measures are almost lacking.
Collapse
Affiliation(s)
- Aruna Pal
- West Bengal University of Animal and Fishery Sciences, 37, K.B. Sarani, Kolkata 37, India.
| | - Abantika Pal
- Indian Institute of technology, Kharagpur, West Bengal, India
| | | | - P Biswas
- West Bengal University of Animal and Fishery Sciences, 37, K.B. Sarani, Kolkata 37, India
| | - P N Chatterjee
- West Bengal University of Animal and Fishery Sciences, 37, K.B. Sarani, Kolkata 37, India
| |
Collapse
|
3
|
Canales Vergara AM, Landi V, Delgado Bermejo JV, Martínez A, Cervantes Acosta P, Pons Barro Á, Bigi D, Sponenberg P, Helal M, Hossein Banabazi M, Camacho Vallejo ME. Tracing Worldwide Turkey Genetic Diversity Using D-loop Sequence Mitochondrial DNA Analysis. Animals (Basel) 2019; 9:ani9110897. [PMID: 31683884 PMCID: PMC6912331 DOI: 10.3390/ani9110897] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 10/19/2019] [Accepted: 10/22/2019] [Indexed: 01/01/2023] Open
Abstract
Simple Summary The development of new production lines of turkeys has relegated native breeds to a second position. This has increased the need for new research to ensure the conservation of local turkey breeds and the maintenance of biodiversity. The objective of the present study was to identify turkey populations, their origins, and maternal lines through mitochondrial DNA analysis. For this study, mitochondrial DNA samples from 93 turkeys (Meleagris gallopavo) were used. The animals belonged to populations in Brazil, Mexico, Spain (Andalusia and Majorca) Italy, Iran, Egypt, and the United States. The haplogroup network that formed suggested that turkey domestic populations group into a single haplotype. However, genetic differences within the haplogroup were found. The present study may provide a better approach for the implementation of conservation strategies for domestic turkey populations. Abstract According to recent archeological evidence, turkey (Meleagris gallopavo gallopavo) domestication may have occurred in Mexico around 2000 years ago. However, little is known about the phylogenetic and genealogical background underlying domestic turkey populations. This study aimed to further understand the domestication process and identify inter- or intraspecific connections between turkey populations to determine their origins, trace their global expansion, and define the species’ genetic value. Ninety-three domestic turkeys (local breeds) were sampled from populations in Brazil, Mexico, USA, Spain, Italy, Iran, and Egypt. Publicly available sequences from previous studies were also included. Standard mitochondrial DNA, genetic diversity, and haplotype network analyses were performed. Seventy-six polymorphic sites were identified. Turkeys from Mexico showed the greatest number of polymorphic sites (40), while turkeys from Italy and Brazil reported only one site each. Nucleotide diversity was also highest in Mexico and the USA (π = 0.0175 and 0.0102, respectively) and lowest in Brazil and Italy. Of the six major haplogroups defined, the Mexican and USA populations appeared to have remained more stable and diverse than the other populations. This may be due to conservative husbandry policies in the rural areas of other populations, which have prevented the introduction of commercial turkey lines.
Collapse
Affiliation(s)
| | - Vincenzo Landi
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, ceiA3. 14071 Cordoba, Spain.
| | | | - Amparo Martínez
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, ceiA3. 14071 Cordoba, Spain.
| | | | - Águeda Pons Barro
- Serveis de Millora Agrària (SEMILLA), 07009 Palma de Mallorca, Spain.
| | - Daniele Bigi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127 Bologna, Italy.
| | - Phillip Sponenberg
- Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA 24060, USA.
| | - Mostafa Helal
- Faculty of Agriculture, Cairo University, Giza 12613, Egypt.
