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Qu J, Lu X, Teng X, Xing Z, Wang S, Feng C, Wang X, Wang L. Mitochondrial Genomes of Streptopelia decaocto: Insights into Columbidae Phylogeny. Animals (Basel) 2024; 14:2220. [PMID: 39123752 PMCID: PMC11310995 DOI: 10.3390/ani14152220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 07/18/2024] [Accepted: 07/26/2024] [Indexed: 08/12/2024] Open
Abstract
In this research, the mitochondrial genome of the Streptopelia decaocto was sequenced and examined for the first time to enhance the comprehension of the phylogenetic relationships within the Columbidae. The complete mitochondrial genome of Streptopelia decaocto (17,160 bp) was structurally similar to the recognized members of the Columbidae family, but with minor differences in gene size and arrangement. The structural AT content was 54.12%. Additionally, 150 mitochondrial datasets, representing valid species, were amassed in this investigation. Maximum likelihood (ML) and Bayesian inference (BI) phylogenetic trees and evolutionary time relationships of species were reconstructed based on cytb gene sequences. The findings from the phylogenetic evaluations suggest that the S. decaocto was classified under the Columbinae subfamily, diverging from the Miocene approximately 8.1 million years ago, indicating intricate evolutionary connections with its close relatives, implying a history of species divergence and geographic isolation. The diversification of the Columbidae commenced during the Late Oligocene and extended into the Miocene. This exploration offers crucial molecular data for the S. decaocto, facilitating the systematic taxonomic examination of the Columbidae and Columbiformes, and establishing a scientific foundation for species preservation and genetic resource management.
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Affiliation(s)
- Jiangyong Qu
- College of Life Science, Yantai University, Yantai 264005, China; (J.Q.); (X.L.); (Z.X.); (S.W.); (C.F.)
| | - Xiaofei Lu
- College of Life Science, Yantai University, Yantai 264005, China; (J.Q.); (X.L.); (Z.X.); (S.W.); (C.F.)
| | - Xindong Teng
- Qingdao International Travel Healthcare Center, Qingdao 266071, China;
| | - Zhikai Xing
- College of Life Science, Yantai University, Yantai 264005, China; (J.Q.); (X.L.); (Z.X.); (S.W.); (C.F.)
| | - Shuang Wang
- College of Life Science, Yantai University, Yantai 264005, China; (J.Q.); (X.L.); (Z.X.); (S.W.); (C.F.)
| | - Chunyu Feng
- College of Life Science, Yantai University, Yantai 264005, China; (J.Q.); (X.L.); (Z.X.); (S.W.); (C.F.)
| | - Xumin Wang
- College of Life Science, Yantai University, Yantai 264005, China; (J.Q.); (X.L.); (Z.X.); (S.W.); (C.F.)
| | - Lijun Wang
- College of Life Science, Yantai University, Yantai 264005, China; (J.Q.); (X.L.); (Z.X.); (S.W.); (C.F.)
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French CM, Bertola LD, Carnaval AC, Economo EP, Kass JM, Lohman DJ, Marske KA, Meier R, Overcast I, Rominger AJ, Staniczenko PPA, Hickerson MJ. Global determinants of insect mitochondrial genetic diversity. Nat Commun 2023; 14:5276. [PMID: 37644003 PMCID: PMC10465557 DOI: 10.1038/s41467-023-40936-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 08/15/2023] [Indexed: 08/31/2023] Open
Abstract
Understanding global patterns of genetic diversity is essential for describing, monitoring, and preserving life on Earth. To date, efforts to map macrogenetic patterns have been restricted to vertebrates, which comprise only a small fraction of Earth's biodiversity. Here, we construct a global map of predicted insect mitochondrial genetic diversity from cytochrome c oxidase subunit 1 sequences, derived from open data. We calculate the mitochondrial genetic diversity mean and genetic diversity evenness of insect assemblages across the globe, identify their environmental correlates, and make predictions of mitochondrial genetic diversity levels in unsampled areas based on environmental data. Using a large single-locus genetic dataset of over 2 million globally distributed and georeferenced mtDNA sequences, we find that mitochondrial genetic diversity evenness follows a quadratic latitudinal gradient peaking in the subtropics. Both mitochondrial genetic diversity mean and evenness positively correlate with seasonally hot temperatures, as well as climate stability since the last glacial maximum. Our models explain 27.9% and 24.0% of the observed variation in mitochondrial genetic diversity mean and evenness in insects, respectively, making an important step towards understanding global biodiversity patterns in the most diverse animal taxon.
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Affiliation(s)
- Connor M French
- Biology Department, City College of New York, New York, NY, USA.
- Biology Ph.D. Program, Graduate Center, City University of New York, New York, NY, USA.
| | - Laura D Bertola
- Biology Department, City College of New York, New York, NY, USA
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, N 2200, Denmark
| | - Ana C Carnaval
- Biology Department, City College of New York, New York, NY, USA
- Biology Ph.D. Program, Graduate Center, City University of New York, New York, NY, USA
| | - Evan P Economo
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Jamie M Kass
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
- Macroecology Laboratory, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - David J Lohman
- Biology Department, City College of New York, New York, NY, USA
- Biology Ph.D. Program, Graduate Center, City University of New York, New York, NY, USA
- Entomology Section, National Museum of Natural History, Manila, Philippines
| | | | - Rudolf Meier
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
- Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde Berlin, Berlin, Germany
| | - Isaac Overcast
- Biology Ph.D. Program, Graduate Center, City University of New York, New York, NY, USA
- Institut de Biologie de l'Ecole Normale Superieure, Paris, France
- Department of Vertebrate Zoology, American Museum of Natural History, New York, NY, USA
| | - Andrew J Rominger
- School of Biology and Ecology, University of Maine, Orono, ME, USA
- Maine Center for Genetics in the Environment, University of Maine, Orono, ME, USA
| | | | - Michael J Hickerson
- Biology Department, City College of New York, New York, NY, USA
- Biology Ph.D. Program, Graduate Center, City University of New York, New York, NY, USA
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA
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Duan Y, Fu S, Ye Z, Bu W. Phylogeny of Urostylididae (Heteroptera: Pentatomoidea) reveals rapid radiation and challenges traditional classification. ZOOL SCR 2023. [DOI: 10.1111/zsc.12582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Yujie Duan
- Institute of Entomology, College of Life Sciences Nankai University Tianjin China
| | - Siying Fu
- Institute of Entomology, College of Life Sciences Nankai University Tianjin China
| | - Zhen Ye
- Institute of Entomology, College of Life Sciences Nankai University Tianjin China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences Nankai University Tianjin China
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Zhang L, Sun K, Csorba G, Hughes AC, Jin L, Xiao Y, Feng J. Complete mitochondrial genomes reveal robust phylogenetic signals and evidence of positive selection in horseshoe bats. BMC Ecol Evol 2021; 21:199. [PMID: 34732135 PMCID: PMC8565063 DOI: 10.1186/s12862-021-01926-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 10/25/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In genus Rhinolophus, species in the Rhinolophus philippinensis and R. macrotis groups are unique because the horseshoe bats in these group have relatively low echolocation frequencies and flight speeds compared with other horseshoe bats with similar body size. The different characteristics among bat species suggest particular evolutionary processes may have occurred in this genus. To study the adaptive evidence in the mitochondrial genomes (mitogenomes) of rhinolophids, especially the mitogenomes of the species with low echolocation frequencies, we sequenced eight mitogenomes and used them for comparative studies of molecular phylogeny and adaptive evolution. RESULTS Phylogenetic analysis using whole mitogenome sequences produced robust results and provided phylogenetic signals that were better than those obtained using single genes. The results supported the recent establishment of the separate macrotis group. The signals of adaptive evolution discovered in the Rhinolophus species were tested for some of the codons in two genes (ND2 and ND6) that encode NADH dehydrogenases in oxidative phosphorylation system complex I. These genes have a background of widespread purifying selection. Signals of relaxed purifying selection and positive selection were found in ND2 and ND6, respectively, based on codon models and physicochemical profiles of amino acid replacements. However, no pronounced overlap was found for non-synonymous sites in the mitogenomes of all the species with low echolocation frequencies. A signal of positive selection for ND5 was found in the branch-site model when R. philippinensis was set as the foreground branch. CONCLUSIONS The mitogenomes provided robust phylogenetic signals that were much more informative than the signals obtained using single mitochondrial genes. Two mitochondrial genes that encoding proteins in the oxidative phosphorylation system showed some evidence of adaptive evolution in genus Rhinolophus and the positive selection signals were tested for ND5 in R. philippinensis. These results indicate that mitochondrial protein-coding genes were targets of adaptive evolution during the evolution of Rhinolophus species, which might have contributed to a diverse range of acoustic adaptations in this genus.
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Affiliation(s)
- Lin Zhang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117, China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117, China.
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, China.
| | - Gábor Csorba
- Department of Zoology, Hungarian Natural History Museum, Budapest, Hungary
| | - Alice Catherine Hughes
- Centre for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla County, 666303, Yunnan, China
| | - Longru Jin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117, China
| | - Yanhong Xiao
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117, China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117, China.
- College of Life Science, Jilin Agricultural University, Changchun, 130118, China.
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5
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Protein Structure, Models of Sequence Evolution, and Data Type Effects in Phylogenetic Analyses of Mitochondrial Data: A Case Study in Birds. DIVERSITY 2021. [DOI: 10.3390/d13110555] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Phylogenomic analyses have revolutionized the study of biodiversity, but they have revealed that estimated tree topologies can depend, at least in part, on the subset of the genome that is analyzed. For example, estimates of trees for avian orders differ if protein-coding or non-coding data are analyzed. The bird tree is a good study system because the historical signal for relationships among orders is very weak, which should permit subtle non-historical signals to be identified, while monophyly of orders is strongly corroborated, allowing identification of strong non-historical signals. Hydrophobic amino acids in mitochondrially-encoded proteins, which are expected to be found in transmembrane helices, have been hypothesized to be associated with non-historical signals. We tested this hypothesis by comparing the evolution of transmembrane helices and extramembrane segments of mitochondrial proteins from 420 bird species, sampled from most avian orders. We estimated amino acid exchangeabilities for both structural environments and assessed the performance of phylogenetic analysis using each data type. We compared those relative exchangeabilities with values calculated using a substitution matrix for transmembrane helices estimated using a variety of nuclear- and mitochondrially-encoded proteins, allowing us to compare the bird-specific mitochondrial models with a general model of transmembrane protein evolution. To complement our amino acid analyses, we examined the impact of protein structure on patterns of nucleotide evolution. Models of transmembrane and extramembrane sequence evolution for amino acids and nucleotides exhibited striking differences, but there was no evidence for strong topological data type effects. However, incorporating protein structure into analyses of mitochondrially-encoded proteins improved model fit. Thus, we believe that considering protein structure will improve analyses of mitogenomic data, both in birds and in other taxa.
