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Serrano MJ, Goudet J, Cumer T. Characterization of the diversity of barn owl's mitochondrial genome reveals high copy number variations in the control region. PLoS One 2024; 19:e0295595. [PMID: 38271341 PMCID: PMC10810427 DOI: 10.1371/journal.pone.0295595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 11/24/2023] [Indexed: 01/27/2024] Open
Abstract
Mitochondria are known to play an essential role in the cell. These organelles contain their own DNA, which is divided in a coding and non-coding region (NCR). While much of the NCR's function is unknown, tandem repeats have been observed in several vertebrates, with extreme intra-individual, intraspecific and interspecific variation. Taking advantage of a new complete reference for the mitochondrial genome of the Afro-European Barn Owl (Tyto alba), as well as 172 whole genome-resequencing; we (i) describe the reference mitochondrial genome with a special focus on the repeats in the NCR, (ii) quantify the variation in number of copies between individuals, and (iii) explore the possible factors associated with the variation in the number of repetitions. The reference mitochondrial genome revealed a long (256bp) and a short (80bp) tandem repeat in the NCR region. The re-sequenced genomes showed a great variation in number of copies between individuals, with 4 to 38 copies of the Long and 6 to 135 copies of the short repeat. Among the factors associated with this variation between individuals, the tissue used for extraction was the most significant. The exact mechanisms of the formations of these repeats are still to be discovered and understanding them will help explain the maintenance of the polymorphism in the number of copies, as well as their interactions with the metabolism, the aging and health of the individuals.
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Affiliation(s)
- Marcelo J. Serrano
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Jérôme Goudet
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Tristan Cumer
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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2
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Pinzari CA, Bellinger MR, Price D, Bonaccorso FJ. Genetic diversity, structure, and effective population size of an endangered, endemic hoary bat, 'ōpe'ape'a, across the Hawaiian Islands. PeerJ 2023; 11:e14365. [PMID: 36718450 PMCID: PMC9884036 DOI: 10.7717/peerj.14365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 10/19/2022] [Indexed: 01/26/2023] Open
Abstract
Island bat species are disproportionately at risk of extinction, and Hawai'i's only native terrestrial land mammal, the Hawaiian hoary bat (Lasiurus semotus) locally known as 'ōpe'ape'a, is no exception. To effectively manage this bat species with an archipelago-wide distribution, it is important to determine the population size on each island and connectivity between islands. We used 18 nuclear microsatellite loci and one mitochondrial gene from 339 individuals collected from 1988-2020 to evaluate genetic diversity, population structure and estimate effective population size on the Islands of Hawai'i, Maui, O'ahu, and Kaua'i. Genetic differentiation occurred between Hawai'i and Maui, both of which were differentiated from O'ahu and Kaua'i. The population on Maui presents the greatest per-island genetic diversity, consistent with their hypothesized status as the original founding population. A signature of isolation by distance was detected between islands, with contemporary migration analyses indicating limited gene flow in recent generations, and male-biased sex dispersal within Maui. Historical and long-term estimates of genetic effective population sizes were generally larger than contemporary estimates, although estimates of contemporary genetic effective population size lacked upper bounds in confidence intervals for Hawai'i and Kaua'i. Contemporary genetic effective population sizes were smaller on O'ahu and Maui. We also detected evidence of past bottlenecks on all islands with the exception of Hawai'i. Our study provides population-level estimates for the genetic diversity and geographic structure of 'ōpe'ape'a, that could be used by agencies tasked with wildlife conservation in Hawai'i.
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Affiliation(s)
- Corinna A. Pinzari
- Tropical Conservation Biology and Environmental Science Graduate Program, University of Hawaiʻi at Hilo, Hilo, Hawaiʻi, United States of America,Hawaiʻi Cooperative Studies Unit, University of Hawaiʻi at Hilo, Hawaiʻi National Park, Hawaiʻi, United States of America
| | - M. Renee Bellinger
- Tropical Conservation Biology and Environmental Science Graduate Program, University of Hawaiʻi at Hilo, Hilo, Hawaiʻi, United States of America,Hawaiʻi Cooperative Studies Unit, University of Hawaiʻi at Hilo, Hawaiʻi National Park, Hawaiʻi, United States of America,Pacific Island Ecosystems Research Center, U.S. Geological Survey, Hawaiʻi National Park, Hawaiʻi, United States of America
| | - Donald Price
- Tropical Conservation Biology and Environmental Science Graduate Program, University of Hawaiʻi at Hilo, Hilo, Hawaiʻi, United States of America,School of Life Sciences, University of Nevada - Las Vegas, Las Vegas, NV, United States of America
| | - Frank J. Bonaccorso
- Pacific Island Ecosystems Research Center, U.S. Geological Survey, Hawaiʻi National Park, Hawaiʻi, United States of America
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3
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Skorupski J. Characterisation of the Complete Mitochondrial Genome of Critically Endangered Mustela lutreola (Carnivora: Mustelidae) and Its Phylogenetic and Conservation Implications. Genes (Basel) 2022; 13:genes13010125. [PMID: 35052465 PMCID: PMC8774856 DOI: 10.3390/genes13010125] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/28/2021] [Accepted: 01/06/2022] [Indexed: 02/07/2023] Open
Abstract
In this paper, a complete mitochondrial genome of the critically endangered European mink Mustela lutreola L., 1761 is reported. The mitogenome was 16,504 bp in length and encoded the typical 13 protein-coding genes, two ribosomal RNA genes and 22 transfer RNA genes, and harboured a putative control region. The A+T content of the entire genome was 60.06% (A > T > C > G), and the AT-skew and GC-skew were 0.093 and −0.308, respectively. The encoding-strand identity of genes and their order were consistent with a collinear gene order characteristic for vertebrate mitogenomes. The start codons of all protein-coding genes were the typical ATN. In eight cases, they were ended by complete stop codons, while five had incomplete termination codons (TA or T). All tRNAs had a typical cloverleaf secondary structure, except tRNASer(AGC) and tRNALys, which lacked the DHU stem and had reduced DHU loop, respectively. Both rRNAs were capable of folding into complex secondary structures, containing unmatched base pairs. Eighty-one single nucleotide variants (substitutions and indels) were identified. Comparative interspecies analyses confirmed the close phylogenetic relationship of the European mink to the so-called ferret group, clustering the European polecat, the steppe polecat and the black-footed ferret. The obtained results are expected to provide useful molecular data, informing and supporting effective conservation measures to save M. lutreola.
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Affiliation(s)
- Jakub Skorupski
- Institute of Marine and Environmental Sciences, University of Szczecin, Adama Mickiewicza 16 St., 70-383 Szczecin, Poland; ; Tel.: +48-91-444-16-85
- Polish Society for Conservation Genetics LUTREOLA, Maciejkowa 21 St., 71-784 Szczecin, Poland
- The European Mink Centre, 71-415 Szczecin, Poland
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4
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Urantówka AD, Kroczak A, Strzała T, Zaniewicz G, Kurkowski M, Mackiewicz P. Mitogenomes of Accipitriformes and Cathartiformes Were Subjected to Ancestral and Recent Duplications Followed by Gradual Degeneration. Genome Biol Evol 2021; 13:evab193. [PMID: 34432018 PMCID: PMC8435663 DOI: 10.1093/gbe/evab193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2021] [Indexed: 11/25/2022] Open
Abstract
The rearrangement of 37 genes with one control region, firstly identified in Gallus gallus mitogenome, is believed to be ancestral for all Aves. However, mitogenomic sequences obtained in recent years revealed that many avian mitogenomes contain duplicated regions that were omitted in previous genomic versions. Their evolution and mechanism of duplication are still poorly understood. The order of Accipitriformes is especially interesting in this context because its representatives contain a duplicated control region in various stages of degeneration. Therefore, we applied an appropriate PCR strategy to look for duplications within the mitogenomes of the early diverged species Sagittarius serpentarius and Cathartiformes, which is a sister order to Accipitriformes. The analyses revealed the same duplicated gene order in all examined taxa and the common ancestor of these groups. The duplicated regions were subjected to gradual degeneration and homogenization during concerted evolution. The latter process occurred recently in the species of Cathartiformes as well as in the early diverged lineages of Accipitriformes, that is, Sagittarius serpentarius and Pandion haliaetus. However, in other lineages, that is, Pernis ptilorhynchus, as well as representatives of Aegypiinae, Aquilinae, and five related subfamilies of Accipitriformes (Accipitrinae, Circinae, Buteoninae, Haliaeetinae, and Milvinae), the duplications were evolving independently for at least 14-47 Myr. Different portions of control regions in Cathartiformes showed conflicting phylogenetic signals indicating that some sections of these regions were homogenized at a frequency higher than the rate of speciation, whereas others have still evolved separately.