| | | | | |
Collapse
|
4
|
Wu Y, Zhang Y, Hou Z, Fan G, Pi J, Sun S, Chen J, Liu H, Du X, Shen J, Hu G, Chen W, Pan A, Yin P, Chen X, Pu Y, Zhang H, Liang Z, Jian J, Zhang H, Wu B, Sun J, Chen J, Tao H, Yang T, Xiao H, Yang H, Zheng C, Bai M, Fang X, Burt DW, Wang W, Li Q, Xu X, Li C, Yang H, Wang J, Yang N, Liu X, Du J. Population genomic data reveal genes related to important traits of quail. Gigascience 2018; 7:4995262. [PMID: 29762663 PMCID: PMC5961004 DOI: 10.1093/gigascience/giy049] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 04/27/2018] [Indexed: 12/18/2022] Open
Abstract
Background Japanese quail (Coturnix japonica), a recently domesticated poultry species, is important not only as an agricultural product, but also as a model bird species for genetic research. However, most of the biological questions concerning genomics, phylogenetics, and genetics of some important economic traits have not been answered. It is thus necessary to complete a high-quality genome sequence as well as a series of comparative genomics, evolution, and functional studies. Results Here, we present a quail genome assembly spanning 1.04 Gb with 86.63% of sequences anchored to 30 chromosomes (28 autosomes and 2 sex chromosomes Z/W). Our genomic data have resolved the long-term debate of phylogeny among Perdicinae (Japanese quail), Meleagridinae (turkey), and Phasianinae (chicken). Comparative genomics and functional genomic data found that four candidate genes involved in early maturation had experienced positive selection, and one of them encodes follicle stimulating hormone beta (FSHβ), which is correlated with different FSHβ levels in quail and chicken. We re-sequenced 31 quails (10 wild, 11 egg-type, and 10 meat-type) and identified 18 and 26 candidate selective sweep regions in the egg-type and meat-type lines, respectively. That only one of them is shared between egg-type and meat-type lines suggests that they were subject to an independent selection. We also detected a haplotype on chromosome Z, which was closely linked with maroon/yellow plumage in quail using population resequencing and a genome-wide association study. This haplotype block will be useful for quail breeding programs. Conclusions This study provided a high-quality quail reference genome, identified quail-specific genes, and resolved quail phylogeny. We have identified genes related to quail early maturation and a marker for plumage color, which is significant for quail breeding. These results will facilitate biological discovery in quails and help us elucidate the evolutionary processes within the Phasianidae family.
Collapse
Affiliation(s)
- Yan Wu
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China.,Key Laboratory of Animal Embryo Engineering and Molecular Breeding of Hubei Province,Wuhan 430064, China.,Hubei Innovation Center of Agricultural Science and Technology, Wuhan, Hubei, 430064, China
| | - Yaolei Zhang
- BGI-Shenzhen, Shenzhen 518083, China.,BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China.,China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Zhuocheng Hou
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, China; Agricultural University, Beijing 100193, China
| | - Guangyi Fan
- BGI-Shenzhen, Shenzhen 518083, China.,BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China.,State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, Macao, China.,China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Jinsong Pi
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China
| | - Shuai Sun
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Jiang Chen
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Huaqiao Liu
- Hubei Shendan Healthy Food Co., Ltd., Wuhan 430206, China
| | - Xiao Du
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Jie Shen
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China
| | - Gang Hu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | | | - Ailuan Pan
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China
| | - Pingping Yin
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | | | - Yuejin Pu
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China
| | - He Zhang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Zhenhua Liang
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China
| | | | - Hao Zhang
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China
| | - Bin Wu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Jing Sun
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China
| | | | - Hu Tao
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China
| | - Ting Yang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Hongwei Xiao
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China
| | - Huan Yang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Chuanwei Zheng
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China
| | | | | | - David W Burt
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Wen Wang
- Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, China
| | - Qingyi Li
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Chengfeng Li
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China.,James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen 518083, China.,James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Ning Yang
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, China; Agricultural University, Beijing 100193, China
| | - Xin Liu
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Jinping Du
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China
| |
Collapse
|
5
|
Schiavo G, Strillacci MG, Ribani A, Bovo S, Roman-Ponce SI, Cerolini S, Bertolini F, Bagnato A, Fontanesi L. Few mitochondrial DNA sequences are inserted into the turkey (Meleagris gallopavo) nuclear genome: evolutionary analyses and informativity in the domestic lineage. Anim Genet 2018. [PMID: 29521475 DOI: 10.1111/age.12648] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mitochondrial DNA (mtDNA) insertions have been detected in the nuclear genome of many eukaryotes. These sequences are pseudogenes originated by horizontal transfer of mtDNA fragments into the nuclear genome, producing nuclear DNA sequences of mitochondrial origin (numt). In this study we determined the frequency and distribution of mtDNA-originated pseudogenes in the turkey (Meleagris gallopavo) nuclear genome. The turkey reference genome (Turkey_2.01) was aligned with the reference linearized mtDNA sequence using last. A total of 32 numt sequences (corresponding to 18 numt regions derived by unique insertional events) were identified in the turkey nuclear genome (size ranging from 66 to 1415 bp; identity against the modern turkey mtDNA corresponding region ranging from 62% to 100%). Numts were distributed in nine chromosomes and in one scaffold. They derived from parts of 10 mtDNA protein-coding genes, ribosomal genes, the control region and 10 tRNA genes. Seven numt regions reported in the turkey genome were identified in orthologues positions in the Gallus gallus genome and therefore were present in the ancestral genome that in the Cretaceous originated the lineages of the modern crown Galliformes. Five recently integrated turkey numts were validated by PCR in 168 turkeys of six different domestic populations. None of the analysed numts were polymorphic (i.e. absence of the inserted sequence, as reported in numts of recent integration in other species), suggesting that the reticulate speciation model is not useful for explaining the origin of the domesticated turkey lineage.