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Sanno R, Kataoka K, Hayakawa S, Ide K, Nguyen CN, Nguyen TP, Le BTN, Kim OTP, Mineta K, Takeyama H, Takeda M, Sato T, Suzuki T, Yura K, Asahi T. Comparative Analysis of Mitochondrial Genomes in Gryllidea (Insecta: Orthoptera): Implications for Adaptive Evolution in Ant-Loving Crickets. Genome Biol Evol 2021; 13:evab222. [PMID: 34554226 PMCID: PMC8511664 DOI: 10.1093/gbe/evab222] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2021] [Indexed: 12/24/2022] Open
Abstract
Species of infraorder Gryllidea, or crickets, are useful invertebrate models for studying developmental biology and neuroscience. They have also attracted attention as alternative protein sources for human food and animal feed. Mitochondrial genomic information on related invertebrates, such as katydids, and locusts, has recently become available in attempt to clarify the controversial classification schemes, although robust phylogenetic relationships with emphasis on crickets remain elusive. Here, we report newly sequenced complete mitochondrial genomes of crickets to study their phylogeny, genomic rearrangements, and adaptive evolution. First, we conducted de novo assembly of mitochondrial genomes from eight cricket species and annotated protein-coding genes and transfer and ribosomal RNAs using automatic annotations and manual curation. Next, by combining newly described protein-coding genes with public data of the complete Gryllidea genomes and gene annotations, we performed phylogenetic analysis and found gene order rearrangements in several branches. We further analyzed genetic signatures of selection in ant-loving crickets (Myrmecophilidae), which are small wingless crickets that inhabit ant nests. Three distinct approaches revealed two positively selected sites in the cox1 gene in these crickets. Protein 3D structural analyses suggested that these selected sites could influence the interaction of respiratory complex proteins, conferring benefits to ant-loving crickets with a unique ecological niche and morphology. These findings enhance our understanding of the genetic basis of cricket evolution without relying on estimates based on a limited number of molecular markers.
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Affiliation(s)
- Ryuto Sanno
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Kosuke Kataoka
- Comprehensive Research Organization, Waseda University, Tokyo, Japan
| | - Shota Hayakawa
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Keigo Ide
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Department of Health Data Science Research, Healthy Aging Innovation Center, Tokyo Metropolitan Geriatric Medical Center, Tokyo, Japan
| | - Chuong N Nguyen
- Applied Biotechnology for Crop Development Research Unit, School of Biotechnology, International University, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Thao P Nguyen
- Applied Biotechnology for Crop Development Research Unit, School of Biotechnology, International University, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Binh T N Le
- Institute of Genome Research, Vietnam Academy of Science and Technology, Cau Giay, Hanoi, Vietnam
| | - Oanh T P Kim
- Institute of Genome Research, Vietnam Academy of Science and Technology, Cau Giay, Hanoi, Vietnam
| | - Katsuhiko Mineta
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Haruko Takeyama
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Comprehensive Research Organization, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
- Research Organization for Nano & Life Innovation, Waseda University, Tokyo, Japan
| | - Makio Takeda
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Hyogo, Japan
| | - Toshiyuki Sato
- Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Takeshi Suzuki
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Japan
| | - Kei Yura
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan
| | - Toru Asahi
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Comprehensive Research Organization, Waseda University, Tokyo, Japan
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
- Research Organization for Nano & Life Innovation, Waseda University, Tokyo, Japan
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7
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Miller CD, Forthman M, Miller CW, Kimball RT. Extracting ‘legacy loci’ from an invertebrate sequence capture data set. ZOOL SCR 2021. [DOI: 10.1111/zsc.12513] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Caroline D. Miller
- Department of Entomology & Nematology University of Florida Gainesville FL USA
| | - Michael Forthman
- Department of Entomology & Nematology University of Florida Gainesville FL USA
- California State Collection of Arthropods Plant Pest Diagnostics Branch California Department of Food & Agriculture Sacramento CA USA
| | - Christine W. Miller
- Department of Entomology & Nematology University of Florida Gainesville FL USA
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De Panis D, Lambertucci SA, Wiemeyer G, Dopazo H, Almeida FC, Mazzoni CJ, Gut M, Gut I, Padró J. Mitogenomic analysis of extant condor species provides insight into the molecular evolution of vultures. Sci Rep 2021; 11:17109. [PMID: 34429448 PMCID: PMC8384887 DOI: 10.1038/s41598-021-96080-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/31/2021] [Indexed: 02/07/2023] Open
Abstract
The evolution of large vultures linked to mountainous habitats was accompanied by extreme physiological and behavioral specializations for energetically efficient flights. However, little is known on the genetic traits associated with the evolution of these obligate soaring scavengers. Mitochondrial DNA plays a vital role in regulating oxidative stress and energy production, and hence may be an important target of selection for flight performance. Herein, we characterized the first mitogenomes of the Andean and California condors, the world's heaviest flying birds and the only living representatives of the Vultur and Gymnogyps genus. We reconstructed the phylogenetic relationships and evaluated possible footprints of convergent evolution associated to the life-history traits and distributional range of vultures. Our phylogenomic analyses supported the independent evolution of vultures, with the origin of Cathartidae in the early Paleogene (~ 61 Mya), and estimated the radiation of extant condors during the late Miocene (~ 11 Mya). Selection analyses indicated that vultures exhibit signals of relaxation of purifying selection relative to other accipitrimorph raptors, possibly indicating the degeneration of flapping flight ability. Overall, our results suggest that the extreme specialization of vultures for efficient soaring flight has compensated the evolution of large body sizes mitigating the selection pressure on mtDNA.
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Affiliation(s)
- D. De Panis
- grid.412234.20000 0001 2112 473XGrupo de Investigaciones en Biología de la Conservación, INIBIOMA, Universidad Nacional del Comahue-CONICET, 8400 Bariloche, Argentina ,grid.7345.50000 0001 0056 1981Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Universidad de Buenos Aires-CONICET, Intendente Güiraldes 2160, 1428 Ciudad Autónoma de Buenos Aires, Argentina
| | - S. A. Lambertucci
- grid.412234.20000 0001 2112 473XGrupo de Investigaciones en Biología de la Conservación, INIBIOMA, Universidad Nacional del Comahue-CONICET, 8400 Bariloche, Argentina
| | - G. Wiemeyer
- grid.412234.20000 0001 2112 473XGrupo de Investigaciones en Biología de la Conservación, INIBIOMA, Universidad Nacional del Comahue-CONICET, 8400 Bariloche, Argentina ,Ecoparque Buenos Aires-Argentina, República de la India 3000, 1425 Ciudad Autónoma de Buenos Aires, Argentina ,Fundación Cabure-Í, Mcal Antonio Sucre 2842, 1428 Ciudad Autónoma de Buenos Aires, Argentina ,grid.7345.50000 0001 0056 1981Present Address: Hospital Escuela, Facultad de Ciencias Veterinarias, Universidad de Buenos Aires, Av. Chorroarín 280, 1427 Ciudad Autónoma de Buenos Aires, Argentina
| | - H. Dopazo
- grid.7345.50000 0001 0056 1981Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Universidad de Buenos Aires-CONICET, Intendente Güiraldes 2160, 1428 Ciudad Autónoma de Buenos Aires, Argentina
| | - F. C. Almeida
- grid.7345.50000 0001 0056 1981Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Universidad de Buenos Aires-CONICET, Intendente Güiraldes 2160, 1428 Ciudad Autónoma de Buenos Aires, Argentina
| | - C. J. Mazzoni
- grid.511553.6Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Königin-Luise-Straße 6-8, 14195 Berlin, Germany
| | - M. Gut
- grid.11478.3bCNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - I. Gut
- grid.11478.3bCNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - J. Padró
- grid.412234.20000 0001 2112 473XGrupo de Investigaciones en Biología de la Conservación, INIBIOMA, Universidad Nacional del Comahue-CONICET, 8400 Bariloche, Argentina
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9
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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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10
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Plazzi F, Puccio G, Passamonti M. HERMES: An improved method to test mitochondrial genome molecular synapomorphies among clades. Mitochondrion 2021; 58:285-295. [PMID: 33639269 DOI: 10.1016/j.mito.2021.02.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 01/10/2021] [Accepted: 02/12/2021] [Indexed: 02/06/2023]
Abstract
Mitochondrial chromosomes have diversified among eukaryotes and many different architectures and features are now acknowledged for this genome. Here we present the improved HERMES index, which can measure and quantify the amount of molecular change experienced by mitochondrial genomes. We test the improved approach with ten molecular phylogenetic studies based on complete mitochondrial genomes, representing six bilaterian Phyla. In most cases, HERMES analysis spotted out clades or single species with peculiar molecular synapomorphies, allowing to identify phylogenetic and ecological patterns. The software presented herein handles linear, circular, and multi-chromosome genomes, thus widening the HERMES scope to the complete eukaryotic domain.
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Affiliation(s)
- Federico Plazzi
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi, 3, 40126 Bologna, Italy.
| | - Guglielmo Puccio
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi, 3, 40126 Bologna, Italy.
| | - Marco Passamonti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi, 3, 40126 Bologna, Italy.