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Affiliation(s)
- Adam Dawid Urantówka
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, Poland
| | - Aleksandra Kroczak
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, Poland
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, Wrocław University, Poland
| | - Tomasz Strzała
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, Poland
| | - Grzegorz Zaniewicz
- Department of Vertebrate Ecology and Zoology, Avian Ecophysiology Unit, University of Gdańsk, Poland
| | - Marcin Kurkowski
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, Poland
| | - Paweł Mackiewicz
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, Wrocław University, Poland
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Vivas-Toro I, Ortega J, Baeza JA. The complete mitochondrial genome of the Honduran white bat Ectophylla alba (Allen 1982) (Chiroptera: Phyllostomidae). Gene 2021; 802:145868. [PMID: 34364911 DOI: 10.1016/j.gene.2021.145868] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/01/2021] [Accepted: 07/30/2021] [Indexed: 11/18/2022]
Abstract
The Honduran white bat, Ectophylla alba (Allen 1982), is one of eight species belonging to the family Phyllostomidae that exclusively roosts in tents. Due to its restricted distribution, habitat specificity, and diet requirements, E. alba has been strongly affected by habitat loss and fragmentation during the last decade. In this study, we developed the first genomic resource for this species; we assembled and analyzed in detail the complete mitochondrial genome of E. alba. The mitogenome of E. alba is 16,664 bp in length and is comprised of 13 protein coding genes (PCGs), 2 ribosomal RNA genes, 22 transfer RNA genes (tRNAs), and a putative Control Region (CR) 1,232 bp in length. Gene arrangement in the mitochondrial chromosome of E. alba is identical to that reported before in other species of co-familiar bats. All PCGs are under purifying selection, with atp8 experiencing the least selective pressure. In all PCGs, codons ending with adenine are preferred over others ending in thymine and cytosine. Except tRNA-Serine 1, all tRNAs exhibit a cloverleaf secondary structure. The CR of E. alba exhibits three domains commonly described in other mammals, including bats; extended terminal associated sequences (ETAS), central, and conserved sequence block (CSB). A ML phylogenetic reconstruction of the family Phyllostomidae based on all 13 mitochondrial PCGs confirms the monophyletic status of the subfamily Sternodermatinae and indicates the close relationship between E. alba and the genus Artibeus. This is the first genomic resource developed for E. alba and represents the first step to improving our understanding of the genomic underpinnings involved in the evolution of specialization as well as acclimatization and adaptation to local and global change of specialist bats.
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Affiliation(s)
- Isabela Vivas-Toro
- Laboratorio de Bioconservación y Manejo, Posgrado en Ciencias Quimicobiológicas, Departamento de Zoologia, Escuela Nacional de Ciencias Biologicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Col. Sto. Tomas, 11340 CDMX, Mexico
| | - Jorge Ortega
- Laboratorio de Bioconservación y Manejo, Posgrado en Ciencias Quimicobiológicas, Departamento de Zoologia, Escuela Nacional de Ciencias Biologicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Col. Sto. Tomas, 11340 CDMX, Mexico
| | - J Antonio Baeza
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC 29634, USA; Smithsonian Marine Station at Fort Pierce, 701 Seaway Drive, Fort Pierce, FL 34949, USA; Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile.
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6
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Male condition and group heterogeneity predict extra-group paternity in a Neotropical bat. Behav Ecol Sociobiol 2020. [DOI: 10.1007/s00265-020-02919-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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7
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Complete mitochondrial genome of a blue-tailed skink Plestiodon capito (Reptilia, Squamata, Scincidae) and comparison with other Scincidae lizards. Genetica 2020; 148:229-241. [PMID: 33044712 DOI: 10.1007/s10709-020-00107-1] [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: 03/15/2020] [Revised: 09/24/2020] [Accepted: 10/03/2020] [Indexed: 10/23/2022]
Abstract
Vertebrate mitochondrial genomes (mitogenomes) are valuable for studying phylogeny, evolutionary genetics and genomics. To date, however, compared to other vertebrate groups, our knowledge about the mitogenomes of skinks (the family Scincidae), even of reptile, has been relatively limited. In the present study, we determined the complete mitogenome of a blue-tailed skink Plestiodon capito for the first time, and compared it with other skinks available in GenBank. The circular genome is 17,344 bp long, showing a typical vertebrate pattern with 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and one control region (CR). The gene organization, nucleotide composition, and codon usage are similar to those from skinks previously published. Twelve out of 13 PCGs initiates with canonical start codon (ATG), while COX1 starts with GTG. The codon usage analysis revealed a preferential use of the LeuCUN (Leu1), Pro, and Thr codons with the A/U ending. All tRNAs in P. capito were predicted to fold into typical clover-leaf secondary structure, except tRNA-Ser AGY. The secondary structures of 12S rRNA and 16S rRNA comprises 34 helices and 56 helices, respectively. The alignment of the Plesitodon species CRs exhibited high genetic variability and rich A + T content. Besides, variable types and numbers of tandem repeat units were also identified in the CR of Plestiodon. Phylogenetic analyses recovered P. capito as the sister species to P. tunganus; monophyly of the Scincidae is well supported. Our results will help to better understand structure and evolution of the mitochondrial DNA control region in reptiles as well as the evolutionary status of P. capito, and to lay foundation for further phylogenetic study of skinks in a mitogenomic framework.
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8
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Hao X. Complete mitochondrial genome of the East Asian fish-eating bat: Myotis ricketti (Chiroptera, Vespertilionidae). Mitochondrial DNA B Resour 2019; 4:3748-3749. [PMID: 33366172 PMCID: PMC7707413 DOI: 10.1080/23802359.2019.1681316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 10/13/2019] [Indexed: 11/05/2022] Open
Abstract
I report the complete mitochondrial genome (mitogenome) of the East Asian fish-eating bat (Myotis ricketti or M. pilosus), also known as the Rickett's big footed bat. The total length of the circular M. ricketti mitogenome is 17,098 base pairs, containing 13 protein-coding genes (PCGs), two ribosomal RNAs, 22 transfer RNAs, and a non-coding control region (D-loop region). The gene order and organisation of this mitogenome are similar to most of other determined vertebrate mitogenomes, with the nucleotide base composition of A 34.22%, T 30.32%, C 22.80%, and G 12.66%. Besides, the mitogenomic D-loop region contains 29 copies of a tandem repeat sequence of six nucleotides (CATACG). The phylogenetic analysis indicates that M. ricketti is closely related to M. macrodactylus and M. petax. This study will contribute to the investigations of phylogeny and evolution for Myotis and its relevant taxa.
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Affiliation(s)
- Xiangyu Hao
- College of Life Sciences, Northwest A&F University, Yangling, China
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9
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Tang Y, Zheng X, Zhong H, Li Q. Phylogenetics and comparative analysis of the mitochondrial genomes of three violet‐ringed octopuses. ZOOL SCR 2019. [DOI: 10.1111/zsc.12359] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yan Tang
- Key Laboratory of Mariculture Ocean University of China Qingdao China
- Institute of Evolution and Marine Biodiversity Ocean University of China Qingdao China
| | - Xiaodong Zheng
- Key Laboratory of Mariculture Ocean University of China Qingdao China
- Institute of Evolution and Marine Biodiversity Ocean University of China Qingdao China
| | - Hong Zhong
- Shenzhen BGTX Foods Co., Ltd. Shenzhen China
| | - Qi Li
- Key Laboratory of Mariculture Ocean University of China Qingdao China
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10
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Jebb D, Foley NM, Whelan CV, Touzalin F, Puechmaille SJ, Teeling EC. Population level mitogenomics of long-lived bats reveals dynamic heteroplasmy and challenges the Free Radical Theory of Ageing. Sci Rep 2018; 8:13634. [PMID: 30206380 PMCID: PMC6134106 DOI: 10.1038/s41598-018-31093-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 07/26/2018] [Indexed: 12/30/2022] Open
Abstract
Bats are the only mammals capable of true, powered flight, which drives an extremely high metabolic rate. The "Free Radical Theory of Ageing" (FTRA) posits that a high metabolic rate causes mitochondrial heteroplasmy and the progressive ageing phenotype. Contrary to this, bats are the longest-lived order of mammals given their small size and high metabolic rate. To investigate if bats exhibit increased mitochondrial heteroplasmy with age, we performed targeted, deep sequencing of mitogenomes and measured point heteroplasmy in wild, long lived Myotis myotis. Blood was sampled from 195 individuals, aged between <1 and at 6+ years old, and whole mitochondria deep-sequenced, with a subset sampled over multiple years. The majority of heteroplasmies were at a low frequency and were transitions. Oxidative mutations were present in only a small number of individuals, suggesting local oxidative stress events. Cohort data showed no significant increase in heteroplasmy with age, while longitudinal data from recaptured individuals showed heteroplasmy is dynamic, and does not increase uniformly over time. We show that bats do not suffer from the predicted, inevitable increase in heteroplasmy as posited by the FRTA, instead heteroplasmy was found to be dynamic, questioning its presumed role as a primary driver of ageing.
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Affiliation(s)
- David Jebb
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Nicole M Foley
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Conor V Whelan
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Frédéric Touzalin
- Laboratoire Evolution et Diversité Biologique, Université Toulouse 3, Paul Sabatier, 31062, Toulouse Cedex 09, France
| | - Sebastien J Puechmaille
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
- Applied Zoology and Conservation, Zoological Institute, Greifswald University, Greifswald, Germany
| | - Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland.
