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DeRaad DA, McCullough JM, DeCicco LH, Hime PM, Joseph L, Andersen MJ, Moyle RG. Mitonuclear discordance results from incomplete lineage sorting, with no detectable evidence for gene flow, in a rapid radiation of Todiramphus kingfishers. Mol Ecol 2023; 32:4844-4862. [PMID: 37515525 DOI: 10.1111/mec.17080] [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: 12/28/2022] [Revised: 03/15/2023] [Accepted: 06/19/2023] [Indexed: 07/31/2023]
Abstract
Many organisms possess multiple discrete genomes (i.e. nuclear and organellar), which are inherited separately and may have unique and even conflicting evolutionary histories. Phylogenetic reconstructions from these discrete genomes can yield different patterns of relatedness, a phenomenon known as cytonuclear discordance. In many animals, mitonuclear discordance (i.e. discordant evolutionary histories between the nuclear and mitochondrial genomes) has been widely documented, but its causes are often considered idiosyncratic and inscrutable. We show that a case of mitonuclear discordance in Todiramphus kingfishers can be explained by extensive genome-wide incomplete lineage sorting (ILS), likely a result of the explosive diversification history of this genus. For these kingfishers, quartet frequencies reveal that the nuclear genome is dominated by discordant topologies, with none of the internal branches in our consensus nuclear tree recovered in >50% of genome-wide gene trees. Meanwhile, a lack of inter-species shared ancestry, non-significant pairwise tests for gene flow, and little evidence for meaningful migration edges between species, leads to the conclusion that gene flow cannot explain the mitonuclear discordance we observe. This lack of evidence for gene flow combined with evidence for extensive genome-wide gene tree discordance, a hallmark of ILS, leads us to conclude that the mitonuclear discordance we observe likely results from ILS, specifically deep coalescence of the mitochondrial genome. Based on this case study, we hypothesize that similar demographic histories in other 'great speciator' taxa across the Indo-Pacific likely predispose these groups to high levels of ILS and high likelihoods of mitonuclear discordance.
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Affiliation(s)
- Devon A DeRaad
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, USA
| | - Jenna M McCullough
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Lucas H DeCicco
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, USA
| | - Paul M Hime
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, USA
| | - Leo Joseph
- Australian National Wildlife Collection, CSIRO National Research Collections Australia, Canberra, Australian Capital Territory, Australia
| | - Michael J Andersen
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Robert G Moyle
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, USA
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2
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Ding L, Luo G, Zhou Q, Sun Y, Liao J. Comparative Mitogenome Analysis of Gerbils and the Mitogenome Phylogeny of Gerbillinae (Rodentia: Muridae). Biochem Genet 2022; 60:2226-2249. [PMID: 35314913 DOI: 10.1007/s10528-022-10213-8] [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: 06/12/2019] [Accepted: 02/24/2022] [Indexed: 11/02/2022]
Abstract
To enrich the mitogenomic database of Gerbillinae (Rodentia: Muridae), mitogenomes of three gerbils from different genera, Meriones tamariscinus (16,393 bp), Brachiones przewalskii (16,357 bp), and Rhombomys opimus (16,352 bp), were elaborated and compared with those of other gerbils in the present study. The three gerbil mitogenomes consisted of 2 ribosomal RNA genes, 13 protein-coding genes (PCGs), 22 transfer RNA genes, and one control region. Here, gerbil mitogenomes have shown unique characteristics in terms of base composition, codon usage, non-coding region, and the replication origin of the light strand. There was no significant correlation between the nucleotide percentage of G + C and the phylogenetic status in gerbils, and between the GC content of PCGs and the leucine count. Phylogenetic relationships of the subfamily Gerbillinae were reconstructed by 7 gerbils that represented four genera based on concatenated mitochondrial DNA data using both Bayesian Inference and Maximum Likelihood. The phylogenetic analysis indicated that M. tamariscinus was phylogenetically distant from the genus Meriones, but has a close relationship with R. opimus. B. przewalskii was closely related to the genus Meriones rather than that of R. opimus.
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Affiliation(s)
- Li Ding
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China.,School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Guangjie Luo
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Quan Zhou
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Yuanhai Sun
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Jicheng Liao
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.