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11
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Kimball RT, Hosner PA, Braun EL. A phylogenomic supermatrix of Galliformes (Landfowl) reveals biased branch lengths. Mol Phylogenet Evol 2021; 158:107091. [PMID: 33545275 DOI: 10.1016/j.ympev.2021.107091] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 01/16/2021] [Accepted: 01/27/2021] [Indexed: 11/25/2022]
Abstract
Building taxon-rich phylogenies is foundational for macroevolutionary studies. One approach to improve taxon sampling beyond individual studies is to build supermatricies of publicly available data, incorporating taxa sampled across different studies and utilizing different loci. Most existing supermatrix studies have focused on loci commonly sequenced with Sanger technology ("legacy" markers, such as mitochondrial data and small numbers of nuclear loci). However, incorporating phylogenomic studies into supermatrices allows problem nodes to be targeted and resolved with considerable amounts of data, while improving taxon sampling with legacy data. Here we estimate phylogeny from a galliform supermatrix which includes well-known model and agricultural species such as the chicken and turkey. We assembled a supermatrix comprising 4500 ultra-conserved elements (UCEs) collected as part of recent phylogenomic studies in this group and legacy mitochondrial and nuclear (intron and exon) sequences. Our resulting phylogeny included 88% of extant species and recovered well-accepted relationships with strong support. However, branch lengths, which are particularly important in down-stream macroevolutionary studies, appeared vastly skewed. Taxa represented only by rapidly evolving mitochondrial data had high proportions of missing data and exhibited long terminal branches. Conversely, taxa sampled for slowly evolving UCEs with low proportions of missing data exhibited substantially shorter terminal branches. We explored several branch length re-estimation methods with particular attention to terminal branches and conclude that re-estimation using well-sampled mitochondrial sequences may be a pragmatic approach to obtain trees suitable for macroevolutionary analysis.
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Affiliation(s)
- Rebecca T Kimball
- Department of Biology, University of Florida, Gainesville, FL 32607, USA.
| | - Peter A Hosner
- Department of Biology, University of Florida, Gainesville, FL 32607, USA; Natural History Museum of Denmark and Center for Macroecology, Evolution and Climate, University of Copenhagen, Copenhagen, Denmark
| | - Edward L Braun
- Department of Biology, University of Florida, Gainesville, FL 32607, USA
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12
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Miller MJ, Bermingham E, Turner BL, Touchon JC, Johnson AB, Winker K. Demographic consequences of foraging ecology explain genetic diversification in Neotropical bird species. Ecol Lett 2021; 24:563-571. [PMID: 33389805 DOI: 10.1111/ele.13674] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/23/2020] [Accepted: 12/02/2020] [Indexed: 11/30/2022]
Abstract
Despite evidence that species' traits affect rates of bird diversification, biogeographic studies tend to prioritise earth history in Neotropical bird speciation. Here we compare mitochondrial genetic differentiation among 56 co-distributed Neotropical bird species with varying ecologies. The trait 'diet' best predicted divergence, with plant-dependent species (mostly frugivores and nectivores) showing lower levels of genetic divergence than insectivores or mixed-diet species. We propose that the greater vagility and demographic instability of birds whose diets rely on fruit, seeds, or nectar known to vary in abundance seasonally and between years relative to birds that eat primarily insects, drives episodic re-unification of otherwise isolated populations, resetting the divergence 'clock'. Testing this prediction using coalescent simulations, we find that plant-dependent species show stronger signals of recent demographic expansion compared to insectivores or mixed-diet species, consistent with this hypothesis. Our study provides evidence that localised ecological phenomena scale up to generate larger macroevolutionary patterns.
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Affiliation(s)
- Matthew J Miller
- Department of Biology & Wildlife, University of Alaska Museum, 907 Yukon Drive, Fairbanks, AK, 99775, USA.,Smithsonian Tropical Research Institute, Apartado, Balboa, Ancón, 0843-03092, Republic of Panama
| | - Eldredge Bermingham
- Smithsonian Tropical Research Institute, Apartado, Balboa, Ancón, 0843-03092, Republic of Panama.,Patricia and Phillip Frost Museum of Science, Miami, FL, 33129, USA
| | - Benjamin L Turner
- Smithsonian Tropical Research Institute, Apartado, Balboa, Ancón, 0843-03092, Republic of Panama
| | - Justin C Touchon
- Smithsonian Tropical Research Institute, Apartado, Balboa, Ancón, 0843-03092, Republic of Panama.,Biology Department, Vassar College, 124 Raymond Ave., Poughkeepsie, NY, 12604, USA
| | - Andrew B Johnson
- Department of Biology & Wildlife, University of Alaska Museum, 907 Yukon Drive, Fairbanks, AK, 99775, USA.,Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Kevin Winker
- Department of Biology & Wildlife, University of Alaska Museum, 907 Yukon Drive, Fairbanks, AK, 99775, USA
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Zeng X, Xu H, Gu J, Mao B, Chen Z, Huang Y, Huang J. Phylogenetic position of the genera Caryandoides, Paratoacris, Fer and Longchuanacris (Orthoptera:Acrididae) revealed by complete mitogenome sequences. INVERTEBR SYST 2021. [DOI: 10.1071/is20077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Many taxa in the Acrididae have controversial phylogenetic positions. A typical example of such controversies is the phylogenetic positions of the genera Caryandoides, Paratoacris, Fer and Longchuanacris, as well as some other related taxa, which were placed in Oxyinae by some authors, but were considered members of the subfamily Catantopinae by others. In this study, the complete mitogenomes of nine species were sequenced using next-generation sequencing, the characteristics of the newly sequenced mitogenomes are presented briefly, and the phylogeny of the Oxyinae and Catantopinae are reconstructed using a selected dataset of mitogenome sequences under maximum likelihood and Bayesian inference frameworks. The results show that the four controversial genera were consistently assigned to the subfamily Oxyinae rather than Catantopinae in all phylogenetic trees deduced from different datasets under different frameworks, and this finding is entirely consistent with their morphological characters. Therefore, it is more appropriate to place them in Oxyinae rather than Catantopinae. In addition, the results from our analysis also confirm the membership of the genus Apalacris in Coptacrinae rather than Catantopinae, and indicate the uncertainty in the phylogenetic position of the genus Traulia, and a more in-depth study is necessary to resolve the relationship of Traulia with other catantopine groups or Coptacrinae.
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14
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Mariadassou M, Suez M, Sathyakumar S, Vignal A, Arca M, Nicolas P, Faraut T, Esquerré D, Nishibori M, Vieaud A, Chen CF, Manh Pham H, Roman Y, Hospital F, Zerjal T, Rognon X, Tixier-Boichard M. Unraveling the history of the genus Gallus through whole genome sequencing. Mol Phylogenet Evol 2020; 158:107044. [PMID: 33346111 DOI: 10.1016/j.ympev.2020.107044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 10/23/2020] [Accepted: 12/14/2020] [Indexed: 12/16/2022]
Abstract
The genus Gallus is distributed across a large part of Southeast Asia and has received special interest because the domestic chicken, Gallus gallus domesticus, has spread all over the world and is a major protein source for humans. There are four species: the red junglefowl (G. gallus), the green junglefowl (G. varius), the Lafayette's junglefowl (G. lafayettii) and the grey junglefowl (G. sonneratii). The aim of this study is to reconstruct the history of these species by a whole genome sequencing approach and resolve inconsistencies between well supported topologies inferred using different data and methods. Using deep sequencing, we identified over 35 million SNPs and reconstructed the phylogeny of the Gallus genus using both distance (BioNJ) and maximum likelihood (ML) methods. We observed discrepancies according to reconstruction methods and genomic components. The two most supported topologies were previously reported and were discriminated by using phylogenetic and gene flow analyses, based on ABBA statistics. Terminology fix requested by the deputy editor led to support a scenario with G. gallus as the earliest branching lineage of the Gallus genus, instead of G. varius. We discuss the probable causes for the discrepancy. A likely one is that G. sonneratii samples from parks or private collections are all recent hybrids, with roughly 10% of their autosomal genome originating from G. gallus. The removal of those regions is needed to provide reliable data, which was not done in previous studies. We took care of this and additionally included two wild G. sonneratii samples from India, showing no trace of introgression. This reinforces the importance of carefully selecting and validating samples and genomic components in phylogenomics.
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Affiliation(s)
| | - Marie Suez
- Université Paris Saclay, INRAE, MaIAGE, 78350 Jouy-en-Josas, France
| | | | - Alain Vignal
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326 Castanet Tolosan, France
| | - Mariangela Arca
- Université Paris Saclay, INRAE, MaIAGE, 78350 Jouy-en-Josas, France
| | - Pierre Nicolas
- Université Paris Saclay, INRAE, MaIAGE, 78350 Jouy-en-Josas, France
| | - Thomas Faraut
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326 Castanet Tolosan, France
| | - Diane Esquerré
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326 Castanet Tolosan, France; Get-PlaGe, INRAE, 31326 Castanet Tolosan, France
| | - Masahide Nishibori
- Lab. of Animal Genetics, Department of Animal Life Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8528, Japan
| | - Agathe Vieaud
- Université Paris Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France
| | - Chih-Feng Chen
- Department of Animal Science, iEGG and Animal Biotechnology Center, National Chung-Hsing University, Taichung 40227, Taiwan
| | - Hung Manh Pham
- Faculty of Animal Science, Vietnam National University of Agriculture, Trau Quy Town, Gia Lam District, Ha Noi City, Viet Nam
| | | | - Frédéric Hospital
- Université Paris Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France
| | - Tatiana Zerjal
- Université Paris Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France
| | - Xavier Rognon
- Université Paris Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France
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15
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Urantówka AD, Kroczak A, Mackiewicz P. New view on the organization and evolution of Palaeognathae mitogenomes poses the question on the ancestral gene rearrangement in Aves. BMC Genomics 2020; 21:874. [PMID: 33287726 PMCID: PMC7720580 DOI: 10.1186/s12864-020-07284-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 11/26/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bird mitogenomes differ from other vertebrates in gene rearrangement. The most common avian gene order, identified first in Gallus gallus, is considered ancestral for all Aves. However, other rearrangements including a duplicated control region and neighboring genes have been reported in many representatives of avian orders. The repeated regions can be easily overlooked due to inappropriate DNA amplification or genome sequencing. This raises a question about the actual prevalence of mitogenomic duplications and the validity of the current view on the avian mitogenome evolution. In this context, Palaeognathae is especially interesting because is sister to all other living birds, i.e. Neognathae. So far, a unique duplicated region has been found in one palaeognath mitogenome, that of Eudromia elegans. RESULTS Therefore, we applied an appropriate PCR strategy to look for omitted duplications in other palaeognaths. The analyses revealed the duplicated control regions with adjacent genes in Crypturellus, Rhea and Struthio as well as ND6 pseudogene in three moas. The copies are very similar and were subjected to concerted evolution. Mapping the presence and absence of duplication onto the Palaeognathae phylogeny indicates that the duplication was an ancestral state for this avian group. This feature was inherited by early diverged lineages and lost two times in others. Comparison of incongruent phylogenetic trees based on mitochondrial and nuclear sequences showed that two variants of mitogenomes could exist in the evolution of palaeognaths. Data collected for other avian mitogenomes revealed that the last common ancestor of all birds and early diverging lineages of Neoaves could also possess the mitogenomic duplication. CONCLUSIONS The duplicated control regions with adjacent genes are more common in avian mitochondrial genomes than it was previously thought. These two regions could increase effectiveness of replication and transcription as well as the number of replicating mitogenomes per organelle. In consequence, energy production by mitochondria may be also more efficient. However, further physiological and molecular analyses are necessary to assess the potential selective advantages of the mitogenome duplications.