Collapse
Affiliation(s)
- G Schiavo
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy
| | - M G Strillacci
- Department of Veterinary Medicine, University of Milan, Via Celoria 10, 20133, Milano, Italy
| | - A Ribani
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy
| | - S Bovo
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy.,Biocomputing Group, Department of Biological, Geological, and Environmental Sciences, University of Bologna, Via San Giacomo 9/2, 40126, Bologna, Italy
| | - S I Roman-Ponce
- Centro Nacional de Investigación en Fisiología y Mejoramiento Animal, Instituto Nacional de Investigaciones Forestales, Agricola y Pecuarias (INIFAP), Km.1 Carretera a Colón, Auchitlán, 76280, Querétaro, Mexico
| | - S Cerolini
- Department of Veterinary Medicine, University of Milan, Via Celoria 10, 20133, Milano, Italy
| | - F Bertolini
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy.,Department of Animal Science, Iowa State University, 2255 Kildee Hall, 50011, Ames, IA, USA
| | - A Bagnato
- Department of Veterinary Medicine, University of Milan, Via Celoria 10, 20133, Milano, Italy
| | - L Fontanesi
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy
| |
Collapse
|
6
|
Hirimuthugoda NY, Adeola AC, Chen X, Perera PWA, Gunawardena WWDA, Gunwardana HGTN, Yin TT, Wang MS, Li GM, Peng MS, Zhang YP. Complete mitochondrial genome of Sri Lankan Junglefowl ( Gallus lafayetti) and phylogenetic study. MITOCHONDRIAL DNA PART B-RESOURCES 2018; 3:83-84. [PMID: 33474074 PMCID: PMC7799929 DOI: 10.1080/23802359.2017.1422409] [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: 11/26/2022]
Abstract
The complete mitochondrial genomes of two Sri Lankan junglefowl (Gallus lafayetti: CJF) individuals were sequenced by using next-generation sequencing technique. Samples were collected from Rathnapura and Pelmadulla areas in Sri Lanka. The complete mitochondrial DNA is 16,839 bp in length, with a typical mitogenome structure composed of a non-coding control region, 22 tRNA, two rRNA, and 13 protein-coding genes. Overall base composition is 30% A, 23.9% T, 32.3% C, and 13.6% G indicating high content of 54.0% A + T for both individuals. Phylogenetic analysis reveals that CJF samples cluster with the clade of the green junglefowl (Gallus varius) and red junglefowl (Gallus gallus) than to grey junglefowl (Gallus sonerattii: GyJF). This result can be subsequently used to provide essential information for junglefowl evolution.
Collapse
Affiliation(s)
| | - Adeniyi C Adeola
- Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Xing Chen
- Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | | | | | | | - Ting-Ting Yin
- Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Ming-Shan Wang
- Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Gui-Mei Li
- Kunming Biological Diversity Regional Center of Large Apparatus and Equipments, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Min-Sheng Peng
- Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Ya-Ping Zhang
- Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, China
| |
Collapse
|
7
|
Kemp BM, Judd K, Monroe C, Eerkens JW, Hilldorfer L, Cordray C, Schad R, Reams E, Ortman SG, Kohler TA. Prehistoric mitochondrial DNA of domesticate animals supports a 13th century exodus from the northern US southwest. PLoS One 2017; 12:e0178882. [PMID: 28746407 PMCID: PMC5528258 DOI: 10.1371/journal.pone.0178882] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 05/19/2017] [Indexed: 01/24/2023] Open
Abstract
The 13th century Puebloan depopulation of the Four Corners region of the US Southwest is an iconic episode in world prehistory. Studies of its causes, as well as its consequences, have a bearing not only on archaeological method and theory, but also social responses to climate change, the sociology of social movements, and contemporary patterns of cultural diversity. Previous research has debated the demographic scale, destinations, and impacts of Four Corners migrants. Much of this uncertainty stems from the substantial differences in material culture between the Four Corners vs. hypothesized destination areas. Comparable biological evidence has been difficult to obtain due to the complete departure of farmers from the Four Corners in the 13th century CE and restrictions on sampling human remains. As an alternative, patterns of genetic variation among domesticated species were used to address the role of migration in this collapse. We collected mitochondrial haplotypic data from dog (Canis lupus familiaris) and turkey (Meleagris gallopavo) remains from archaeological sites in the most densely-populated portion of the Four Corners region, and the most commonly proposed destination area for that population under migration scenarios. Results are consistent with a large-scale migration of humans, accompanied by their domestic turkeys, during the 13th century CE. These results support scenarios that suggest contemporary Pueblo peoples of the Northern Rio Grande are biological and cultural descendants of Four Corners populations.