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Ding L, Zhou Q, Sun Y, Feoktistova NY, Liao J. Two novel cricetine mitogenomes: Insight into the mitogenomic characteristics and phylogeny in Cricetinae (Rodentia: Cricetidae). Genomics 2019; 112:1716-1725. [PMID: 31669701 DOI: 10.1016/j.ygeno.2019.09.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 09/06/2019] [Accepted: 09/18/2019] [Indexed: 01/30/2023]
Abstract
Both Cricetus cricetus and Phodopus sungorus mitochondrial genomes (mitogenomes) were sequenced and elaborated for the first time in the present study. Their mitogenomes contained 37 genes and showed typical characteristics of the vertebrate mitogenome. Comparative analysis of 10 cricetine mitogenomes indicated that they shared similar characteristics with those of other cricetines in terms of genes arrangement, nucleotide composition, codon usage, tRNA structure, nucleotide skew and the origin of replication of light strand. Phylogenetic relationship of the subfamily Cricetinae was reconstructed using mitogenomes data with the methods of Bayesian Inference and Maximum Likelihood. Phylogenetic analysis indicated that Cricetulus kamensis was at basal position and phylogenetically distant from all other Cricetulus species but had a close relationship with the group of Phodopus, and supported that the genus Urocricetus deserved as a separate genus rank. The phylogenetic status of Tscherskia triton represented a separate clade corresponding to a diversified cricetine lineage (Cricetulus, Allocricetulus, and Cricetus).
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Affiliation(s)
- Li Ding
- School of Life Sciences, Lanzhou University, Lanzhou 730000, PR China.
| | - Quan Zhou
- School of Life Sciences, Lanzhou University, Lanzhou 730000, PR China
| | - Yuanhai Sun
- School of Life Sciences, Lanzhou University, Lanzhou 730000, PR China
| | - Natalia Yu Feoktistova
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow 119071, Russia
| | - Jicheng Liao
- School of Life Sciences, Lanzhou University, Lanzhou 730000, PR China.
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4
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De Ré FC, Robe LJ, Wallau GL, Loreto ELS. Inferring the phylogenetic position of the Drosophila flavopilosa
group: Incongruence within and between mitochondrial and nuclear multilocus datasets. J ZOOL SYST EVOL RES 2017. [DOI: 10.1111/jzs.12170] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Francine C. De Ré
- Programa de Pós Graduação em Biodiversidade Animal; Universidade Federal de Santa Maria (UFSM); Santa Maria Rio Grande do Sul Brazil
| | - Lizandra J. Robe
- Programa de Pós Graduação em Biodiversidade Animal; Universidade Federal de Santa Maria (UFSM); Santa Maria Rio Grande do Sul Brazil
- Programa de Pós-Graduação em Biologia de Ambientes Aquáticos Continentais; Universidade Federal do Rio Grande (FURG); Rio Grande Rio Grande do Sul Brazil
| | - Gabriel L. Wallau
- Programa de Pós Graduação em Biodiversidade Animal; Universidade Federal de Santa Maria (UFSM); Santa Maria Rio Grande do Sul Brazil
- Departamento de Entomologia; Instituto Aggeu Magalhães - FIOCRUZ-IAM; Recife PE Brazil
| | - Elgion L. S. Loreto
- Programa de Pós Graduação em Biodiversidade Animal; Universidade Federal de Santa Maria (UFSM); Santa Maria Rio Grande do Sul Brazil
- Departamento de Bioquímica e Biologia Molecular; Universidade Federal de Santa Maria (UFSM); Santa Maria Rio Grande do Sul Brazil
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Lin MF, Chou WH, Kitahara MV, Chen CLA, Miller DJ, Forêt S. Corallimorpharians are not "naked corals": insights into relationships between Scleractinia and Corallimorpharia from phylogenomic analyses. PeerJ 2016; 4:e2463. [PMID: 27761308 PMCID: PMC5068439 DOI: 10.7717/peerj.2463] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 08/19/2016] [Indexed: 01/01/2023] Open
Abstract
Calcification is one of the most distinctive traits of scleractinian corals. Their hard skeletons form the substratum of reef ecosystems and confer on corals their remarkable diversity of shapes. Corallimorpharians are non-calcifying, close relatives of scleractinian corals, and the evolutionary relationship between these two groups is key to understanding the evolution of calcification in the coral lineage. One pivotal question is whether scleractinians are a monophyletic group, paraphyly being an alternative possibility if corallimorpharians are corals that have lost their ability to calcify, as is implied by the “naked-coral” hypothesis. Despite major efforts, relationships between scleractinians and corallimorpharians remain equivocal and controversial. Although the complete mitochondrial genomes of a range of scleractinians and corallimorpharians have been obtained, heterogeneity in composition and evolutionary rates means that mitochondrial sequences are insufficient to understand the relationship between these two groups. To overcome these limitations, transcriptome data were generated for three representative corallimorpharians. These were used in combination with sequences available for a representative range of scleractinians to identify 291 orthologous single copy protein-coding nuclear markers. Unlike the mitochondrial sequences, these nuclear markers do not display any distinct compositional bias in their nucleotide or amino-acid sequences. A range of phylogenomic approaches congruently reveal a topology consistent with scleractinian monophyly and corallimorpharians as the sister clade of scleractinians.