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Affiliation(s)
- Adam Dawid Urantówka
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, 7 Kozuchowska Street, 51-631 Wroclaw, Poland
| | - Aleksandra Kroczak
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, 7 Kozuchowska Street, 51-631 Wroclaw, Poland
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, 14a Fryderyka Joliot-Curie Street, 50-383 Wrocław, Poland
| | - Paweł Mackiewicz
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, 14a Fryderyka Joliot-Curie Street, 50-383 Wrocław, Poland
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Chen D, Liu Y, Davison G, Yong DL, Gao S, Hu J, Li SH, Zhang Z. Disentangling the evolutionary history and biogeography of hill partridges (Phasianidae, Arborophila) from low coverage shotgun sequences. Mol Phylogenet Evol 2020; 151:106895. [PMID: 32562823 DOI: 10.1016/j.ympev.2020.106895] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 05/06/2020] [Accepted: 06/12/2020] [Indexed: 11/18/2022]
Abstract
The advent of the phylogenomic era has significantly improved our understanding of the evolutionary history and biogeography of Southeast Asia's diverse avian fauna. However, the taxonomy and phylogenetic relationships of many Southeast Asian birds remain poorly resolved, especially for those with large geographic ranges, which might have experienced both ancient and recent geological and environmental changes. In this study, we examined the evolutionary history and biogeography of the hill partridges (Galliformes: Phasianidae: Arborophila spp.), currently the second most speciose galliform genus, and thought to have colonized Southeast Asia from Africa. We present a well-resolved phylogeny of 14 Arborophila species inferred from ultra-conserved elements, exons, and mitochondrial genomes from both fresh and museum samples, which representing almost complete coverage of the genus. Our fossil-calibrated divergence time estimates and biogeographic modeling showed the ancestor of Arborophila arrived in Indochina during the early Miocene, but the initial divergence within Arborophila did not occur until ~10 Ma when global cooling intensified. Subsequent dispersal and diversification within Arborophila were driven by several tectonic and climatic events. In particular, we found evidence of rapid radiation in Indochinese Arborophila during the Pliocene global cooling and extensive dispersal and speciation of Sundaic Arborophila during the Pleistocene sea-level fluctuations. Taken together, these results suggest that the evolutionary history and biogeography of Arborophila were influenced by complex interactions among historical, geological and climatic events in Southeast Asia.
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Affiliation(s)
- De Chen
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Yang Liu
- State Key Laboratory of Biocontrol, School of Ecology/School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Geoffrey Davison
- National Biodiversity Centre, National Parks Board, 1 Cluny Road, 259569, Singapore
| | - Ding Li Yong
- BirdLife International (Asia), 354 Tanglin Road, #01-16/17, Tanglin International Centre, Singapore 247672, Singapore; Fenner School of Environment and Society, The Australian National University, Linnaeus Way, Canberra, ACT 2601, Australia
| | - Shenghan Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Junhua Hu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Shou-Hsien Li
- Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan, China
| | - Zhengwang Zhang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China.
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17
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Murtskhvaladze M, Tarkhnishvili D, Anderson CL, Kotorashvili A. Phylogeny of caucasian rock lizards (Darevskia) and other true lizards based on mitogenome analysis: Optimisation of the algorithms and gene selection. PLoS One 2020; 15:e0233680. [PMID: 32511235 PMCID: PMC7279592 DOI: 10.1371/journal.pone.0233680] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 05/11/2020] [Indexed: 11/18/2022] Open
Abstract
We generated a phylogeny for Caucasian rock lizards (Darevskia), and included six other families of true lizards (Lacertini), based on complete mitochondrial genome analysis. Next-generation sequencing (NGS) of genomic DNA was used to obtain 16 new mitogenomes of Darevskia. These, along with 35 sequences downloaded from GenBank: genera Darevskia, Zootoca, Podarcis, Phoenicolacerta, Takydromus, Lacerta, and Eremias-were used in the analysis. All four analytical methods (Bayesian Inference, BI; Maximum Likelihood, ML; Maximum Parsimony, MP; and Neighbor-Joining, NJ) showed almost congruent intra-generic topologies for Darevskia and other lizard genera. However, ML and NJ methods on one side, and BI and MP methods on the other harvested conflicting phylogenies. The ML/NJ topology supports earlier published separation of Darevskia into three mitochondrial clades (Murphy, Fu, Macculloch, Darevsky, and Kupinova, 2000), but BI and MP topologies support that the basal branching occurred between D. parvula from the western Lesser Caucasus and the rest of Darevskia. All topologies altered the phylogenetic position of some individual species, including D. daghestanica, D. derjugini, and D. chlorogaster. Reanalysis after excluding four saturated genes from the data set, and excluding genus Eremias gives fully convergent topologies. The most basal branching for true lizards was between Far Eastern Takydromus and the Western Eurasian genera (BI). Comparing phylogenetic performance of individual genes relative to whole mitogenome data, concatenated 16S RNA (the least saturated gene in our analyses) and Cytochrome b genes generate a robust phylogeny that is fully congruent with that based on the complete mitogenome.
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Affiliation(s)
- Marine Murtskhvaladze
- School of Natural Sciences and Engineering, Ilia State University, Tbilisi, Georgia
- L. Sakvarelidze National Center for Disease Control and Public Health, Tbilisi, Georgia
| | - David Tarkhnishvili
- School of Natural Sciences and Engineering, Ilia State University, Tbilisi, Georgia
| | - Cort L. Anderson
- School of Natural Sciences and Engineering, Ilia State University, Tbilisi, Georgia
| | - Adam Kotorashvili
- L. Sakvarelidze National Center for Disease Control and Public Health, Tbilisi, Georgia
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18
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Allio R, Schomaker-Bastos A, Romiguier J, Prosdocimi F, Nabholz B, Delsuc F. MitoFinder: Efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics. Mol Ecol Resour 2020; 20:892-905. [PMID: 32243090 PMCID: PMC7497042 DOI: 10.1111/1755-0998.13160] [Citation(s) in RCA: 631] [Impact Index Per Article: 157.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 02/21/2020] [Accepted: 03/12/2020] [Indexed: 11/27/2022]
Abstract
Thanks to the development of high-throughput sequencing technologies, target enrichment sequencing of nuclear ultraconserved DNA elements (UCEs) now allows routine inference of phylogenetic relationships from thousands of genomic markers. Recently, it has been shown that mitochondrial DNA (mtDNA) is frequently sequenced alongside the targeted loci in such capture experiments. Despite its broad evolutionary interest, mtDNA is rarely assembled and used in conjunction with nuclear markers in capture-based studies. Here, we developed MitoFinder, a user-friendly bioinformatic pipeline, to efficiently assemble and annotate mitogenomic data from hundreds of UCE libraries. As a case study, we used ants (Formicidae) for which 501 UCE libraries have been sequenced whereas only 29 mitogenomes are available. We compared the efficiency of four different assemblers (IDBA-UD, MEGAHIT, MetaSPAdes, and Trinity) for assembling both UCE and mtDNA loci. Using MitoFinder, we show that metagenomic assemblers, in particular MetaSPAdes, are well suited to assemble both UCEs and mtDNA. Mitogenomic signal was successfully extracted from all 501 UCE libraries, allowing us to confirm species identification using CO1 barcoding. Moreover, our automated procedure retrieved 296 cases in which the mitochondrial genome was assembled in a single contig, thus increasing the number of available ant mitogenomes by an order of magnitude. By utilizing the power of metagenomic assemblers, MitoFinder provides an efficient tool to extract complementary mitogenomic data from UCE libraries, allowing testing for potential mitonuclear discordance. Our approach is potentially applicable to other sequence capture methods, transcriptomic data and whole genome shotgun sequencing in diverse taxa. The MitoFinder software is available from GitHub (https://github.com/RemiAllio/MitoFinder).