Collapse
Affiliation(s)
- Brian M. Kemp
- Department of Anthropology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Kathleen Judd
- Laboratory of Molecular Anthropology and Ancient DNA, Washington State University, Pullman, Washington, United States of America
| | - Cara Monroe
- Department of Anthropology, Washington State University, Pullman, Washington, United States of America
| | - Jelmer W. Eerkens
- Department of Anthropology, University of California, Davis, California, United States of America
| | - Lindsay Hilldorfer
- School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
| | - Connor Cordray
- Laboratory of Molecular Anthropology and Ancient DNA, Washington State University, Pullman, Washington, United States of America
| | - Rebecca Schad
- Laboratory of Molecular Anthropology and Ancient DNA, Washington State University, Pullman, Washington, United States of America
| | - Erin Reams
- Laboratory of Molecular Anthropology and Ancient DNA, Washington State University, Pullman, Washington, United States of America
| | - Scott G. Ortman
- Department of Anthropology, University of Colorado, Boulder, Colorado, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
- Crow Canyon Archaeological Center, Cortez, Colorado, United States of America
| | - Timothy A. Kohler
- Department of Anthropology, Washington State University, Pullman, Washington, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
- Crow Canyon Archaeological Center, Cortez, Colorado, United States of America
| |
Collapse
|
8
|
Halley YA, Oldeschulte DL, Bhattarai EK, Hill J, Metz RP, Johnson CD, Presley SM, Ruzicka RE, Rollins D, Peterson MJ, Murphy WJ, Seabury CM. Northern Bobwhite (Colinus virginianus) Mitochondrial Population Genomics Reveals Structure, Divergence, and Evidence for Heteroplasmy. PLoS One 2015; 10:e0144913. [PMID: 26713762 PMCID: PMC4699210 DOI: 10.1371/journal.pone.0144913] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 11/26/2015] [Indexed: 01/09/2023] Open
Abstract
Herein, we evaluated the concordance of population inferences and conclusions resulting from the analysis of short mitochondrial fragments (i.e., partial or complete D-Loop nucleotide sequences) versus complete mitogenome sequences for 53 bobwhites representing six ecoregions across TX and OK (USA). Median joining (MJ) haplotype networks demonstrated that analyses performed using small mitochondrial fragments were insufficient for estimating the true (i.e., complete) mitogenome haplotype structure, corresponding levels of divergence, and maternal population history of our samples. Notably, discordant demographic inferences were observed when mismatch distributions of partial (i.e., partial D-Loop) versus complete mitogenome sequences were compared, with the reduction in mitochondrial genomic information content observed to encourage spurious inferences in our samples. A probabilistic approach to variant prediction for the complete bobwhite mitogenomes revealed 344 segregating sites corresponding to 347 total mutations, including 49 putative nonsynonymous single nucleotide variants (SNVs) distributed across 12 protein coding genes. Evidence of gross heteroplasmy was observed for 13 bobwhites, with 10 of the 13 heteroplasmies involving one moderate to high frequency SNV. Haplotype network and phylogenetic analyses for the complete bobwhite mitogenome sequences revealed two divergent maternal lineages (dXY = 0.00731; FST = 0.849; P < 0.05), thereby supporting the potential for two putative subspecies. However, the diverged lineage (n = 103 variants) almost exclusively involved bobwhites geographically classified as Colinus virginianus texanus, which is discordant with the expectations of previous geographic subspecies designations. Tests of adaptive evolution for functional divergence (MKT), frequency distribution tests (D, FS) and phylogenetic analyses (RAxML) provide no evidence for positive selection or hybridization with the sympatric scaled quail (Callipepla squamata) as being explanatory factors for the two bobwhite maternal lineages observed. Instead, our analyses support the supposition that two diverged maternal lineages have survived from pre-expansion to post-expansion population(s), with the segregation of some slightly deleterious nonsynonymous mutations.