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11
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Barshad G, Marom S, Cohen T, Mishmar D. Mitochondrial DNA Transcription and Its Regulation: An Evolutionary Perspective. Trends Genet 2018; 34:682-692. [DOI: 10.1016/j.tig.2018.05.009] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 05/19/2018] [Accepted: 05/31/2018] [Indexed: 12/15/2022]
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12
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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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13
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Halczok TK, Brändel SD, Flores V, Puechmaille SJ, Tschapka M, Page RA, Kerth G. Male-biased dispersal and the potential impact of human-induced habitat modifications on the Neotropical bat Trachops cirrhosus. Ecol Evol 2018; 8:6065-6080. [PMID: 29988406 PMCID: PMC6024115 DOI: 10.1002/ece3.4161] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 03/26/2018] [Accepted: 04/16/2018] [Indexed: 12/25/2022] Open
Abstract
Gene flow, maintained through natal dispersal and subsequent mating events, is one of the most important processes in both ecology and population genetics. Among mammalian populations, gene flow is strongly affected by a variety of factors, including the species' ability to disperse, and the composition of the environment which can limit dispersal. Information on dispersal patterns is thus crucial both for conservation management and for understanding the social system of a species. We used 16 polymorphic nuclear microsatellite loci in addition to mitochondrial DNA sequences (1.61 kbp) to analyse the population structure and the sex-specific pattern of natal dispersal in the frog-eating fringe-lipped bat, Trachops cirrhosus, in Central Panama. Our study revealed that-unlike most of the few other investigated Neotropical bats-gene flow in this species is mostly male-mediated. Nevertheless, distinct genetic clusters occur in both sexes. In particular, the presence of genetic differentiation in the dataset only consisting of the dispersing sex (males) indicates that gene flow is impeded within our study area. Our data are in line with the Panama Canal in connection with the widening of the Río Chagres during the canal construction acting as a recent barrier to gene flow. The sensitivity of T. cirrhosus to human-induced habitat modifications is further indicated by an extremely low capture success in highly fragmented areas. Taken together, our genetic and capture data provide evidence for this species to be classified as less mobile and thus vulnerable to habitat change, information that is important for conservation management.
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Affiliation(s)
- Tanja K. Halczok
- Zoological Institute and MuseumGreifswald UniversityGreifswaldGermany
- Smithsonian Tropical Research InstituteBalboa, AncónRepublic of Panamá
| | - Stefan D. Brändel
- Smithsonian Tropical Research InstituteBalboa, AncónRepublic of Panamá
- Institute of Evolutionary Ecology and Conservation GenomicsUniversity of UlmUlmGermany
| | - Victoria Flores
- Smithsonian Tropical Research InstituteBalboa, AncónRepublic of Panamá
- Committee on Evolutionary BiologyUniversity of ChicagoChicagoIllinois
| | | | - Marco Tschapka
- Smithsonian Tropical Research InstituteBalboa, AncónRepublic of Panamá
- Institute of Evolutionary Ecology and Conservation GenomicsUniversity of UlmUlmGermany
| | - Rachel A. Page
- Smithsonian Tropical Research InstituteBalboa, AncónRepublic of Panamá
| | - Gerald Kerth
- Zoological Institute and MuseumGreifswald UniversityGreifswaldGermany
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14
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Lv C, Li Q, Kong L. Comparative analyses of the complete mitochondrial genomes of Dosinia clams and their phylogenetic position within Veneridae. PLoS One 2018; 13:e0196466. [PMID: 29718949 PMCID: PMC5931646 DOI: 10.1371/journal.pone.0196466] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 04/13/2018] [Indexed: 11/19/2022] Open
Abstract
Mitochondrial genomes have proved to be a powerful tool in resolving phylogenetic relationship. In order to understand the mitogenome characteristics and phylogenetic position of the genus Dosinia, we sequenced the complete mitochondrial genomes of Dosinia altior and Dosinia troscheli (Bivalvia: Veneridae), compared them with that of Dosinia japonica and established a phylogenetic tree for Veneridae. The mitogenomes of D. altior (17,536 bp) and D. troscheli (17,229 bp) are the two smallest in Veneridae, which include 13 protein-coding genes, 2 ribosomal RNA genes, 22 tRNA genes, and non-coding regions. The mitogenomes of the Dosinia species are similar in size, gene content, AT content, AT- and GC- skews, and gene arrangement. The phylogenetic relationships of family Veneridae were established based on 12 concatenated protein-coding genes using maximum likelihood and Bayesian analyses, which supported that Dosininae and Meretricinae have a closer relationship, with Tapetinae being the sister taxon. The information obtained in this study will contribute to further understanding of the molecular features of bivalve mitogenomes and the evolutionary history of the genus Dosinia.
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Affiliation(s)
- Changda Lv
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
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15
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du Toit Z, du Plessis M, Dalton DL, Jansen R, Paul Grobler J, Kotzé A. Mitochondrial genomes of African pangolins and insights into evolutionary patterns and phylogeny of the family Manidae. BMC Genomics 2017; 18:746. [PMID: 28934931 PMCID: PMC5609056 DOI: 10.1186/s12864-017-4140-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 09/14/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND This study used next generation sequencing to generate the mitogenomes of four African pangolin species; Temminck's ground pangolin (Smutsia temminckii), giant ground pangolin (S. gigantea), white-bellied pangolin (Phataginus tricuspis) and black-bellied pangolin (P. tetradactyla). RESULTS The results indicate that the mitogenomes of the African pangolins are 16,558 bp for S. temminckii, 16,540 bp for S. gigantea, 16,649 bp for P. tetradactyla and 16,565 bp for P. tricuspis. Phylogenetic comparisons of the African pangolins indicated two lineages with high posterior probabilities providing evidence to support the classification of two genera; Smutsia and Phataginus. The total GC content between African pangolins was observed to be similar between species (36.5% - 37.3%). The most frequent codon was found to be A or C at the 3rd codon position. Significant variations in GC-content and codon usage were observed for several regions between African and Asian pangolin species which may be attributed to mutation pressure and/or natural selection. Lastly, a total of two insertions of 80 bp and 28 bp in size respectively was observed in the control region of the black-bellied pangolin which were absent in the other African pangolin species. CONCLUSIONS The current study presents reference mitogenomes of all four African pangolin species and thus expands on the current set of reference genomes available for six of the eight extant pangolin species globally and represents the first phylogenetic analysis with six pangolin species using full mitochondrial genomes. Knowledge of full mitochondrial DNA genomes will assist in providing a better understanding on the evolution of pangolins which will be essential for conservation genetic studies.
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Affiliation(s)
- Zelda du Toit
- Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
- Centre for Conservation Science, National Zoological Gardens of South Africa, P.O. Box 754, Pretoria, 0001, South Africa
| | - Morné du Plessis
- Centre for Conservation Science, National Zoological Gardens of South Africa, P.O. Box 754, Pretoria, 0001, South Africa
| | - Desiré L Dalton
- Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa.
- Centre for Conservation Science, National Zoological Gardens of South Africa, P.O. Box 754, Pretoria, 0001, South Africa.
- Department of Zoology, University of Venda, Thohoyandou, South Africa.
| | - Raymond Jansen
- Department of Environmental, Water and Earth Sciences, Tshwane University of Technology, Private Bag X680, Pretoria, 0001, South Africa
| | - J Paul Grobler
- Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | - Antoinette Kotzé
- Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
- Centre for Conservation Science, National Zoological Gardens of South Africa, P.O. Box 754, Pretoria, 0001, South Africa
- Department of Environmental, Water and Earth Sciences, Tshwane University of Technology, Private Bag X680, Pretoria, 0001, South Africa
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16
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Piaggio AJ, Russell AL, Osorio IA, Jiménez Ramírez A, Fischer JW, Neuwald JL, Tibbels AE, Lecuona L, McCracken GF. Genetic demography at the leading edge of the distribution of a rabies virus vector. Ecol Evol 2017; 7:5343-5351. [PMID: 28770072 PMCID: PMC5528231 DOI: 10.1002/ece3.3087] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 04/21/2017] [Accepted: 05/02/2017] [Indexed: 11/21/2022] Open
Abstract
The common vampire bat, Desmodus rotundus, ranges from South America into northern Mexico in North America. This sanguivorous species of bat feeds primarily on medium to large-sized mammals and is known to rely on livestock as primary prey. Each year, there are hotspot areas of D. rotundus-specific rabies virus outbreaks that lead to the deaths of livestock and economic losses. Based on incidental captures in our study area, which is an area of high cattle mortality from D. rotundus transmitted rabies, it appears that D. rotundus are being caught regularly in areas and elevations where they previously were thought to be uncommon. Our goal was to investigate demographic processes and genetic diversity at the north eastern edge of the range of D. rotundus in Mexico. We generated control region sequences (441 bp) and 12-locus microsatellite genotypes for 602 individuals of D. rotundus. These data were analyzed using network analyses, Bayesian clustering approaches, and standard population genetic statistical analyses. Our results demonstrate panmixia across our sampling area with low genetic diversity, low population differentiation, loss of intermediate frequency alleles at microsatellite loci, and very low mtDNA haplotype diversity with all haplotypes being very closely related. Our study also revealed strong signals of population expansion. These results follow predictions from the leading-edge model of expanding populations and supports conclusions from another study that climate change may allow this species to find suitable habitat within the U.S. border.