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Affiliation(s)
- Rémi Allio
- Institut des Sciences de l'Évolution de Montpellier (ISEM), CNRS, EPHE, IRD, Université de Montpellier, Montpellier, France
| | - Alex Schomaker-Bastos
- Laboratório Multidisciplinar para Análise de Dados (LAMPADA), Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jonathan Romiguier
- Institut des Sciences de l'Évolution de Montpellier (ISEM), CNRS, EPHE, IRD, Université de Montpellier, Montpellier, France
| | - Francisco Prosdocimi
- Laboratório Multidisciplinar para Análise de Dados (LAMPADA), Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Benoit Nabholz
- Institut des Sciences de l'Évolution de Montpellier (ISEM), CNRS, EPHE, IRD, Université de Montpellier, Montpellier, France
| | - Frédéric Delsuc
- Institut des Sciences de l'Évolution de Montpellier (ISEM), CNRS, EPHE, IRD, Université de Montpellier, Montpellier, France
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Liu YY, Zhou ZC, Chen XS. Characterization of the Complete Mitochondrial Genome of Epicauta impressicornis (Coleoptera: Meloidae) and Its Phylogenetic Implications for the Infraorder Cucujiformia. JOURNAL OF INSECT SCIENCE (ONLINE) 2020; 20:16. [PMID: 32302386 PMCID: PMC7164779 DOI: 10.1093/jisesa/ieaa021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Indexed: 06/11/2023]
Abstract
The complete mitochondrial genome (mitogenome) of Epicauta impressicornis Pic (Coleoptera: Meloidae) was determined. The circular genome is 15,713-bp long, and encodes 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region (CR). The 13 PCGs start with the typical ATN codon and terminate with the typical stop codon TAA (ND2, ND4L, ND6, ATP6, ATP8, and CYTB), TAG (ND1 and ND3), and T- (COX1, COX2, COX3, ND4, and ND5). The two rRNA genes (rrn12S and rrn16S) are encoded on the minority strand. All tRNAs genes except trnS1 (AGN) are predicted to fold into the typical cloverleaf structure. The longest overlap (10 bp) is observed between ATP8 and ATP6. CR mainly harbors a conserved poly-T stretch (15 bp), a short repeat unit (17 bp), some universal microsatellite-like repeats, and a canonical poly-A tail. Phylogenetic analysis using Bayesian inferences and maximum likelihood based on nucleotide and corresponding amino acid sequences of the 13 PCGs showed that E. impressicornis is closely related to E. chinensis, this relationship is and supported within Cucujiformia belonging to Meloidae (Tenebrionoidea). Our results further confirmed the monophyly of Tenebrionoidea, Lymexyloidea, Curculionoidea, Chrysomeloidea, Cucujoidea, Coccinelloidea, and Cleroidea within Cucujiformia, and revealed the sister relationships of (Cleroidea + Coccinelloidea), (Lymexyloidea + Tenebrionoidea), and ((Chrysomeloidea + Cucujoidea) + Curculionoidea). We believe that the complete mitogenome of E. impressicornis will contribute to further studies on molecular bases for the classification and phylogeny of Meloidae or even Cucujiformia.
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Affiliation(s)
- Yang-Yang Liu
- Institute of Entomology and Special Key Laboratory for Development and Utilization of Insect Resources of Guizhou, Guizhou University, Guiyang, China
| | - Zhi-Cheng Zhou
- Institute of Entomology and Special Key Laboratory for Development and Utilization of Insect Resources of Guizhou, Guizhou University, Guiyang, China
| | - Xiang-Sheng Chen
- Institute of Entomology and Special Key Laboratory for Development and Utilization of Insect Resources of Guizhou, Guizhou University, Guiyang, China
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20
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Mackiewicz P, Urantówka AD, Kroczak A, Mackiewicz D. Resolving Phylogenetic Relationships within Passeriformes Based on Mitochondrial Genes and Inferring the Evolution of Their Mitogenomes in Terms of Duplications. Genome Biol Evol 2019; 11:2824-2849. [PMID: 31580435 PMCID: PMC6795242 DOI: 10.1093/gbe/evz209] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/30/2019] [Indexed: 12/29/2022] Open
Abstract
Mitochondrial genes are placed on one molecule, which implies that they should carry consistent phylogenetic information. Following this advantage, we present a well-supported phylogeny based on mitochondrial genomes from almost 300 representatives of Passeriformes, the most numerous and differentiated Aves order. The analyses resolved the phylogenetic position of paraphyletic Basal and Transitional Oscines. Passerida occurred divided into two groups, one containing Paroidea and Sylvioidea, whereas the other, Passeroidea and Muscicapoidea. Analyses of mitogenomes showed four types of rearrangements including a duplicated control region (CR) with adjacent genes. Mapping the presence and absence of duplications onto the phylogenetic tree revealed that the duplication was the ancestral state for passerines and was maintained in early diverged lineages. Next, the duplication could be lost and occurred independently at least four times according to the most parsimonious scenario. In some lineages, two CR copies have been inherited from an ancient duplication and highly diverged, whereas in others, the second copy became similar to the first one due to concerted evolution. The second CR copies accumulated over twice as many substitutions as the first ones. However, the second CRs were not completely eliminated and were retained for a long time, which suggests that both regions can fulfill an important role in mitogenomes. Phylogenetic analyses based on CR sequences subjected to the complex evolution can produce tree topologies inconsistent with real evolutionary relationships between species. Passerines with two CRs showed a higher metabolic rate in relation to their body mass.
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Affiliation(s)
- Paweł Mackiewicz
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, Poland
| | - Adam Dawid Urantówka
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, Poland
| | - Aleksandra Kroczak
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, Poland
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, Poland
| | - Dorota Mackiewicz
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, Poland
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21
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Cornetti L, Fields PD, Van Damme K, Ebert D. A fossil-calibrated phylogenomic analysis of Daphnia and the Daphniidae. Mol Phylogenet Evol 2019; 137:250-262. [DOI: 10.1016/j.ympev.2019.05.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 05/03/2019] [Accepted: 05/20/2019] [Indexed: 11/16/2022]
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Abstract
It has long been appreciated that analyses of genomic data (e.g., whole genome sequencing or sequence capture) have the potential to reveal the tree of life, but it remains challenging to move from sequence data to a clear understanding of evolutionary history, in part due to the computational challenges of phylogenetic estimation using genome-scale data. Supertree methods solve that challenge because they facilitate a divide-and-conquer approach for large-scale phylogeny inference by integrating smaller subtrees in a computationally efficient manner. Here, we combined information from sequence capture and whole-genome phylogenies using supertree methods. However, the available phylogenomic trees had limited overlap so we used taxon-rich (but not phylogenomic) megaphylogenies to weave them together. This allowed us to construct a phylogenomic supertree, with support values, that included 707 bird species (~7% of avian species diversity). We estimated branch lengths using mitochondrial sequence data and we used these branch lengths to estimate divergence times. Our time-calibrated supertree supports radiation of all three major avian clades (Palaeognathae, Galloanseres, and Neoaves) near the Cretaceous-Paleogene (K-Pg) boundary. The approach we used will permit the continued addition of taxa to this supertree as new phylogenomic data are published, and it could be applied to other taxa as well.
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23
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Zhang D, Zou H, Hua CJ, Li WX, Mahboob S, Al-Ghanim KA, Al-Misned F, Jakovlić I, Wang GT. Mitochondrial Architecture Rearrangements Produce Asymmetrical Nonadaptive Mutational Pressures That Subvert the Phylogenetic Reconstruction in Isopoda. Genome Biol Evol 2019; 11:1797-1812. [PMID: 31192351 PMCID: PMC6601869 DOI: 10.1093/gbe/evz121] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2019] [Indexed: 01/04/2023] Open
Abstract
The phylogeny of Isopoda, a speciose order of crustaceans, remains unresolved, with different data sets (morphological, nuclear, mitochondrial) often producing starkly incongruent phylogenetic hypotheses. We hypothesized that extreme diversity in their life histories might be causing compositional heterogeneity/heterotachy in their mitochondrial genomes, and compromising the phylogenetic reconstruction. We tested the effects of different data sets (mitochondrial, nuclear, nucleotides, amino acids, concatenated genes, individual genes, gene orders), phylogenetic algorithms (assuming data homogeneity, heterogeneity, and heterotachy), and partitioning; and found that almost all of them produced unique topologies. As we also found that mitogenomes of Asellota and two Cymothoida families (Cymothoidae and Corallanidae) possess inversed base (GC) skew patterns in comparison to other isopods, we concluded that inverted skews cause long-branch attraction phylogenetic artifacts between these taxa. These asymmetrical skews are most likely driven by multiple independent inversions of origin of replication (i.e., nonadaptive mutational pressures). Although the PhyloBayes CAT-GTR algorithm managed to attenuate some of these artifacts (and outperform partitioning), mitochondrial data have limited applicability for reconstructing the phylogeny of Isopoda. Regardless of this, our analyses allowed us to propose solutions to some unresolved phylogenetic debates, and support Asellota are the most likely candidate for the basal isopod branch. As our findings show that architectural rearrangements might produce major compositional biases even on relatively short evolutionary timescales, the implications are that proving the suitability of data via composition skew analyses should be a prerequisite for every study that aims to use mitochondrial data for phylogenetic reconstruction, even among closely related taxa.
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Affiliation(s)
- Dong Zhang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
- University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Hong Zou
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
| | - Cong-Jie Hua
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
| | - Wen-Xiang Li
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
| | - Shahid Mahboob
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Zoology, GC University, Faisalabad, Pakistan
| | | | - Fahad Al-Misned
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | | | - Gui-Tang Wang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
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What are the roles of taxon sampling and model fit in tests of cyto-nuclear discordance using avian mitogenomic data? Mol Phylogenet Evol 2019; 130:132-142. [DOI: 10.1016/j.ympev.2018.10.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 09/11/2018] [Accepted: 10/09/2018] [Indexed: 11/23/2022]
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25
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A simple strategy for recovering ultraconserved elements, exons, and introns from low coverage shotgun sequencing of museum specimens: Placement of the partridge genus Tropicoperdix within the galliformes. Mol Phylogenet Evol 2018; 129:304-314. [DOI: 10.1016/j.ympev.2018.09.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 07/23/2018] [Accepted: 09/06/2018] [Indexed: 11/19/2022]
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26
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Richards EJ, Brown JM, Barley AJ, Chong RA, Thomson RC. Variation Across Mitochondrial Gene Trees Provides Evidence for Systematic Error: How Much Gene Tree Variation Is Biological? Syst Biol 2018; 67:847-860. [PMID: 29471536 DOI: 10.1093/sysbio/syy013] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 02/15/2018] [Indexed: 12/28/2022] Open
Abstract
The use of large genomic data sets in phylogenetics has highlighted extensive topological variation across genes. Much of this discordance is assumed to result from biological processes. However, variation among gene trees can also be a consequence of systematic error driven by poor model fit, and the relative importance of biological vs. methodological factors in explaining gene tree variation is a major unresolved question. Using mitochondrial genomes to control for biological causes of gene tree variation, we estimate the extent of gene tree discordance driven by systematic error and employ posterior prediction to highlight the role of model fit in producing this discordance. We find that the amount of discordance among mitochondrial gene trees is similar to the amount of discordance found in other studies that assume only biological causes of variation. This similarity suggests that the role of systematic error in generating gene tree variation is underappreciated and critical evaluation of fit between assumed models and the data used for inference is important for the resolution of unresolved phylogenetic questions.