Collapse
Affiliation(s)
- Yvette A. Halley
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
| | - David L. Oldeschulte
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
| | - Eric K. Bhattarai
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
| | - Joshua Hill
- Genomics and Bioinformatics Core, Texas A&M AgriLife Research, College Station, Texas, United States of America
| | - Richard P. Metz
- Genomics and Bioinformatics Core, Texas A&M AgriLife Research, College Station, Texas, United States of America
| | - Charles D. Johnson
- Genomics and Bioinformatics Core, Texas A&M AgriLife Research, College Station, Texas, United States of America
| | - Steven M. Presley
- Department of Environmental Toxicology, Institute of Environmental and Human Health, Texas Tech University, Lubbock, Texas, United States of America
| | - Rebekah E. Ruzicka
- Texas A&M AgriLife Extension Service, Dallas, Texas, United States of America
| | - Dale Rollins
- Rolling Plains Quail Research Ranch, 1262 U.S. Highway 180 W., Rotan, Texas, United States of America
| | - Markus J. Peterson
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, United States of America
| | - William J. Murphy
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
| | - Christopher M. Seabury
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
- * E-mail:
| |
Collapse
|
9
|
Liu G, Zhou L, Gu C. The complete mitochondrial genome of Brown wood owl Strix leptogrammica (Strigiformes: Strigidae). ACTA ACUST UNITED AC 2015; 25:370-1. [PMID: 25204537 DOI: 10.3109/19401736.2013.803540] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The mitochondrial genome of Brown wood owl is a 16,308-bp circular molecule, which contains 37 typical mitochondrial genes (13 protein-coding genes, 2 rRNAs and 22 tRNAs) and a 741-bp A+T-rich region. Its gene arrangement pattern is identical with typical bird species. All protein-coding genes start with an ATG codon. TAA is the most frequent stop codon, and TAG and T- are also occurred very common. The mtDNA sequence contains 12S rRNA and 16S rRNA of rRNA. Except for tRNA(Ser) ((AGY)) and tRNA(Leu) ((CUN)) without the dihydrouridine (DHU) arm, all tRNAs could be folded into canonical cloverleaf secondary structures.
Collapse
Affiliation(s)
- Gang Liu
- School of Resources and Environmental Engineering, Anhui University , Hefei 230601 , P.R. China
| | | | | |
Collapse
|
10
|
Bao D, Zhao G, Zhou L, Li B. The complete mitochondrial genome of Spotted Munia Lonchura punctulata topela (Passeriformes: Estrildidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3022-3. [PMID: 26162053 DOI: 10.3109/19401736.2015.1063049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Spotted Munia Lonchura punctulata is a sparrow-sized estrildid finch native to tropical Asia. In this study, we used PCR-based method to determine the complete mitochondrial genome of Lonchura punctulata topela. The mitochondrial genome of Spotted Munia is a 16 824-bp circular molecule, which contains 37 typical mitochondrial genes (13 protein-coding genes, two rRNAs, and 22 tRNAs) and a 1247-bp A + T- rich region. The gene arrangement pattern is identical to Taeniopygia guttata and Passer montanus. All the start codons of PCGs are typical ATG, except for the COI and ND3 genes. TAN is the most frequent stop codon, and TAN and T- are also found very common. The non-coding region contains some inter-genic spacers and a control region. The phylogenetic trees from the Bayesian and neighbor-joining analyses, based on the complete mtDNA of 12 Passeriformes species, share similar topologies and high node support values. Lonchura punctulata topela has close relative with Taeniopygia guttata.
Collapse
Affiliation(s)
- Di Bao
- a School of Resources and Environmental Engineering, Anhui University , Hefei , PR China and.,b Department of Animal Genetic Diversity , Anhui Biodiversity Information Center , Hefei , PR China
| | - Guanghong Zhao
- a School of Resources and Environmental Engineering, Anhui University , Hefei , PR China and.,b Department of Animal Genetic Diversity , Anhui Biodiversity Information Center , Hefei , PR China
| | - Lizhi Zhou
- a School of Resources and Environmental Engineering, Anhui University , Hefei , PR China and.,b Department of Animal Genetic Diversity , Anhui Biodiversity Information Center , Hefei , PR China
| | - Bo Li
- a School of Resources and Environmental Engineering, Anhui University , Hefei , PR China and.,b Department of Animal Genetic Diversity , Anhui Biodiversity Information Center , Hefei , PR China
| |
Collapse
|
11
|
Guan X, Silva P, Gyenai K, Xu J, Geng T, Smith E. Mitochondrial DNA-Based Analyses of Relatedness Among Turkeys, Meleagris gallopavo. Biochem Genet 2015; 53:29-41. [PMID: 25820210 DOI: 10.1007/s10528-015-9668-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 02/27/2015] [Indexed: 10/23/2022]
Abstract
The domesticated turkey, Meleagris gallopavo, is believed to be a single breed with several varieties whose relatedness and origins remain poorly understood. Using the mitochondrial genome sequence (GenBank accession no. EF153719) that our group first reported, we investigated the relationships among 15 of the most widely occurring turkey varieties using D-loop and 16S RNA sequences. We included, as a non-traditional outgroup, mtDNA sequence information from wild turkey varieties. A total of 24 SNPs, including 18 in the D-loop and 6 in the 16S rRNA, was identified, validated and used. Of the 15 haplotypes detected based on these SNPs, 7 were unique to wild turkeys. Nucleotide diversity estimates were relatively low when compared to those reported for chickens and other livestock. Network and phylogenetic analyses showed a closer relationship among heritage varieties than between heritage and wild turkeys. The mtDNA data provide additional evidence that suggest a recent divergence of turkey varieties.