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Affiliation(s)
| | - Amy L. Russell
- Department of BiologyGrand Valley State UniversityAllendaleMIUSA
| | - Ignacio A. Osorio
- Committee of Promotion and Animal Health ProtectionRabies Campaign, San Luis Potosi CitySan Luis PotosiMéxico
| | - Alejandro Jiménez Ramírez
- Former State Chief of the National Campaign of Bovine Paralytic Rabies SENASICA/SAGARPAMéxico CityMéxico
- Present address:
MVZ.Marcelino Champagnat 505 Colonia Guadalupe Tepatitlán de MorelosJaliscoMexico
| | | | | | | | - Luis Lecuona
- USDA/APHIS/International ServicesDistrito FederalMéxico
| | - Gary F. McCracken
- Department of Ecology and Evolutionary BiologyUniversity of TennesseeKnoxvilleTNUSA
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17
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Adrian-Kalchhauser I, Svensson O, Kutschera VE, Alm Rosenblad M, Pippel M, Winkler S, Schloissnig S, Blomberg A, Burkhardt-Holm P. The mitochondrial genome sequences of the round goby and the sand goby reveal patterns of recent evolution in gobiid fish. BMC Genomics 2017; 18:177. [PMID: 28209125 PMCID: PMC5314710 DOI: 10.1186/s12864-017-3550-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 02/02/2017] [Indexed: 11/15/2022] Open
Abstract
Background Vertebrate mitochondrial genomes are optimized for fast replication and low cost of RNA expression. Accordingly, they are devoid of introns, are transcribed as polycistrons and contain very little intergenic sequences. Usually, vertebrate mitochondrial genomes measure between 16.5 and 17 kilobases (kb). Results During genome sequencing projects for two novel vertebrate models, the invasive round goby and the sand goby, we found that the sand goby genome is exceptionally small (16.4 kb), while the mitochondrial genome of the round goby is much larger than expected for a vertebrate. It is 19 kb in size and is thus one of the largest fish and even vertebrate mitochondrial genomes known to date. The expansion is attributable to a sequence insertion downstream of the putative transcriptional start site. This insertion carries traces of repeats from the control region, but is mostly novel. To get more information about this phenomenon, we gathered all available mitochondrial genomes of Gobiidae and of nine gobioid species, performed phylogenetic analyses, analysed gene arrangements, and compared gobiid mitochondrial genome sizes, ecological information and other species characteristics with respect to the mitochondrial phylogeny. This allowed us amongst others to identify a unique arrangement of tRNAs among Ponto-Caspian gobies. Conclusions Our results indicate that the round goby mitochondrial genome may contain novel features. Since mitochondrial genome organisation is tightly linked to energy metabolism, these features may be linked to its invasion success. Also, the unique tRNA arrangement among Ponto-Caspian gobies may be helpful in studying the evolution of this highly adaptive and invasive species group. Finally, we find that the phylogeny of gobiids can be further refined by the use of longer stretches of linked DNA sequence. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3550-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Irene Adrian-Kalchhauser
- Program Man-Society-Environment, Department of Environmental Sciences, University of Basel, Vesalgasse 1, Basel, 4051, Switzerland.
| | - Ola Svensson
- Department of Biological and Environmental Sciences, University of Gothenburg, Medicinaregatan 18A, 41390, Göteborg, Sweden.,The Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, P.O. Box 460, 40530, Gothenburg, Sweden
| | - Verena E Kutschera
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - Magnus Alm Rosenblad
- The Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, P.O. Box 460, 40530, Gothenburg, Sweden.,Department of Marine Sciences, NBIS Bioinformatics Infrastructure for Life Sciences, University of Gothenburg, Medicinaregatan 9C, 41390, Gothenburg, Sweden
| | - Martin Pippel
- Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany
| | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - Siegfried Schloissnig
- Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany
| | - Anders Blomberg
- The Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, P.O. Box 460, 40530, Gothenburg, Sweden.,Department of Marine Sciences, University of Gothenburg, Medicinaregatan 9C, 41390, Gothenburg, Sweden
| | - Patricia Burkhardt-Holm
- Program Man-Society-Environment, Department of Environmental Sciences, University of Basel, Vesalgasse 1, Basel, 4051, Switzerland.,Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB, Canada
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18
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Ma H, O'Farrell PH. Selfish drive can trump function when animal mitochondrial genomes compete. Nat Genet 2016; 48:798-802. [PMID: 27270106 PMCID: PMC4925267 DOI: 10.1038/ng.3587] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 05/13/2016] [Indexed: 12/11/2022]
Abstract
Mitochondrial genomes compete for transmission from mother to progeny. We explored this competition by introducing a second genome into Drosophila melanogaster to follow transmission. Competitions between closely related genomes favored those functional in electron transport, resulting in a host-beneficial purifying selection. In contrast, matchups between distantly related genomes often favored those with negligible, negative or lethal consequences, indicating selfish selection. Exhibiting powerful selfish selection, a genome carrying a detrimental mutation displaced a complementing genome, leading to population death after several generations. In a different pairing, opposing selfish and purifying selection counterbalanced to give stable transmission of two genomes. Sequencing of recombinant mitochondrial genomes showed that the noncoding region, containing origins of replication, governs selfish transmission. Uniparental inheritance prevents encounters between distantly related genomes. Nonetheless, in each maternal lineage, constant competition among sibling genomes selects for super-replicators. We suggest that this relentless competition drives positive selection, promoting change in the sequences influencing transmission.
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Affiliation(s)
- Hansong Ma
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, USA
| | - Patrick H O'Farrell
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, USA
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19
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Vonhof MJ, Amelon SK, Currie RR, McCracken GF. Genetic structure of winter populations of the endangered Indiana bat (Myotis sodalis) prior to the white nose syndrome epidemic: implications for the risk of disease spread. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0841-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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20
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Phukuntsi MA, Brettschneider H, Dalton DL, Kearney T, Badenhorst J, Kotze A. DNA barcoding for identification of cryptic species in the field and existing museum collections: a case study ofAethomysandMicaelamys(Rodentia: Muridae). AFRICAN ZOOLOGY 2016. [DOI: 10.1080/15627020.2016.1146084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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21
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Gager Y, Tarland E, Lieckfeldt D, Ménage M, Botero-Castro F, Rossiter SJ, Kraus RHS, Ludwig A, Dechmann DKN. The Value of Molecular vs. Morphometric and Acoustic Information for Species Identification Using Sympatric Molossid Bats. PLoS One 2016; 11:e0150780. [PMID: 26943355 PMCID: PMC4778951 DOI: 10.1371/journal.pone.0150780] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 02/17/2016] [Indexed: 11/21/2022] Open
Abstract
A fundamental condition for any work with free-ranging animals is correct species identification. However, in case of bats, information on local species assemblies is frequently limited especially in regions with high biodiversity such as the Neotropics. The bat genus Molossus is a typical example of this, with morphologically similar species often occurring in sympatry. We used a multi-method approach based on molecular, morphometric and acoustic information collected from 962 individuals of Molossus bondae, M. coibensis, and M. molossus captured in Panama. We distinguished M. bondae based on size and pelage coloration. We identified two robust species clusters composed of M. molossus and M. coibensis based on 18 microsatellite markers but also on a more stringently determined set of four markers. Phylogenetic reconstructions using the mitochondrial gene co1 (DNA barcode) were used to diagnose these microsatellite clusters as M. molossus and M. coibensis. To differentiate species, morphological information was only reliable when forearm length and body mass were combined in a linear discriminant function (95.9% correctly identified individuals). When looking in more detail at M. molossus and M. coibensis, only four out of 13 wing parameters were informative for species differentiation, with M. coibensis showing lower values for hand wing area and hand wing length and higher values for wing loading. Acoustic recordings after release required categorization of calls into types, yielding only two informative subsets: approach calls and two-toned search calls. Our data emphasizes the importance of combining morphological traits and independent genetic data to inform the best choice and combination of discriminatory information used in the field. Because parameters can vary geographically, the multi-method approach may need to be adjusted to local species assemblies and populations to be entirely informative.