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Affiliation(s)
- Mei Fang Lin
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia; Comparative Genomics Centre and Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, Australia
| | - Wen Hwa Chou
- Biodiversity Research Center, Academia Sinica , Taipei , Taiwan
| | - Marcelo V Kitahara
- Departamento de Ciências do Mar, Universidade Federal de São Paulo, Santos, São Paulo, Brazil; Centro de Biologia Marinha, Universidade Federal de São Paulo, São Sebastião, São Paulo, Brazil
| | | | - David John Miller
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia; Comparative Genomics Centre and Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, Australia
| | - Sylvain Forêt
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia; Research School of Biology, Australian National University, Canberra, ACT, Australia
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Addamo AM, Vertino A, Stolarski J, García-Jiménez R, Taviani M, Machordom A. Merging scleractinian genera: the overwhelming genetic similarity between solitary Desmophyllum and colonial Lophelia. BMC Evol Biol 2016; 16:108. [PMID: 27193263 PMCID: PMC4870751 DOI: 10.1186/s12862-016-0654-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 04/12/2016] [Indexed: 12/16/2022] Open
Abstract
Background In recent years, several types of molecular markers and new microscale skeletal characters have shown potential as powerful tools for phylogenetic reconstructions and higher-level taxonomy of scleractinian corals. Nonetheless, discrimination of closely related taxa is still highly controversial in scleractinian coral research. Here we used newly sequenced complete mitochondrial genomes and 30 microsatellites to define the genetic divergence between two closely related azooxanthellate taxa of the family Caryophylliidae: solitary Desmophyllum dianthus and colonial Lophelia pertusa. Results In the mitochondrial control region, an astonishing 99.8 % of nucleotides between L. pertusa and D. dianthus were identical. Variability of the mitochondrial genomes of the two species is represented by only 12 non-synonymous out of 19 total nucleotide substitutions. Microsatellite sequence (37 loci) analysis of L. pertusa and D. dianthus showed genetic similarity is about 97 %. Our results also indicated that L. pertusa and D. dianthus show high skeletal plasticity in corallum shape and similarity in skeletal ontogeny, micromorphological (septal and wall granulations) and microstructural characters (arrangement of rapid accretion deposits, thickening deposits). Conclusions Molecularly and morphologically, the solitary Desmophyllum and the dendroid Lophelia appear to be significantly more similar to each other than other unambiguous coral genera analysed to date. This consequently leads to ascribe both taxa under the generic name Desmophyllum (priority by date of publication). Findings of this study demonstrate that coloniality may not be a robust taxonomic character in scleractinian corals. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0654-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anna Maria Addamo
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Agostina Vertino
- Dipartimento di Scienze dell'Ambiente e del Territorio e di Scienze della Terra, Università di Milano Bicocca (UNIMIB), Piazza della Scienza 4, 20126, Milan, Italy.,Department of Geology Renard Centre of Marine Geology, Universiteit Ghent, Krijgslaan 281, B-9000, Ghent, Belgium
| | - Jaroslaw Stolarski
- Polskiej Akademii Nauk, Instytut Paleobiologii, Twarda 51/55, PL-00-818, Warsaw, Poland
| | - Ricardo García-Jiménez
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Marco Taviani
- Consiglio Nazionale delle Ricerche, Istituto di Scienze Marine (ISMAR), Via Gobetti 101, 40129, Bologna, Italy.,Biology Department, Woods Hole Oceanographic Institution, 266 Woods Hole Road, Woods Hole, 02543, MA, USA.,Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Annie Machordom
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006, Madrid, Spain.