Collapse
Affiliation(s)
- Xiaojing Guan
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA, 24061, USA,
| | | | | | | | | | | |
Collapse
|
12
|
Liu G, Zhou L, Li B, Zhang L. The complete mitochondrial genome of Aix galericulata and Tadorna ferruginea: bearings on their phylogenetic position in the Anseriformes. PLoS One 2014; 9:e109701. [PMID: 25375111 PMCID: PMC4222781 DOI: 10.1371/journal.pone.0109701] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 07/22/2014] [Indexed: 11/21/2022] Open
Abstract
Aix galericulata and Tadorna ferruginea are two Anatidae species representing different taxonomic groups of Anseriformes. We used a PCR-based method to determine the complete mtDNAs of both species, and estimated phylogenetic trees based on the complete mtDNA alignment of these and 14 other Anseriforme species, to clarify Anseriform phylogenetics. Phylogenetic trees were also estimated using a multiple sequence alignment of three mitochondrial genes (Cyt b, ND2, and COI) from 68 typical species in GenBank, to further clarify the phylogenetic relationships of several groups among the Anseriformes. The new mtDNAs are circular molecules, 16,651 bp (Aix galericulata) and 16,639 bp (Tadorna ferruginea) in length, containing the 37 typical genes, with an identical gene order and arrangement as those of other Anseriformes. Comparing the protein-coding genes among the mtDNAs of 16 Anseriforme species, ATG is generally the start codon, TAA is the most frequent stop codon, one of three, TAA, TAG, and T-, commonly observed. All tRNAs could be folded into canonical cloverleaf secondary structures except for tRNASer (AGY) and tRNALeu (CUN), which are missing the "DHU" arm.Phylogenetic relationships demonstrate that Aix galericula and Tadorna ferruginea are in the same group, the Tadorninae lineage, based on our analyses of complete mtDNAs and combined gene data. Molecular phylogenetic analysis suggests the 68 species of Anseriform birds be divided into three families: Anhimidae, Anatidae, and Anseranatidae. The results suggest Anatidae birds be divided into five subfamilies: Anatinae, Tadorninae, Anserinae, Oxyurinae, and Dendrocygninae. Oxyurinae and Dendrocygninae should not belong to Anserinae, but rather represent independent subfamilies. The Anatinae includes species from the tribes Mergini, Somaterini, Anatini, and Aythyini. The Anserinae includes species from the tribes Anserini and Cygnini.
Collapse
Affiliation(s)
- Gang Liu
- Institute of Biodiversity and Wetland Ecology, School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui, P. R. China
- Anhui Biodiversity Information Center, Hefei, Anhui, P. R. China
| | - Lizhi Zhou
- Institute of Biodiversity and Wetland Ecology, School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui, P. R. China
- Anhui Biodiversity Information Center, Hefei, Anhui, P. R. China
- * E-mail:
| | - Bo Li
- Institute of Biodiversity and Wetland Ecology, School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui, P. R. China
- Anhui Biodiversity Information Center, Hefei, Anhui, P. R. China
| | - Lili Zhang
- Institute of Biodiversity and Wetland Ecology, School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui, P. R. China
- Anhui Biodiversity Information Center, Hefei, Anhui, P. R. China
| |
Collapse
|
13
|
Li B, Zhu C, Ding P, Bai S, Cui J. Complete mitochondrial genome of black grouse (Lyrurus tetrix). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:134-5. [PMID: 24450707 DOI: 10.3109/19401736.2013.878911] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We sequenced the entire mitochondrial genome of Lyrurus tetrix for the first time. The mitogenome was 16,677 bp in length, encoded with a standard set of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes plus a putative control region. Almost all genes were encoded on the H-strand except the ND6 and eight tRNA genes. All protein-coding genes initiated with ATG, except for COX1 and ND5 (GTG). An 18-bp-nucleotide deletion occurred in the ND6 of Lyrurus tetrix in contrast to other Galliformes. The total base composition of the mitogenome was 30.4% for A, 30.4% for C, 25.8% for T and 13.4% for G. These results provide basic information for phylogenetic analyses among Galliformes.