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Affiliation(s)
- Emilie J Richards
- Department of Biology, University of Hawai'i, 2538 McCarthy Mall, Edmondson Hall 2016, Honolulu, HI 96822, USA.,Department of Biology, University of North Carolina, 120 South Road, Coker Hall CB 3280 Chapel Hill, NC 27599, USA
| | - Jeremy M Brown
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
| | - Anthony J Barley
- Department of Biology, University of Hawai'i, 2538 McCarthy Mall, Edmondson Hall 2016, Honolulu, HI 96822, USA
| | - Rebecca A Chong
- Department of Biology, University of Hawai'i, 2538 McCarthy Mall, Edmondson Hall 2016, Honolulu, HI 96822, USA
| | - Robert C Thomson
- Department of Biology, University of Hawai'i, 2538 McCarthy Mall, Edmondson Hall 2016, Honolulu, HI 96822, USA
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27
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Jaiswal SK, Gupta A, Saxena R, Prasoodanan VPK, Sharma AK, Mittal P, Roy A, Shafer ABA, Vijay N, Sharma VK. Genome Sequence of Peacock Reveals the Peculiar Case of a Glittering Bird. Front Genet 2018; 9:392. [PMID: 30283495 PMCID: PMC6156156 DOI: 10.3389/fgene.2018.00392] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 08/29/2018] [Indexed: 12/03/2022] Open
Abstract
The unique ornamental features and extreme sexual traits of Peacock have always intrigued scientists and naturalists for centuries. However, the genomic basis of these phenotypes are yet unknown. Here, we report the first genome sequence and comparative analysis of peacock with the high quality genomes of chicken, turkey, duck, flycatcher and zebra finch. Genes involved in early developmental pathways including TGF-β, BMP, and Wnt signaling, which have been shown to be involved in feather patterning, bone morphogenesis, and skeletal muscle development, revealed signs of adaptive evolution and provided useful clues on the phenotypes of peacock. Innate and adaptive immune genes involved in complement system and T-cell response also showed signs of adaptive evolution in peacock suggesting their possible role in building a robust immune system which is consistent with the predictions of the Hamilton–Zuk hypothesis. This study provides novel genomic and evolutionary insights into the molecular understanding toward the phenotypic evolution of Indian peacock.
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Affiliation(s)
- Shubham K Jaiswal
- Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Ankit Gupta
- Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Rituja Saxena
- Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Vishnu P K Prasoodanan
- Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Ashok K Sharma
- Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Parul Mittal
- Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Ankita Roy
- Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Aaron B A Shafer
- Forensic Science and Environmental and Life Sciences, Trent University, Peterborough, ON, Canada
| | - Nagarjun Vijay
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Vineet K Sharma
- Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
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28
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Evolutionary progression of mitochondrial gene rearrangements and phylogenetic relationships in Strigidae (Strigiformes). Gene 2018; 674:8-14. [PMID: 29940272 DOI: 10.1016/j.gene.2018.06.066] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 05/30/2018] [Accepted: 06/20/2018] [Indexed: 01/09/2023]
Abstract
The bird mitogenome is generally considered to have a conservative genome size, consistent gene content, and similar gene order. As more mitogenomes are sequenced, mitochondrial (mt) gene rearrangements have been frequently identified among diverse birds. Within two genera (Bubo and Strix) of typical owls (Strigidae, Strigiformes), the rearrangement of the mt gene has been a subject of debate. In the current study, we first sequenced the whole mitogenomes of S. uralensis and B. scandiaca and resequenced the entire mitogenome of B. bubo. By combining our data with previously sequenced mitogenomes in Strigidae, we examined the mt gene rearrangements in the family and attempted to reconstruct the evolutionary progression of these rearrangements. The mitogenomes were then used to review the phylogenies of Strigidae. Most mitogenomes exhibited the ancestral gene order (A) in Strigidae. The ancestral gene order in the previously published mitogenome of B. bubo was found to be incorrect. We determined the mt gene order (the duplicate tRNAThr-CR, B) and discovered two additional mt gene orders (the duplicate tRNAGlu-L-CR and CR, C and D) in the Bubo and Strix genera. Gene order B was likely derived from A by a tandem duplication of the region spanning from tRNAThr to CR. The other two modified gene orders, C and D, were likely derived from B by further degenerations or deletions of one copy of specific duplicated genes. We also preliminarily reconstructed the evolutionary progression of mt gene rearrangements and discussed maintenance of the duplicated CR in the genera. Additionally, the phylogenetic trees based on the mitogenomes supported the division of Strigidae into three subfamilies: Ninoxinae + (Surniinae + Striginae). Within the Striginae clade, the four genera formed a phylogenetic relationship: Otus + (Asio + (Bubo + Strix)). This suggests that Otus firstly diverges in their evolutionary history, and Bubo and Strix show a close relationship. B. bubo, B. blakistoni and B. scandiaca form a clade should be considered members of the same genus. The well-supported topology obtained in our Bayesian inference (BI) and maximum likelihood (ML) analyses of Strigid mitogenomes suggests that these genomes are informative for constructing phylogenetic relationships.
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Reddy S, Kimball RT, Pandey A, Hosner PA, Braun MJ, Hackett SJ, Han KL, Harshman J, Huddleston CJ, Kingston S, Marks BD, Miglia KJ, Moore WS, Sheldon FH, Witt CC, Yuri T, Braun EL. Why Do Phylogenomic Data Sets Yield Conflicting Trees? Data Type Influences the Avian Tree of Life more than Taxon Sampling. Syst Biol 2018; 66:857-879. [PMID: 28369655 DOI: 10.1093/sysbio/syx041] [Citation(s) in RCA: 150] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 03/22/2017] [Indexed: 01/27/2023] Open
Abstract
Phylogenomics, the use of large-scale data matrices in phylogenetic analyses, has been viewed as the ultimate solution to the problem of resolving difficult nodes in the tree of life. However, it has become clear that analyses of these large genomic data sets can also result in conflicting estimates of phylogeny. Here, we use the early divergences in Neoaves, the largest clade of extant birds, as a "model system" to understand the basis for incongruence among phylogenomic trees. We were motivated by the observation that trees from two recent avian phylogenomic studies exhibit conflicts. Those studies used different strategies: 1) collecting many characters [$\sim$ 42 mega base pairs (Mbp) of sequence data] from 48 birds, sometimes including only one taxon for each major clade; and 2) collecting fewer characters ($\sim$ 0.4 Mbp) from 198 birds, selected to subdivide long branches. However, the studies also used different data types: the taxon-poor data matrix comprised 68% non-coding sequences whereas coding exons dominated the taxon-rich data matrix. This difference raises the question of whether the primary reason for incongruence is the number of sites, the number of taxa, or the data type. To test among these alternative hypotheses we assembled a novel, large-scale data matrix comprising 90% non-coding sequences from 235 bird species. Although increased taxon sampling appeared to have a positive impact on phylogenetic analyses the most important variable was data type. Indeed, by analyzing different subsets of the taxa in our data matrix we found that increased taxon sampling actually resulted in increased congruence with the tree from the previous taxon-poor study (which had a majority of non-coding data) instead of the taxon-rich study (which largely used coding data). We suggest that the observed differences in the estimates of topology for these studies reflect data-type effects due to violations of the models used in phylogenetic analyses, some of which may be difficult to detect. If incongruence among trees estimated using phylogenomic methods largely reflects problems with model fit developing more "biologically-realistic" models is likely to be critical for efforts to reconstruct the tree of life. [Birds; coding exons; GTR model; model fit; Neoaves; non-coding DNA; phylogenomics; taxon sampling.].