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Affiliation(s)
- Yann Gager
- Department of Migration and Immuno-Ecology, Max Planck Institute for Ornithology, Radolfzell, Germany
- Department of Biology, University of Konstanz, Konstanz, Germany
- International Max Planck Research School for Organismal Biology, University of Konstanz, Konstanz, Germany
- * E-mail:
| | - Emilia Tarland
- Swedish University of Agricultural Sciences, Department of Animal Breeding and Genetics, Uppsala, Sweden
- Department of Evolutionary Genetics, Leibniz-Institute of Zoo and Wildlife Research, Berlin, Germany
| | - Dietmar Lieckfeldt
- Department of Evolutionary Genetics, Leibniz-Institute of Zoo and Wildlife Research, Berlin, Germany
| | - Matthieu Ménage
- Department of Migration and Immuno-Ecology, Max Planck Institute for Ornithology, Radolfzell, Germany
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Fidel Botero-Castro
- Institut des Sciences de l’Evolution, UMR 5554-CNRS-IRD, Université de Montpellier, Montpellier, France
| | - Stephen J. Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Robert H. S. Kraus
- Department of Migration and Immuno-Ecology, Max Planck Institute for Ornithology, Radolfzell, Germany
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Arne Ludwig
- Department of Evolutionary Genetics, Leibniz-Institute of Zoo and Wildlife Research, Berlin, Germany
| | - Dina K. N. Dechmann
- Department of Migration and Immuno-Ecology, Max Planck Institute for Ornithology, Radolfzell, Germany
- Department of Biology, University of Konstanz, Konstanz, Germany
- Smithsonian Tropical Research Institute, Panamá, Rep. of Panamá
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22
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Rahman MM, Yoon KB, Kim JY, Hussin MZ, Park YC. Complete mitochondrial genome sequence of the Indian pipistrellePipistrellus coromandra(Vespertilioninae). Anim Cells Syst (Seoul) 2016. [DOI: 10.1080/19768354.2016.1150877] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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23
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Naidoo T, Schoeman MC, Goodman SM, Taylor PJ, Lamb JM. Discordance between mitochondrial and nuclear genetic structure in the bat Chaerephon pumilus (Chiroptera: Molossidae) from southern Africa. Mamm Biol 2016. [DOI: 10.1016/j.mambio.2015.11.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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24
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Dool SE, Puechmaille SJ, Foley NM, Allegrini B, Bastian A, Mutumi GL, Maluleke TG, Odendaal LJ, Teeling EC, Jacobs DS. Nuclear introns outperform mitochondrial DNA in inter-specific phylogenetic reconstruction: Lessons from horseshoe bats (Rhinolophidae: Chiroptera). Mol Phylogenet Evol 2016; 97:196-212. [PMID: 26826601 DOI: 10.1016/j.ympev.2016.01.003] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 01/07/2016] [Accepted: 01/08/2016] [Indexed: 01/22/2023]
Abstract
Despite many studies illustrating the perils of utilising mitochondrial DNA in phylogenetic studies, it remains one of the most widely used genetic markers for this purpose. Over the last decade, nuclear introns have been proposed as alternative markers for phylogenetic reconstruction. However, the resolution capabilities of mtDNA and nuclear introns have rarely been quantified and compared. In the current study we generated a novel ∼5kb dataset comprising six nuclear introns and a mtDNA fragment. We assessed the relative resolution capabilities of the six intronic fragments with respect to each other, when used in various combinations together, and when compared to the traditionally used mtDNA. We focused on a major clade in the horseshoe bat family (Afro-Palaearctic clade; Rhinolophidae) as our case study. This old, widely distributed and speciose group contains a high level of conserved morphology. This morphological stasis renders the reconstruction of the phylogeny of this group with traditional morphological characters complex. We sampled multiple individuals per species to represent their geographic distributions as best as possible (122 individuals, 24 species, 68 localities). We reconstructed the species phylogeny using several complementary methods (partitioned Maximum Likelihood and Bayesian and Bayesian multispecies-coalescent) and made inferences based on consensus across these methods. We computed pairwise comparisons based on Robinson-Foulds tree distance metric between all Bayesian topologies generated (27,000) for every gene(s) and visualised the tree space using multidimensional scaling (MDS) plots. Using our supported species phylogeny we estimated the ancestral state of key traits of interest within this group, e.g. echolocation peak frequency which has been implicated in speciation. Our results revealed many potential cryptic species within this group, even in taxa where this was not suspected a priori and also found evidence for mtDNA introgression. We demonstrated that by using just two introns one can recover a better supported species tree than when using the mtDNA alone, despite the shorter overall length of the combined introns. Additionally, when combining any single intron with mtDNA, we showed that the result is highly similar to the mtDNA gene tree and far from the true species tree and therefore this approach should be avoided. We caution against the indiscriminate use of mtDNA in phylogenetic studies and advocate for pilot studies to select nuclear introns. The selection of marker type and number is a crucial step that is best based on critical examination of preliminary or previously published data. Based on our findings and previous publications, we recommend the following markers to recover phylogenetic relationships between recently diverged taxa (<20 My) in bats and other mammals: ACOX2, COPS7A, BGN, ROGDI and STAT5A.
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Affiliation(s)
- Serena E Dool
- Department of Biological Sciences, Animal Evolution and Systematics Group, University of Cape Town, Cape Town, South Africa; Zoological Institute and Museum, University of Greifswald, Soldmann-Straße 14, D-17487 Greifswald, Germany.
| | - Sebastien J Puechmaille
- Zoological Institute and Museum, University of Greifswald, Soldmann-Straße 14, D-17487 Greifswald, Germany; Midi-Pyrénées bat group (CREN-GCMP), Toulouse, France; School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Nicole M Foley
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland.
| | | | - Anna Bastian
- Department of Biological Sciences, Animal Evolution and Systematics Group, University of Cape Town, Cape Town, South Africa.
| | - Gregory L Mutumi
- Department of Biological Sciences, Animal Evolution and Systematics Group, University of Cape Town, Cape Town, South Africa.
| | - Tinyiko G Maluleke
- Department of Biological Sciences, Animal Evolution and Systematics Group, University of Cape Town, Cape Town, South Africa.
| | - Lizelle J Odendaal
- Department of Biological Sciences, Animal Evolution and Systematics Group, University of Cape Town, Cape Town, South Africa.
| | - Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland.
| | - David S Jacobs
- Department of Biological Sciences, Animal Evolution and Systematics Group, University of Cape Town, Cape Town, South Africa.
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25
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Korkmaz EM, Budak M, Ördek MN, Başıbüyük HH. The complete mitogenomes of Calameuta filiformis (Eversmann, 1847) and Calameuta idolon (Rossi, 1794) (Hymenoptera: Cephidae): The remarkable features of the elongated A+T rich region in Cephini. Gene 2015; 576:404-11. [PMID: 26515518 DOI: 10.1016/j.gene.2015.10.050] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 10/17/2015] [Accepted: 10/20/2015] [Indexed: 11/28/2022]
Abstract
Two complete mitogenomes of the stem borers, Calameuta filiformis and Calameuta idolon, and the complete A+T-rich region of Trachelus iudaicus (Hymenoptera: Cephidae), are reported. The mitogenomes of these species are the longest reported from hymenopterans to date. A remarkable increase in length of the A+T-rich region, the longest for Hymenoptera, was found and compared across the tribe Cephini. The presence of the tRNA- and rRNA-like sequences were reported in the A+T-rich region of sawflies and they were suggested to play a role in replication and/or transcription. The long and short tandem repeats were orderly located in both sides of the A+T-rich region producing stable secondary structures. We suggest that the short tandem repeats are likely to function as a replication fork barrier.
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Affiliation(s)
- E Mahir Korkmaz
- Department of Molecular Biology and Genetics, Faculty of Science, Cumhuriyet University, Sivas, 58140, Turkey.
| | - Mahir Budak
- Department of Molecular Biology and Genetics, Faculty of Science, Cumhuriyet University, Sivas, 58140, Turkey
| | - Merve Nur Ördek
- Department of Molecular Biology and Genetics, Faculty of Science, Cumhuriyet University, Sivas, 58140, Turkey
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26
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Huang Z, Gallot A, Lao NT, Puechmaille SJ, Foley NM, Jebb D, Bekaert M, Teeling EC. A nonlethal sampling method to obtain, generate and assemble whole blood transcriptomes from small, wild mammals. Mol Ecol Resour 2015; 16:150-62. [PMID: 26186236 DOI: 10.1111/1755-0998.12447] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 07/08/2015] [Accepted: 07/13/2015] [Indexed: 12/01/2022]
Abstract
The acquisition of tissue samples from wild populations is a constant challenge in conservation biology, especially for endangered species and protected species where nonlethal sampling is the only option. Whole blood has been suggested as a nonlethal sample type that contains a high percentage of bodywide and genomewide transcripts and therefore can be used to assess the transcriptional status of an individual, and to infer a high percentage of the genome. However, only limited quantities of blood can be nonlethally sampled from small species and it is not known if enough genetic material is contained in only a few drops of blood, which represents the upper limit of sample collection for some small species. In this study, we developed a nonlethal sampling method, the laboratory protocols and a bioinformatic pipeline to sequence and assemble the whole blood transcriptome, using Illumina RNA-Seq, from wild greater mouse-eared bats (Myotis myotis). For optimal results, both ribosomal and globin RNAs must be removed before library construction. Treatment of DNase is recommended but not required enabling the use of smaller amounts of starting RNA. A large proportion of protein-coding genes (61%) in the genome were expressed in the blood transcriptome, comparable to brain (65%), kidney (63%) and liver (58%) transcriptomes, and up to 99% of the mitogenome (excluding D-loop) was recovered in the RNA-Seq data. In conclusion, this nonlethal blood sampling method provides an opportunity for a genomewide transcriptomic study of small, endangered or critically protected species, without sacrificing any individuals.