Collapse
Affiliation(s)
- Bo Li
- a College of Wildlife Resources, Northeast Forestry University , Harbin , China and.,b State Forestry Administration Detecting Center of Wildlife , Harbin , China
| | - Can Zhu
- a College of Wildlife Resources, Northeast Forestry University , Harbin , China and
| | - Peng Ding
- a College of Wildlife Resources, Northeast Forestry University , Harbin , China and
| | - Suying Bai
- a College of Wildlife Resources, Northeast Forestry University , Harbin , China and
| | - Jie Cui
- a College of Wildlife Resources, Northeast Forestry University , Harbin , China and
| |
Collapse
|
14
|
The complete mitochondrial genome of bean goose (Anser fabalis) and implications for anseriformes taxonomy. PLoS One 2013; 8:e63334. [PMID: 23717412 PMCID: PMC3662773 DOI: 10.1371/journal.pone.0063334] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Accepted: 03/30/2013] [Indexed: 11/29/2022] Open
Abstract
Mitochondrial DNA plays an important role in living organisms, and has been used as a powerful molecular marker in a variety of evolutionary studies. In this study, we determined the complete mtDNA of Bean goose (Anser fabalis), which is 16,688 bp long and contains 13 protein-coding genes, 2 rRNAs, 22 tRNAs and a control region. The arrangement is similar to that of typical Anseriform species. All protein-coding genes, except for Cyt b, ND5, COI, and COII, start with an ATG codon. The ATG start codon is also generally observed in the 12 other Anseriform species, including 2 Anser species, with sequenced mitochondrial genomes. TAA is the most frequent stop codon, one of three–TAA, TAG, and T- –commonly observed in Anseriformes. All tRNAs could be folded into canonical cloverleaf secondary structures except for tRNASer(AGY) and tRNALeu(CUN), which are missing the dihydrouridine (DHU) arm. The control region of Bean goose mtDNA, with some conserved sequence boxes, such as F, E, D, and C, identified in its central domain. Phylogenetic analysis of complete mtDNA data for 13 Anseriform species supports the classification of them into four major branches: Anatinae, Anserinae, Dendrocygninae and Anseranatidae. Phylogenetic analyses were also conducted on 36 Anseriform birds using combined Cyt b, ND2, and COI sequences. The results clearly support the genus Somateria as an independent lineage classified in its own tribe, the Somaterini. Recovered topologies from both complete mtDNA and combined DNA sequences strongly indicate that Dendrocygninae is an independent subfamily within the family Anatidae and Anseranatidae represents an independent family. Based on the results of this study, we conclude that combining ND2, Cyt b, and COI sequence data is a workable solution at present for resolving phylogenetic relationships among Anseriform species in the absence of sufficient complete mtDNA data.
Collapse
|
15
|
Li HM, Shi JP, Zeng DL, Zeng ZH, Qin XM. The complete mitochondrial genome of Chrysolophus pictus (Galliformes: Phasianidae) and a phylogenetic analysis with related species. MITOCHONDRIAL DNA 2011; 22:159-61. [PMID: 22165827 DOI: 10.3109/19401736.2011.636433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The 16,678 bp mitochondrial genome of the Chrysolophus pictus has been sequenced in this paper. To determine the phylogentic position of C. pictus with related species within Phasianidae, the phylogenetic tree was reconstructed with the concatenated nucleotide dataset of the 12 heavy-strand-encoded protein genes. The phylogenetic analysis was carried out using maximum parsimony (MP) and Bayesian inference (BI) methods. MP and BI phylogenetic trees here showed similar topology and consistently suggested that C. pictus shared a close relationship with Phasianus versicolor. The results also showed that the Meleagris gallopavo possessed a basal phylogenetic position within Phasianidae, which may imply that it should be classified into the Phasianidae.