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Affiliation(s)
- Sushma Reddy
- Biology Department, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, USA
| | - Rebecca T Kimball
- Department of Biology, University of Florida, Gainesville, FL 32607, USA
| | - Akanksha Pandey
- Department of Biology, University of Florida, Gainesville, FL 32607, USA
| | - Peter A Hosner
- Department of Biology, University of Florida, Gainesville, FL 32607, USA.,Florida Museum of Natural History, University of Florida, Gainesville, FL 32607, USA
| | - Michael J Braun
- Behavior, Ecology, Evolution, and Systematics Program, University of Maryland, College Park, MD 20742, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution-MRC 163, PO Box 37012, Washington, DC 20013-7012, USA
| | - Shannon J Hackett
- Zoology Department, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, USA
| | - Kin-Lan Han
- Department of Biology, University of Florida, Gainesville, FL 32607, USA
| | | | - Christopher J Huddleston
- Collections Program, National Museum of Natural History, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746, USA
| | - Sarah Kingston
- Behavior, Ecology, Evolution, and Systematics Program, University of Maryland, College Park, MD 20742, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution-MRC 163, PO Box 37012, Washington, DC 20013-7012, USA.,Bowdoin College, Department of Biology and Coastal Studies Center, 6500 College Station, Brunwick, ME 04011, USA
| | - Ben D Marks
- Zoology Department, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, USA
| | - Kathleen J Miglia
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202, USA
| | - William S Moore
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202, USA
| | - Frederick H Sheldon
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, 119 Foster Hall, Baton Rouge, LA 70803, USA
| | - Christopher C Witt
- Department of Biology and Museum of Southwestern Biology, University 15 of New Mexico, Albuquerque, New Mexico 87131, USA
| | - Tamaki Yuri
- Department of Biology, University of Florida, Gainesville, FL 32607, USA.,Sam Noble Museum, University of Oklahoma, 2401 Chautauqua Avenue, Norman, OK 73072, USA
| | - Edward L Braun
- Department of Biology, University of Florida, Gainesville, FL 32607, USA.,Genetics Institute, University of Florida, Gainesville, FL 32607, USA
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30
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Advances in Using Non-invasive, Archival, and Environmental Samples for Population Genomic Studies. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_45] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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31
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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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32
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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: 12] [Impact Index Per Article: 1.7] [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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Laggis A, Baxevanis AD, Charalampidou A, Maniatsi S, Triantafyllidis A, Abatzopoulos TJ. Microevolution of the noble crayfish (Astacus astacus) in the Southern Balkan Peninsula. BMC Evol Biol 2017; 17:122. [PMID: 28558646 PMCID: PMC5450353 DOI: 10.1186/s12862-017-0971-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 05/17/2017] [Indexed: 12/02/2022] Open
Abstract
Background The noble crayfish (Astacus astacus) displays a complex historical and contemporary genetic status in Europe. The species divergence has been shaped by geological events (i.e. Pleistocene glaciations) and humanly induced impacts (i.e. translocations, pollution, etc.) on its populations due to species commercial value and its niche degradation. Until now, limited genetic information has been procured for the Balkan area and especially for the southernmost distribution of this species (i.e. Greece). It is well known that the rich habitat diversity of the Balkan Peninsula offers suitable conditions for genetically diversified populations. Thus, the present manuscript revisits the phylogenetic relationships of the noble crayfish in Europe and identifies the genetic make-up and the biogeographical patterns of the species in its southern range limit. Results Mitochondrial markers (i.e. COI and 16S) were used in order to elucidate the genetic structure and diversity of the noble crayfish in Europe. Two of the six European haplotypic lineages, were found exclusively in Greece. These two lineages exhibited greater haplotypic richness when compared with the rest four (of “Central European” origin) while they showed high genetic diversity. Divergence time analysis identified that the majority of this divergence was captured through Pleistocene, suggesting a southern glacial refugium (Greece, southern Balkans). Furthermore, six microsatellite markers were used in order to define the factors affecting the genetic structure and demographic history of the species in Greece. The population structure analysis revealed six to nine genetic clusters and eight putative genetic barriers. Evidence of bottleneck effects in the last ~5000 years (due to climatic and geological events and human activities) is also afforded. Findings from several other research fields (e.g. life sciences, geology or even archaeology) have been utilized to perceive the genetic make-up of the noble crayfish. Conclusions The southernmost part of Balkans has played a major role as a glacial refugium for A. astacus. Such refugia have served as centres of expansion to northern regions. Recent history of the noble crayfish in southern Balkans reveals the influence of environmental (climate, geology and/or topology) and anthropogenic factors. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0971-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anastasia Laggis
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Macedonia, Greece
| | - Athanasios D Baxevanis
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Macedonia, Greece
| | - Alexandra Charalampidou
- Scientific Computing Office, Information Technology (IT) Center, School of Sciences, Aristotle University of Thessaloniki, 541 24, Thessaloniki, Macedonia, Greece
| | - Stefania Maniatsi
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Macedonia, Greece
| | - Alexander Triantafyllidis
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Macedonia, Greece
| | - Theodore J Abatzopoulos
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Macedonia, Greece.
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34
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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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35
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Zhou Z, Zhao L, Liu N, Guo H, Guan B, Di J, Shi F. Towards a higher-level Ensifera phylogeny inferred from mitogenome sequences. Mol Phylogenet Evol 2017; 108:22-33. [PMID: 28188878 DOI: 10.1016/j.ympev.2017.01.014] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 01/24/2017] [Accepted: 01/31/2017] [Indexed: 11/15/2022]
Abstract
Although mitogenomes are useful tools for inferring evolutionary history, only a few representative ones can be used for most Ensifera lineages. Thirty-two ensiferan mitogenomes were determined using ABI Sanger sequencing and standard primer walking of 2-3 overlapping Long-PCR fragments, or Illumina® HiSeq2000 for "shotgun" sequenced long-PCR-amplified mitochondrial or total genomic DNA. Six patterns of gene arrangements, including the novel trnR-trnSAGN-trnA-trnN-trnG-nad3 in Lipotactes tripyrga (Lipotactinae), were identified from 59 ensiferan mitogenomes. The results suggest that trnM-trnI-trnQ and trnA-trnR-trnE-trnSAGN-trnN-trnF rearrangements might be a shared derived character in Pseudophyllinae and Gryllidae, respectively. We found base composition biases in our dataset, which potentially complicate the inference of higher-level ensiferan phylogeny. Site-heterogeneous Bayesian inference (BI) and site-homogeneous maximum likelihood (ML) analyses recovered all ensiferan superfamilies as monophyletic. The site-homogeneous BI analysis failed to recover the monophyly of Stenopelmatoidea. As Schizodactyloidea was only represented by Comicus campestris, its monophyly could not be tested. In the Triassic/Jurassic boundary, Ensifera diverged into grylloid and non-grylloid clades. All analyses confirmed Grylloidea and Gryllotalpoidea as sister groups. Site-heterogeneous BI analysis found Schizodactyloidea as the most basal lineage and sister to the clade formed by Grylloidea and Gryllotalpoidea, but the site-homogeneous analyses placed it basally to the non-grylloid clade and recovered a sister relationship between Tettigonioidea and (Hagloidea, Rhaphidophoroidea, Stenopelmatoidea), although this clade had a low support. The site-heterogeneous BI analysis found Tettigonioidea and Hagloidea were sister groups (posterior probability (PP)=0.99), Stenopelmatoidea was sister to (Tettigonioidea, Hagloidea) (PP>0.91), and Rhaphidophoroidea was basal to the non-grylloid clade. At a lower level, all analyses divided Tettigonioidea into Phaneropteridae and Tettigoniidae.
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Affiliation(s)
- Zhijun Zhou
- Key Laboratory of Invertebrate Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China.
| | - Ling Zhao
- College of Life Sciences and Biotechnology, Mianyang Normal University, Mianyang, Sichuan 621000, China
| | - Nian Liu
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710062, China
| | - Huifang Guo
- Key Laboratory of Invertebrate Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China
| | - Bei Guan
- Key Laboratory of Invertebrate Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China
| | - Juanxia Di
- Key Laboratory of Invertebrate Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China
| | - Fuming Shi
- Key Laboratory of Invertebrate Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China.
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The mitogenomes of three beetles (Coleoptera: Polyphaga: Cucujiformia): New gene rearrangement and phylogeny. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.08.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Complete mitochondrial genomes are not necessarily more informative than individual mitochondrial genes to recover a well-established annelid phylogeny. GENE REPORTS 2016. [DOI: 10.1016/j.genrep.2016.07.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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38
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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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Grass AA, Hosie C, McDowall IL. The complete mitochondrial genome and phylogenetic position of the critically endangered Trinidad Piping Guan, Pipile pipile synonym Aburria pipile (Aves: Galliformes). Mitochondrial DNA B Resour 2016; 1:649-650. [PMID: 34395876 PMCID: PMC7875200 DOI: 10.1080/23802359.2016.1219622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 07/20/2016] [Accepted: 07/29/2016] [Indexed: 12/02/2022] Open
Abstract
The complete mitochondrial genome of the Critically Endangered Trinidad Piping Guan, Pipile pipile (Jacquin 1784) synonym Aburria pipile was sequenced for the first time in this study. The genome is 16,665 bp in length with overall base compositions of 30.1, 23.7, 32.3 and 13.9% for A, T, C, and G, respectively. Structurally, the P. pipile mitogenome is comparable to that of other Galliformes, thereby demonstrating typical avian gene organization. The mitogenome was subsequently used to produce a revised phylogenetic placement of P. pipile within the Galliforme order, positioning the Pipile genus basal within the Cracidae family. It is further envisaged that this novel genomic data will contribute to a wider understanding of genetic relationships within the genus Pipile and the analysis of the evolutionary relationships of the Galliforme order in a wider avian context.
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Affiliation(s)
- Amelia A. Grass
- Department of Biological Sciences, University of Chester, Chester, UK
| | - Charlotte Hosie
- Department of Biological Sciences, University of Chester, Chester, UK
| | - Ian L. McDowall
- Department of Biological Sciences, University of Chester, Chester, UK
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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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Simmons MP, Gatesy J. Biases of tree-independent-character-subsampling methods. Mol Phylogenet Evol 2016; 100:424-443. [DOI: 10.1016/j.ympev.2016.04.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 03/16/2016] [Accepted: 04/15/2016] [Indexed: 12/21/2022]
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Persons NW, Hosner PA, Meiklejohn KA, Braun EL, Kimball RT. Sorting out relationships among the grouse and ptarmigan using intron, mitochondrial, and ultra-conserved element sequences. Mol Phylogenet Evol 2016; 98:123-32. [DOI: 10.1016/j.ympev.2016.02.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 11/14/2015] [Accepted: 02/03/2016] [Indexed: 11/24/2022]
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Zhang D, Yan L, Zhang M, Chu H, Cao J, Li K, Hu D, Pape T. Phylogenetic inference of calyptrates, with the first mitogenomes for Gasterophilinae (Diptera: Oestridae) and Paramacronychiinae (Diptera: Sarcophagidae). Int J Biol Sci 2016; 12:489-504. [PMID: 27019632 PMCID: PMC4807417 DOI: 10.7150/ijbs.12148] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 12/22/2015] [Indexed: 11/05/2022] Open
Abstract
The complete mitogenome of the horse stomach bot fly Gasterophilus pecorum (Fabricius) and a near-complete mitogenome of Wohlfahrt's wound myiasis fly Wohlfahrtia magnifica (Schiner) were sequenced. The mitogenomes contain the typical 37 mitogenes found in metazoans, organized in the same order and orientation as in other cyclorrhaphan Diptera. Phylogenetic analyses of mitogenomes from 38 calyptrate taxa with and without two non-calyptrate outgroups were performed using Bayesian Inference and Maximum Likelihood. Three sub-analyses were performed on the concatenated data: (1) not partitioned; (2) partitioned by gene; (3) 3rd codon positions of protein-coding genes omitted. We estimated the contribution of each of the mitochondrial genes for phylogenetic analysis, as well as the effect of some popular methodologies on calyptrate phylogeny reconstruction. In the favoured trees, the Oestroidea are nested within the muscoid grade. Relationships at the family level within Oestroidea are (remaining Calliphoridae (Sarcophagidae (Oestridae, Pollenia + Tachinidae))). Our mito-phylogenetic reconstruction of the Calyptratae presents the most extensive taxon coverage so far, and the risk of long-branch attraction is reduced by an appropriate selection of outgroups. We find that in the Calyptratae the ND2, ND5, ND1, COIII, and COI genes are more phylogenetically informative compared with other mitochondrial protein-coding genes. Our study provides evidence that data partitioning and the inclusion of conserved tRNA genes have little influence on calyptrate phylogeny reconstruction, and that the 3rd codon positions of protein-coding genes are not saturated and therefore should be included.