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Affiliation(s)
- Zixia Huang
- UCD School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Aurore Gallot
- UCD School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland.,Laboratoire de Biométrie et Biologie Évolutive, UMR 5558, Centre National de la Recherche Scientifique, Université Lyon 1, Lyon, France
| | - Nga T Lao
- UCD School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland.,Molecular Biology Laboratory, National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Sébastien J Puechmaille
- UCD School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland.,Applied Zoology and Nature Conservation, Greifswald University, J.-S.-Bach-Str. 11/12, 17489, Greifswald, Germany
| | - Nicole M Foley
- UCD School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - David Jebb
- UCD School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Michaël Bekaert
- NSilico Lifescience Limited, Melbourn Building, CIT Campus, Bishopstown, Co., Cork, Ireland
| | - Emma C Teeling
- UCD School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
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27
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O’ Donnell CFJ, Richter S, Dool S, Monks JM, Kerth G. Genetic diversity is maintained in the endangered New Zealand long-tailed bat (Chalinolobus tuberculatus) despite a closed social structure and regular population crashes. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0763-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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28
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Hu QX, Fan Y, Xu L, Pang W, Wang S, Zheng YT, Lv LB, Yao YG. Analysis of the complete mitochondrial genome and characterization of diverse NUMTs of Macaca leonina. Gene 2015; 571:279-85. [PMID: 26151895 DOI: 10.1016/j.gene.2015.06.085] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Revised: 06/08/2015] [Accepted: 06/26/2015] [Indexed: 11/19/2022]
Abstract
As a non-human primate, the pig-tailed macaque has received wide attention because it can be infected by HIV-1. In this study, we determined the complete mtDNA sequence of the northern pig-tailed macaque (Macaca leonina). Unexpectedly, during the amplification of the mtDNA control region (D-loop region) we observed several D-loop-like sequences, which were NUMTs (nuclear mitochondrial sequences) and a total of 14 D-loop-like NUMT haplotypes were later identified in five individuals. The neighbor-joining tree and estimated divergence time based on these D-loop-like NUMT sequences of M. leonina provide some insights into the understanding of the evolutionary history of NUMTs. D-loop-like haplotypes G and H, which also exist in the nuclear genome of mulatta, appear to have been translocated into the nuclear genome before the divergence of M. mulatta and M. leonina. The other D-loop-like NUMT haplotypes were translocated into the nuclear genome of M. leonina after the divergence of the two species. Later sequence conversion was predicted to occur among these 14 D-loop-like NUMT haplotypes. The overall structure of the mtDNA of M. leonina was found to be similar to that seen in other mammalian mitochondrial genomes. Phylogenetic analysis based on the maximum likelihood method shows M. leonina clustered with Macaca silenus among the analyzed mammalian species.
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Affiliation(s)
- Qiu-Xiang Hu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Yu Fan
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Ling Xu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Wei Pang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China
| | - Shuang Wang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Kunming Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Long-Bao Lv
- Kunming Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Kunming Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
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Volleth M, Loidl J, Mayer F, Yong HS, Müller S, Heller KG. Surprising Genetic Diversity inRhinolophus luctus(Chiroptera: Rhinolophidae) from Peninsular Malaysia: Description of a New Species Based on Genetic and Morphological Characters. ACTA CHIROPTEROLOGICA 2015. [DOI: 10.3161/15081109acc2015.17.1.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Arnold BD, Wilkinson GS. Female natal philopatry and gene flow between divergent clades of pallid bats (Antrozous pallidus). J Mammal 2015. [DOI: 10.1093/jmammal/gyv058] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Lakshmanan LN, Gruber J, Halliwell B, Gunawan R. Are mutagenic non D-loop direct repeat motifs in mitochondrial DNA under a negative selection pressure? Nucleic Acids Res 2015; 43:4098-108. [PMID: 25855815 PMCID: PMC4417187 DOI: 10.1093/nar/gkv299] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 03/26/2015] [Indexed: 12/22/2022] Open
Abstract
Non D-loop direct repeats (DRs) in mitochondrial DNA (mtDNA) have been commonly implicated in the mutagenesis of mtDNA deletions associated with neuromuscular disease and ageing. Further, these DRs have been hypothesized to put a constraint on the lifespan of mammals and are under a negative selection pressure. Using a compendium of 294 mammalian mtDNA, we re-examined the relationship between species lifespan and the mutagenicity of such DRs. Contradicting the prevailing hypotheses, we found no significant evidence that long-lived mammals possess fewer mutagenic DRs than short-lived mammals. By comparing DR counts in human mtDNA with those in selectively randomized sequences, we also showed that the number of DRs in human mtDNA is primarily determined by global mtDNA properties, such as the bias in synonymous codon usage (SCU) and nucleotide composition. We found that SCU bias in mtDNA positively correlates with DR counts, where repeated usage of a subset of codons leads to more frequent DR occurrences. While bias in SCU and nucleotide composition has been attributed to nucleotide mutational bias, mammalian mtDNA still exhibit higher SCU bias and DR counts than expected from such mutational bias, suggesting a lack of negative selection against non D-loop DRs.
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Affiliation(s)
- Lakshmi Narayanan Lakshmanan
- Institute for Chemical and Bioengineering, ETH Zurich, Zurich 8093, Switzerland Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
| | - Jan Gruber
- Yale-NUS College, Department of Biochemistry, Neurobiology and Ageing Program, National University of Singapore, Singapore 117599, Singapore
| | - Barry Halliwell
- Department of Biochemistry, Neurobiology and Ageing Program, Centre for Life Sciences (CeLS), National University of Singapore, Singapore 117599, Singapore
| | - Rudiyanto Gunawan
- Institute for Chemical and Bioengineering, ETH Zurich, Zurich 8093, Switzerland Swiss Institute of Bioinformatics, Quartier Sorge - Batiment Genopode, 1015 Lausanne, Switzerland
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Sun S, Kong L, Yu H, Li Q. The complete mitochondrial DNA of Tegillarca granosa and comparative mitogenomic analyses of three Arcidae species. Gene 2014; 557:61-70. [PMID: 25499696 DOI: 10.1016/j.gene.2014.12.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 12/05/2014] [Accepted: 12/06/2014] [Indexed: 10/24/2022]
Abstract
To better understand the characteristics and the evolutionary dynamics of mt genomes in Arcidae, the complete mitochondrial genome of Tegillarca granosa was firstly determined and compared with other two Arcidae species (Scapharca broughtonii and Scapharca kagoshimensis). The complete mitochondrial genome of T. granosa was 31,589 bp in length, including 12 protein-coding genes, 2 rRNA genes and 23 tRNA genes, and a major non-coding region. Three tandem repeat fragments were identified in the major non-coding region and the tandem repeat motifs of these fragments can be folded into stem-loop structures. The mitochondrial genome of the three species has several common features such as the AT content, the arrangement of the protein-coding genes, the codon usage of the protein-coding genes and AT/GC skew. However, a high level of variability is presented in the size of the genome, the number of tRNA genes and the length of non-coding sequences in the three mitogenomes. According to the phylogenetic analyses, these mitogenome-level characters are correlated with their phylogenetic relationships. It is the absence of the duplicated tRNAs and large non-coding sequences that are responsible for the length divergence of mitogenomes between T. granosa and other two Arcidae species. The phylogenetic analyses were conducted based on 12 partitioned protein genes, which support the relationship at the family level: (((Pectinidae+Ostreidae)+Mytilidae)+Arcidae).
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Affiliation(s)
- Shao'e Sun
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China.
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
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Merker S, Thomas S, Völker E, Perwitasari-Farajallah D, Feldmeyer B, Streit B, Pfenninger M. Control region length dynamics potentially drives amino acid evolution in tarsier mitochondrial genomes. J Mol Evol 2014; 79:40-51. [PMID: 25008552 DOI: 10.1007/s00239-014-9631-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 06/19/2014] [Indexed: 11/25/2022]
Abstract
Patterns and processes of molecular evolution critically influence inferences in phylogeny and phylogeography. Within primates, a shift in evolutionary rates has been identified as the rationale for contrasting findings from mitochondrial and nuclear DNA studies as to the position of Tarsius. While the latter now seems settled, we sequenced complete mitochondrial genomes of three Sulawesi tarsiers (Tarsius dentatus, T. lariang, and T. wallacei) and analyzed substitution rates among tarsiers and other primates to infer driving processes of molecular evolution. We found substantial length polymorphism of the D-loop within tarsier individuals, but little variation of predominant lengths among them, regardless of species. Length variation was due to repetitive elements in the CSB domain-minisatellite motifs of 35 bp length and microsatellite motifs of 6 bp length. Amino acid evolutionary rates were second highest among major primate taxa relative to nucleotide substitution rates. We observed many radical possibly function-altering amino acid changes that were rarely driven by positive selection and thus potentially slightly deleterious or neutral. We hypothesize that the observed pattern of an increased amino acid evolutionary rate in tarsier mitochondrial genomes may be caused by hitchhiking of slightly deleterious mutations with favored D-loop length variants selected for maximizing replication success within the cell or the mitochondrion.