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Everson KM, Soarimalala V, Goodman SM, Olson LE. Multiple Loci and Complete Taxonomic Sampling Resolve the Phylogeny and Biogeographic History of Tenrecs (Mammalia: Tenrecidae) and Reveal Higher Speciation Rates in Madagascar's Humid Forests. Syst Biol 2016; 65:890-909. [DOI: 10.1093/sysbio/syw034] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 04/07/2016] [Indexed: 11/14/2022] Open
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Malyarchuk B, Derenko M, Denisova G. A mitogenomic phylogeny and genetic history of sable (Martes zibellina). Gene 2014; 550:56-67. [PMID: 25110108 DOI: 10.1016/j.gene.2014.08.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Revised: 07/29/2014] [Accepted: 08/06/2014] [Indexed: 12/21/2022]
Abstract
We assessed phylogeny of sable (Martes zibellina, Linnaeus, 1758) by sequence analysis of nearly complete, new mitochondrial genomes in 36 specimens from different localities in northern Eurasia (Primorye, Khabarovsk and Krasnoyarsk regions, the Kamchatka Peninsula, the Kuril Islands and the Urals). Phylogenetic analysis of mtDNA sequences demonstrates that two clades, A and BC, radiated about 200-300 thousandyears ago (kya) according to results of Bayesian molecular clock and RelTime analyses of different mitogenome alignments (nearly complete mtDNA sequences, protein-coding region, and synonymous sites), while the age estimates of clades A, B and C fall within the Late Pleistocene (~50-140 kya). Bayesian skyline plots (BSPs) of sable population size change based on analysis of nearly complete mtDNAs show an expansion around 40 kya in the warm Karganian time, without a decline of population size around the Last Glacial Maximum (21 kya). The BSPs based on synonymous clock rate indicate that M. zibellina experienced demographic expansions later, approximately 22 kya. The A2a clade that colonized Kamchatka ~23-50 kya (depending on the mutation rate used) survived the last glaciation there as demonstrated by the BSP analysis. In addition, we have found evidence of positive selection acting at ND4 and cytochrome b genes, thereby suggesting adaptive evolution of the A2a clade in Kamchatka.
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Affiliation(s)
- Boris Malyarchuk
- Institute of Biological Problems of the North, Magadan, 685000 Russia.
| | - Miroslava Derenko
- Institute of Biological Problems of the North, Magadan, 685000 Russia
| | - Galina Denisova
- Institute of Biological Problems of the North, Magadan, 685000 Russia
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9
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Malyarchuk BA, Derenko MV, Denisova GA. Episodes of adaptive evolution of mitochondrial genome in asiatic salamanders (Amphibia, Caudata, Hynobiidae). RUSS J GENET+ 2014. [DOI: 10.1134/s1022795414020070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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10
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Rothfels CJ, Schuettpelz E. Accelerated Rate of Molecular Evolution for Vittarioid Ferns is Strong and Not Driven by Selection. Syst Biol 2013; 63:31-54. [DOI: 10.1093/sysbio/syt058] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Carl J. Rothfels
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA; 2Department of Zoology, University of British Columbia, #4200-6270 University Blvd., Vancouver, BC V6T 1Z4, Canada; 3Department of Biology and Marine Biology, University of North Carolina Wilmington, 601 South College Road, Wilmington, NC 28403, USA; and 4Department of Botany (MRC 166), National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington DC 20013-7012, USA
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA; 2Department of Zoology, University of British Columbia, #4200-6270 University Blvd., Vancouver, BC V6T 1Z4, Canada; 3Department of Biology and Marine Biology, University of North Carolina Wilmington, 601 South College Road, Wilmington, NC 28403, USA; and 4Department of Botany (MRC 166), National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington DC 20013-7012, USA
| | - Eric Schuettpelz
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA; 2Department of Zoology, University of British Columbia, #4200-6270 University Blvd., Vancouver, BC V6T 1Z4, Canada; 3Department of Biology and Marine Biology, University of North Carolina Wilmington, 601 South College Road, Wilmington, NC 28403, USA; and 4Department of Botany (MRC 166), National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington DC 20013-7012, USA
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA; 2Department of Zoology, University of British Columbia, #4200-6270 University Blvd., Vancouver, BC V6T 1Z4, Canada; 3Department of Biology and Marine Biology, University of North Carolina Wilmington, 601 South College Road, Wilmington, NC 28403, USA; and 4Department of Botany (MRC 166), National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington DC 20013-7012, USA
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