Collapse
Affiliation(s)
- Hui-Min Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, College of Life Sciences, Guangxi Normal University, Guilin, PR China
| | | | | | | | | |
Collapse
|
16
|
Speller CF, Nicholas GP, Yang DY. Feather barbs as a good source of mtDNA for bird species identification in forensic wildlife investigations. INVESTIGATIVE GENETICS 2011; 2:16. [PMID: 21794178 PMCID: PMC3199791 DOI: 10.1186/2041-2223-2-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Accepted: 07/28/2011] [Indexed: 12/01/2022]
Abstract
Background The ability to accurately identify bird species is crucial for wildlife law enforcement and bird-strike investigations. However, such identifications may be challenging when only partial or damaged feathers are available for analysis. Results By applying vigorous contamination controls and sensitive PCR amplification protocols, we found that it was feasible to obtain accurate mitochondrial (mt)DNA-based species identification with as few as two feather barbs. This minimally destructive DNA approach was successfully used and tested on a variety of bird species, including North American wild turkey (Meleagris gallopavo), Canada goose (Branta canadensis), blue heron (Ardea herodias) and pygmy owl (Glaucidium californicum). The mtDNA was successfully obtained from 'fresh' feathers, historic museum specimens and archaeological samples, demonstrating the sensitivity and versatility of this technique. Conclusions By applying appropriate contamination controls, sufficient quantities of mtDNA can be reliably recovered and analyzed from feather barbs. This previously overlooked substrate provides new opportunities for accurate DNA species identification when minimal feather samples are available for forensic analysis.
Collapse
Affiliation(s)
- Camilla F Speller
- Centre for Forensic Research, Ancient DNA Laboratory, Department of Archaeology, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada.
| | | | | |
Collapse
|
17
|
Kan XZ, Li XF, Lei ZP, Wang M, Chen L, Gao H, Yang ZY. Complete mitochondrial genome of Cabot's tragopan, Tragopan caboti (Galliformes: Phasianidae). GENETICS AND MOLECULAR RESEARCH 2010; 9:1204-16. [PMID: 20589618 DOI: 10.4238/vol9-2gmr820] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Cabot's tragopan, Tragopan caboti, is a globally threatened pheasant endemic to southeast China. The complete mitochondrial genome of Cabot's tragopan was sequenced. The circular genome contains 16,727 bp, encoding a standard set of 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes, plus the putative control region, a structure very similar to that of other Galliformes. As found in other vertebrates, most of these genes code on the H-strand, except for the NADH dehydrogenase subunit 6 (nad6) and eight tRNA genes (Gln, Ala, Asn, Cys, Tyr, Ser(UCN), Pro, Glu). All protein-coding genes initiated with ATG, except for cox1, which began with GTG, and had a strong skew of C vs G (GC skew = -0.29 to -0.73). One extra 'C' nucleotide was found in the NADH dehydrogenase subunit 3 (nad3). All the tRNA gene sequences have the potential to fold into typical cloverleaf secondary structures. Conserved sequences in three domains were identified within the control region (D-loop). These results provide basic information for phylogenetic analyses among Galliform birds, and especially Tragopan species.
Collapse
Affiliation(s)
- X Z Kan
- The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, College of Life Sciences, Anhui Normal University, Wuhu, China.
| | | | | | | | | | | | | |
Collapse
|
18
|
Kan XZ, Yang JK, Li XF, Chen L, Lei ZP, Wang M, Qian CJ, Gao H, Yang ZY. Phylogeny of major lineages of galliform birds (Aves: Galliformes) based on complete mitochondrial genomes. GENETICS AND MOLECULAR RESEARCH 2010; 9:1625-33. [DOI: 10.4238/vol9-3gmr898] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
19
|
The complete mitochondrial genomes of the whistling duck (Dendrocygna javanica) and black swan (Cygnus atratus): dating evolutionary divergence in Galloanserae. Mol Biol Rep 2009; 37:3001-15. [PMID: 19823953 DOI: 10.1007/s11033-009-9868-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2009] [Accepted: 09/29/2009] [Indexed: 10/20/2022]
Abstract
Galloanserae is an ancient and diverse avian group, for which comprehensive molecular evidence relevant to phylogenetic analysis in the context of molecular chronology is lacking. In this study, we present two additional mitochondrial genome sequences of Galloanserae (the whistling duck, Dendrocygna javanica, and the black swan, Cygnus atratus) to broaden the scope of molecular phylogenetic reconstruction. The lengths of the whistling duck's and black swan's mitochondrial genomes are 16,753 and 16,748 bases, respectively. Phylogenetic analyses suggest that Dendrocygna is more likely to be in a basal position of the branch consisting of Anatinae and Anserinae, an affiliation that does not conform to its traditional classification. Bayesian approaches were employed to provide a rough timescale for Galloanserae evolution. In general, a narrow range of 95% confidence intervals gave younger estimates than those based on limited genes and estimated that at least two lineages originated before the Coniacian epoch around 90 MYA, well before the Cretaceous-Tertiary boundary. In addition, these results, which were compatible with estimates from fossil evidence, also imply that the origin of numerous genera in Anseriformes took place in the late Oligocene to early Miocene. Taken together, the results presented here provide a working framework for future research on Galloanserae evolution, and they underline the utility of whole mitochondrial genome sequences for the resolution of deep divergence.
Collapse
|