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Affiliation(s)
- Stefan Merker
- Department of Zoology, State Museum of Natural History Stuttgart, Rosenstein 1, 70191, Stuttgart, Germany,
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Mao X, Dong J, Hua P, He G, Zhang S, Rossiter SJ. Heteroplasmy and ancient translocation of mitochondrial DNA to the nucleus in the Chinese Horseshoe Bat (Rhinolophus sinicus) complex. PLoS One 2014; 9:e98035. [PMID: 24842827 PMCID: PMC4026475 DOI: 10.1371/journal.pone.0098035] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 04/28/2014] [Indexed: 11/18/2022] Open
Abstract
The utility and reliability of mitochondrial DNA sequences in phylogenetic and phylogeographic studies may be compromised by widespread and undetected nuclear mitochondrial copies (numts) as well as heteroplasmy within individuals. Both numts and heteroplasmy are likely to be common across diverse taxa yet few studies have characterised their frequencies and variation at the intra-specific level. Here we report the presence of both numts and heteroplasmy in the mitochondrial control region of the Chinese horseshoe bat Rhinolophus sinicus. In total we generated 123 sequences from 18 bats, which contained two different numt clades (i.e. Numt-1 and Numt-2) and one mtDNA clade. The sequence divergence between Numt-1 and Numt-2 was 16.8% and each numt type was found in all four R. sinicus taxa, suggesting either two ancient translocations of mitochondrial DNA into the nucleus from the same source taxon, or a single translocation from different source taxa that occurred before the split of R. sinicus into different lineages. Within the mtDNA clade, phylogenetic relationships among the four taxa of R. sinicus were similar to those seen in previous results. Based on PCR comparisons, heteroplasmy was inferred between almost all individuals of R. sinicus with respect to sequence variation. Consistent with introgression of mtDNA between Central sinicus and septentrionalis, individuals from these two taxa exhibited similar signatures of repeated sequences in the control region. Our study highlights the importance of testing for the presence of numts and heteroplasmy when applying mtDNA markers to phylogenetic studies.
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Affiliation(s)
- Xiuguang Mao
- Institute of Molecular Ecology and Evolution, Institute for Advanced Studies in Multidisciplinary Science and Technology, East China Normal University, Shanghai, China
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Ji Dong
- Institute of Molecular Ecology and Evolution, Institute for Advanced Studies in Multidisciplinary Science and Technology, East China Normal University, Shanghai, China
| | - Panyu Hua
- Institute of Molecular Ecology and Evolution, Institute for Advanced Studies in Multidisciplinary Science and Technology, East China Normal University, Shanghai, China
| | - Guimei He
- Institute of Molecular Ecology and Evolution, Institute for Advanced Studies in Multidisciplinary Science and Technology, East China Normal University, Shanghai, China
| | - Shuyi Zhang
- Institute of Molecular Ecology and Evolution, Institute for Advanced Studies in Multidisciplinary Science and Technology, East China Normal University, Shanghai, China
| | - Stephen J. Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
- * E-mail:
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35
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Dispersal and social organization in the Neotropical Grey sac-winged bat Balantiopteryx plicata. Behav Ecol Sociobiol 2014. [DOI: 10.1007/s00265-014-1702-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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36
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Ba H, Wu L, Liu Z, Li C. An examination of the origin and evolution of additional tandem repeats in the mitochondrial DNA control region of Japanese sika deer (Cervus Nippon). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:276-81. [PMID: 24621225 DOI: 10.3109/19401736.2014.892077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Tandem repeat units are only detected in the left domain of the mitochondrial DNA control region in sika deer. Previous studies showed that Japanese sika deer have more tandem repeat units than its cousins from the Asian continent and Taiwan, which often have only three repeat units. To determine the origin and evolution of these additional repeat units in Japanese sika deer, we obtained the sequence of repeat units from an expanded dataset of the control region from all sika deer lineages. The functional constraint is inferred to act on the first repeat unit because this repeat has the least sequence divergence in comparison to the other units. Based on slipped-strand mispairing mechanisms, the illegitimate elongation model could account for the addition or deletion of these additional repeat units in the Japanese sika deer population. We also report that these additional repeat units could be occurring in the internal positions of tandem repeat regions, possibly via coupling with a homogenization mechanism within and among these lineages. Moreover, the increased number of repeat units in the Japanese sika deer population could reflect a balance between mutation and selection, as well as genetic drift.
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Affiliation(s)
- Hengxing Ba
- a Institute of Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences , Jilin , People's Republic of China .,b State Key Laboratory for Molecular Biology of Special Economical Animals , Chinese Academy of Agricultural Sciences , Jilin , People's Republic of China , and
| | - Lang Wu
- c Center for Clinical and Translational Science, Mayo Clinic , Rochester , MN , USA
| | - Zongyue Liu
- a Institute of Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences , Jilin , People's Republic of China .,b State Key Laboratory for Molecular Biology of Special Economical Animals , Chinese Academy of Agricultural Sciences , Jilin , People's Republic of China , and
| | - Chunyi Li
- a Institute of Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences , Jilin , People's Republic of China .,b State Key Laboratory for Molecular Biology of Special Economical Animals , Chinese Academy of Agricultural Sciences , Jilin , People's Republic of China , and
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Yu JN, Chung CU, Kwak M. The complete mitochondrial genome sequence of the Korean hare (Lepus coreanus). ACTA ACUST UNITED AC 2013; 26:129-30. [PMID: 23883283 DOI: 10.3109/19401736.2013.815170] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitogenome of the Korean hare (Lepus coreanus) was determined by the long and accurate polymerase chain reaction and primer-walking methods. The mitogenome of the Korean hare is 17,472 bp in length and contains sequences that encode 13 protein genes, 22 tRNAs, 2 rRNAs and a noncoding control region. The mitogenome is arranged in an identical order to that found in most other vertebrates. All mitochondrial genes are encoded on the heavy strand, except for eight tRNA genes and the ND6 gene. The control region contains putative termination associated elements, conserved sequence blocks and short and long tandem repeats motifs.
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Affiliation(s)
- Jeong-Nam Yu
- National Institute of Biological Resources , Incheon , Korea and
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Sun K, Luo L, Zhang Z, Liu S, Feng J. Molecular characteristics and evolution of the mitochondrial control region in three genera (Hipposideridae: Hipposideros Aselliscus and Coelops) of leaf-nosed bats. ACTA ACUST UNITED AC 2013; 24:451-61. [PMID: 23406568 DOI: 10.3109/19401736.2013.766176] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The mitochondrial control region (CR) was sequenced for three genera of Hipposideridae to give a detailed overview of its features. The CR of leaf-nosed bats (1288-1560 bp) was divided into three domains like that of other mammals. In addition to the common conserved blocks (ETAS1, ETAS2, F-B boxes, CSB1, CSB2, and CSB3) found in all species, a CSB1-like element was also detected in the conserved sequence blocks (CSB). Repeated motifs were examined in the ETAS of Aselliscus stoliczkanus (26 bp) and Hipposideros bicolor (80 bp) and were present in the CSB of all individuals (6, 8, 16, and 20 bp). Phylogenetic reconstructions using the CR sequences indicated that the phylogenetic relationships among Hipposideros species were consistent with the results of other molecular and phenetic analyses. Aselliscus and Coelops had a closer relationship. But the central domain could not be used for phylogenetic analyses at family and genus levels due to its high conservation.
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Affiliation(s)
- Keping Sun
- Jilin Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130024, China
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Evolution of an Ancient Microsatellite Hotspot in the Conifer Mitochondrial Genome and Comparison with Other Plants. J Mol Evol 2013; 76:146-57. [DOI: 10.1007/s00239-013-9547-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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40
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Liu YG, Kurokawa T, Sekino M, Tanabe T, Watanabe K. Complete mitochondrial DNA sequence of the ark shell Scapharca broughtonii: an ultra-large metazoan mitochondrial genome. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2012; 8:72-81. [PMID: 23291309 DOI: 10.1016/j.cbd.2012.12.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 12/04/2012] [Accepted: 12/04/2012] [Indexed: 11/17/2022]
Abstract
The complete mitochondrial (mt) genome of the ark shell Scapharca broughtonii was determined using long PCR and a genome walking sequencing strategy with genus-specific primers. The S. broughtonii mt genome (GenBank accession number AB729113) contained 12 protein-coding genes (the atp8 gene is missing, as in most bivalves), 2 ribosomal RNA genes, and 42 transfer tRNA genes, in a length of 46,985 nucleotides for the size of mtDNA with only one copy of the heteroplasmic tandem repeat (HTR) unit. Moreover the S. broughtonii mt genome shows size variation; these genomes ranged in size from about 47 kb to about 50 kb because of variation in the number of repeat sequences in the non-coding region. The mt-genome of S. broughtonii is, to date, the longest reported metazoan mtDNA sequence. Sequence duplication in non-coding region and the formation of HTR arrays were two of the factors responsible for the ultra-large size of this mt genome. All the tRNA genes were found within the S. broughtonii mt genome, unlike the other bivalves usually lacking one or more tRNA genes. Twelve additional specimens were used to analyze the patterns of tandem repeat arrays by PCR amplification and agarose electrophoresis. Each of the 12 specimens displayed extensive heteroplasmy and had 8-10 length variants. The motifs of the HTR arrays are about 353-362 bp and the number of repeats ranges from 1 to 11.