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Affiliation(s)
- Dong Zhang
- 1. School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Liping Yan
- 1. School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Ming Zhang
- 1. School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Hongjun Chu
- 3. Wildlife Conservation Office of Altay Prefecture, Altay, Xinjiang, China
| | - Jie Cao
- 4. Xinjiang Research Centre for Breeding Przewalski's Horse, Ürümqi, Xinjiang, China
| | - Kai Li
- 1. School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Defu Hu
- 1. School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Thomas Pape
- 2. Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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Meiklejohn KA, Faircloth BC, Glenn TC, Kimball RT, Braun EL. Analysis of a Rapid Evolutionary Radiation Using Ultraconserved Elements: Evidence for a Bias in Some Multispecies Coalescent Methods. Syst Biol 2016; 65:612-27. [DOI: 10.1093/sysbio/syw014] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 01/25/2016] [Indexed: 01/30/2023] Open
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45
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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.
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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:
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46
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Hosner PA, Faircloth BC, Glenn TC, Braun EL, Kimball RT. Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes). Mol Biol Evol 2015; 33:1110-25. [PMID: 26715628 DOI: 10.1093/molbev/msv347] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Production of massive DNA sequence data sets is transforming phylogenetic inference, but best practices for analyzing such data sets are not well established. One uncertainty is robustness to missing data, particularly in coalescent frameworks. To understand the effects of increasing matrix size and loci at the cost of increasing missing data, we produced a 90 taxon, 2.2 megabase, 4,800 locus sequence matrix of landfowl using target capture of ultraconserved elements. We then compared phylogenies estimated with concatenated maximum likelihood, quartet-based methods executed on concatenated matrices and gene tree reconciliation methods, across five thresholds of missing data. Results of maximum likelihood and quartet analyses were similar, well resolved, and demonstrated increasing support with increasing matrix size and sparseness. Conversely, gene tree reconciliation produced unexpected relationships when we included all informative loci, with certain taxa placed toward the root compared with other approaches. Inspection of these taxa identified a prevalence of short average contigs, which potentially biased gene tree inference and caused erroneous results in gene tree reconciliation. This suggests that the more problematic missing data in gene tree-based analyses are partial sequences rather than entire missing sequences from locus alignments. Limiting gene tree reconciliation to the most informative loci solved this problem, producing well-supported topologies congruent with concatenation and quartet methods. Collectively, our analyses provide a well-resolved phylogeny of landfowl, including strong support for previously problematic relationships such as those among junglefowl (Gallus), and clarify the position of two enigmatic galliform genera (Lerwa, Melanoperdix) not sampled in previous molecular phylogenetic studies.
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Affiliation(s)
| | - Brant C Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge
| | - Travis C Glenn
- Department of Environmental Health Science, University of Georgia
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Raposo do Amaral F, Neves LG, Resende MFR, Mobili F, Miyaki CY, Pellegrino KCM, Biondo C. Ultraconserved Elements Sequencing as a Low-Cost Source of Complete Mitochondrial Genomes and Microsatellite Markers in Non-Model Amniotes. PLoS One 2015; 10:e0138446. [PMID: 26379155 PMCID: PMC4574942 DOI: 10.1371/journal.pone.0138446] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 08/31/2015] [Indexed: 02/06/2023] Open
Abstract
Sequence capture of ultraconserved elements (UCEs) associated with massively parallel sequencing has become a common source of nuclear data for studies of animal systematics and phylogeography. However, mitochondrial and microsatellite variation are still commonly used in various kinds of molecular studies, and probably will complement genomic data in years to come. Here we show that besides providing abundant genomic data, UCE sequencing is an excellent source of both sequences for microsatellite loci design and complete mitochondrial genomes with high sequencing depth. Identification of dozens of microsatellite loci and assembly of complete mitogenomes is exemplified here using three species of Poospiza warbling finches from southern and southeastern Brazil. This strategy opens exciting opportunities to simultaneously analyze genome-wide nuclear datasets and traditionally used mtDNA and microsatellite markers in non-model amniotes at no additional cost.
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Affiliation(s)
- Fábio Raposo do Amaral
- Universidade Federal de São Paulo, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Laboratório de Genética Evolutiva, Rua Professor Artur Riedel, 275, Diadema, SP, 09972–270, Brazil
| | - Leandro G. Neves
- RAPiD Genomics, LLC, 747 SW 2nd Avenue, Gainesville, FL, 32601, United States of America
| | - Márcio F. R. Resende
- RAPiD Genomics, LLC, 747 SW 2nd Avenue, Gainesville, FL, 32601, United States of America
| | - Flávia Mobili
- Universidade Federal de São Paulo, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Laboratório de Genética Evolutiva, Rua Professor Artur Riedel, 275, Diadema, SP, 09972–270, Brazil
| | - Cristina Y. Miyaki
- Universidade de São Paulo, Departamento de Genética e Biologia Evolutiva, Rua do Matão, 277, Cidade Universitária, São Paulo, SP, 05508–090, Brazil
| | - Katia C. M. Pellegrino
- Universidade Federal de São Paulo, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Laboratório de Genética Evolutiva, Rua Professor Artur Riedel, 275, Diadema, SP, 09972–270, Brazil
| | - Cibele Biondo
- Universidade Federal do ABC, Centro de Ciências Naturais e Humanas, Rua Arcturus 03, Jardim Antares, São Bernardo do Campo, SP, 09606–070, Brazil
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48
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Malyarchuk BA, Derenko MV, Denisova GA, Litvinov AN. Topological conflicts in phylogenetic analysis of different regions of the sable (Martes zibellina L.) mitochondrial genome. RUSS J GENET+ 2015. [DOI: 10.1134/s1022795415060095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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49
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Adaptation of the Mitochondrial Genome in Cephalopods: Enhancing Proton Translocation Channels and the Subunit Interactions. PLoS One 2015; 10:e0135405. [PMID: 26285039 PMCID: PMC4540416 DOI: 10.1371/journal.pone.0135405] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 07/21/2015] [Indexed: 01/25/2023] Open
Abstract
Mitochondrial protein-coding genes (mt genes) encode subunits forming complexes of crucial cellular pathways, including those involved in the vital process of oxidative phosphorylation (OXPHOS). Despite the vital role of the mitochondrial genome (mt genome) in the survival of organisms, little is known with respect to its adaptive implications within marine invertebrates. The molluscan Class Cephalopoda is represented by a marine group of species known to occupy contrasting environments ranging from the intertidal to the deep sea, having distinct metabolic requirements, varied body shapes and highly advanced visual and nervous systems that make them highly competitive and successful worldwide predators. Thus, cephalopods are valuable models for testing natural selection acting on their mitochondrial subunits (mt subunits). Here, we used concatenated mt genes from 17 fully sequenced mt genomes of diverse cephalopod species to generate a robust mitochondrial phylogeny for the Class Cephalopoda. We followed an integrative approach considering several branches of interest–covering cephalopods with distinct morphologies, metabolic rates and habitats–to identify sites under positive selection and localize them in the respective protein alignment and/or tridimensional structure of the mt subunits. Our results revealed significant adaptive variation in several mt subunits involved in the energy production pathway of cephalopods: ND5 and ND6 from Complex I, CYTB from Complex III, COX2 and COX3 from Complex IV, and in ATP8 from Complex V. Furthermore, we identified relevant sites involved in protein-interactions, lining proton translocation channels, as well as disease/deficiencies related sites in the aforementioned complexes. A particular case, revealed by this study, is the involvement of some positively selected sites, found in Octopoda lineage in lining proton translocation channels (site 74 from ND5) and in interactions between subunits (site 507 from ND5) of Complex I.
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Govindarajulu R, Parks M, Tennessen JA, Liston A, Ashman TL. Comparison of nuclear, plastid, and mitochondrial phylogenies and the origin of wild octoploid strawberry species. AMERICAN JOURNAL OF BOTANY 2015; 102:544-554. [PMID: 25878088 DOI: 10.3732/ajb.1500026] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 03/05/2015] [Indexed: 06/04/2023]
Abstract
PREMISE OF THE STUDY Molecular phylogenies derived from all three plant genomes can provide insight into the evolutionary history of plant groups influenced by reticulation. We sought to reconstruct mitochondrial exome, chloroplast, and nuclear genome phylogenies for octoploid Fragaria and their diploid ancestors and to document patterns of incongruence between and within the cytoplasmic genomes and interpret these in the context of evolutionary origin of the octoploid strawberries. METHODS Using a genome-skimming approach, we assembled chloroplast genomes and mitochondrial exomes, and we used the POLiMAPS method to assemble nuclear sequence for octoploid species and constructed phylogenies from all three genomes. We assessed incongruence between and within cytoplasmic genomes using topology-based phylogenetic incongruence tests. KEY RESULTS The incongruent cytoplasmic genome phylogeny with respect to the placement of octoploids suggests potential breakage in linkage disequilibrium of cytoplasmic genomes during allopolyploid origin of the octoploids. Furthermore, a single mitochondrial chimeric gene with a putative role in cytoplasmic male sterility yields a phylogeny that is inconsistent with the rest of the mitochondrial genome but consistent with the chloroplast phylogeny, suggesting intracellular gene transfer between heteroplasmic mitochondria, possibly driven by selection to overcome the effects of mito-nuclear incompatibility in octoploid origins. CONCLUSIONS This work expands on the current understanding of evolutionary history of the octoploid ancestors of cultivated strawberry. It demonstrates phylogenetic incongruence between cytoplasmic genomes in octoploids with respect to diploid ancestors, indicating breakage in linkage disequilibrium of cytoplasmic genomes. We discuss potential organism-level processes that may have contributed to the observed incongruence in Fragaria.
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Affiliation(s)
| | - Matthew Parks
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331 USA
| | - Jacob A Tennessen
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon 97331 USA
| | - Aaron Liston
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331 USA
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260 USA
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