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Affiliation(s)
- Yun-Guo Liu
- Tohoku National Fisheries Research Institute, Fisheries Research Agency, Shiogama, Miyagi, Japan.
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Life in a mosaic landscape: anthropogenic habitat fragmentation affects genetic population structure in a frugivorous bat species. CONSERV GENET 2012. [DOI: 10.1007/s10592-012-0434-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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42
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Limited phylogenetic distribution of a long tandem-repeat cluster in the mitochondrial control region in Bubo (Aves, Strigidae) and cluster variation in Blakiston's fish owl (Bubo blakistoni). Mol Phylogenet Evol 2012; 66:889-97. [PMID: 23211719 DOI: 10.1016/j.ympev.2012.11.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 11/15/2012] [Accepted: 11/20/2012] [Indexed: 11/23/2022]
Abstract
To investigate the phylogenetic position of Blakiston's fish owl (Bubo blakistoni), we sequenced the mitochondrial (mt) DNA control region and cytochrome b (cyt b) for nine Bubo species. Maximum-likelihood analyses of combined control region and cyt b sequences, and cyt b sequences alone, showed that species formerly placed in genus Ketupa comprise a monophyletic group. Unexpectedly, we discovered a long cluster of 20-25 tandem repeat units 77 or 78bp long in the third control region domain in four of the nine Bubo species for which the control region was sequenced (B. blakistoni, B. flavipes, and B. ketupu in the Ketupa clade; B. lacteus), leading to overall control region lengths of 3.0-3.8kpb estimated from agarose gel electrophoresis. The control region in B. lacteus is the longest (3.8kbp) reported to date in vertebrates. Sequencing of eight repeat units at each end of the cluster in 20 B. blakistoni individuals detected several types of repeat units 77 or 78bp long, and six patterns in the order of unit types. The occurrence of a repeat cluster in all three species examined in the Ketupa clade suggests their common ancestor also had a cluster, whereas a maximum parsimony tree showed repeat-unit types grouping by species, rather than by paralog groups, suggesting independent origins of the clusters. We reconcile these results with a turnover model, in which the range in cluster-length variation and unit types at the 5' end are hypothetically functionally constrained by the protein-binding function of the control region, but otherwise there is a continual turnover of units in evolutionary time, with new unit types arising through mutations, proliferating by duplication of single and double repeat blocks, and being lost through deletion. Estimated free energies for reconstructed secondary structures of single and especially pairs of repeat units were higher than for homologous single-unit blocks in species lacking a repeat cluster, supporting slipped-strand mispairing as the mechanism of cluster turnover.
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Song N, Liang AP, Bu CP. A molecular phylogeny of Hemiptera inferred from mitochondrial genome sequences. PLoS One 2012; 7:e48778. [PMID: 23144967 PMCID: PMC3493603 DOI: 10.1371/journal.pone.0048778] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 10/01/2012] [Indexed: 11/18/2022] Open
Abstract
Classically, Hemiptera is comprised of two suborders: Homoptera and Heteroptera. Homoptera includes Cicadomorpha, Fulgoromorpha and Sternorrhyncha. However, according to previous molecular phylogenetic studies based on 18S rDNA, Fulgoromorpha has a closer relationship to Heteroptera than to other hemipterans, leaving Homoptera as paraphyletic. Therefore, the position of Fulgoromorpha is important for studying phylogenetic structure of Hemiptera. We inferred the evolutionary affiliations of twenty-five superfamilies of Hemiptera using mitochondrial protein-coding genes and rRNAs. We sequenced three mitogenomes, from Pyrops candelaria, Lycorma delicatula and Ricania marginalis, representing two additional families in Fulgoromorpha. Pyrops and Lycorma are representatives of an additional major family Fulgoridae in Fulgoromorpha, whereas Ricania is a second representative of the highly derived clade Ricaniidae. The organization and size of these mitogenomes are similar to those of the sequenced fulgoroid species. Our consensus phylogeny of Hemiptera largely supported the relationships (((Fulgoromorpha,Sternorrhyncha),Cicadomorpha),Heteroptera), and thus supported the classic phylogeny of Hemiptera. Selection of optimal evolutionary models (exclusion and inclusion of two rRNA genes or of third codon positions of protein-coding genes) demonstrated that rapidly evolving and saturated sites should be removed from the analyses.
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Affiliation(s)
- Nan Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
- Henan Entry-Exit Inspection and Quarantine Bureau, Jinshui District, Zhengzhou, China
| | - Ai-Ping Liang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Cui-Ping Bu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
- Jiangsu Key Laboratory for Eco-agricultural Biotechnology, Huaiyin Normal University, Huaiyin, China
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Sindičić M, Gomerčić T, Galov A, Polanc P, Huber Đ, Slavica A. Repetitive sequences in Eurasian lynx (Lynx lynx L.) mitochondrial DNA control region. ACTA ACUST UNITED AC 2012; 23:201-7. [DOI: 10.3109/19401736.2012.668894] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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45
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Tikochinski Y, Bendelac R, Barash A, Daya A, Levy Y, Friedmann A. Mitochondrial DNA STR analysis as a tool for studying the green sea turtle (Chelonia mydas) populations: the Mediterranean Sea case study. Mar Genomics 2012; 6:17-24. [PMID: 22578655 DOI: 10.1016/j.margen.2012.01.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Revised: 01/09/2012] [Accepted: 01/15/2012] [Indexed: 11/28/2022]
Abstract
The Mediterranean population of the green sea turtle Chelonia mydas is critically endangered. Genetic analysis of this population using the ordinary haplotyping system, based on sequence analysis of a segment of the mitochondrial DNA (mtDNA) D-loop (control region), revealed very little variation. The most common haplotype, CM-A13, was observed in all but three individuals in hundreds of samples in previous studies. In search for a more informative marker we sequenced the 3' of the mitochondrial control region which contains an AT-rich microsatellite. We found a unique pattern that consists of four AT short tandem repeats (STRs) with varying copy numbers. This allowed us to construct a new haplotyping system composed of four different STR sizes for each mtDNA sequence. Our new mitochondrial STR (mtSTR) haplotyping approach revealed 33 different haplotypes within the nesting and stranded sea turtles along the Mediterranean Israeli seashore. The Israeli coast nesting females had 10 different haplotypes that can be used for monitoring and conservation purposes. The mtSTR haplotyping system can clearly assist in fingerprinting of individual turtles. Moreover, it can be used for estimating phylogenetic distances within populations. This case study shows that the mtSTR haplotyping is applicable for the study of global green sea turtle populations and could also be considered as markers of genetic variability in other species.
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Affiliation(s)
- Y Tikochinski
- School of Marine Sciences, Ruppin Academic Center, Michmoret, Israel.
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46
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Nalls AV, Ammerman LK, Dowler RC. Genetic and Morphologic Variation in the Davis Mountains Cottontail (Sylvilagus robustus). SOUTHWEST NAT 2012. [DOI: 10.1894/0038-4909-57.1.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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47
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Meganathan P, Pagan HJ, McCulloch ES, Stevens RD, Ray DA. Complete mitochondrial genome sequences of three bats species and whole genome mitochondrial analyses reveal patterns of codon bias and lend support to a basal split in Chiroptera. Gene 2012; 492:121-9. [DOI: 10.1016/j.gene.2011.10.038] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2011] [Revised: 10/14/2011] [Accepted: 10/15/2011] [Indexed: 11/26/2022]
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48
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Kim YM, Choi EH, Kim SK, Jang KH, Ryu SH, Hwang UW. Complete mitochondrial genome of the Hodgson's batMyotis formosus(Mammalia, Chiroptera, Vespertilionidae). ACTA ACUST UNITED AC 2011; 22:71-3. [DOI: 10.3109/19401736.2011.624598] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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49
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Yu H, Li Q. Complete mitochondrial DNA sequence of Crassostrea nippona: comparative and phylogenomic studies on seven commercial Crassostrea species. Mol Biol Rep 2011; 39:999-1009. [PMID: 21562763 DOI: 10.1007/s11033-011-0825-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Accepted: 05/03/2011] [Indexed: 02/07/2023]
Abstract
The complete mitochondrial genome of Crassostrea nippona was determined and compared with six other Crassostrea mitogenomes from GenBank in an attempt to shed light on the evolutionary relatedness within Crassostrea. The total length of the mitogenome was 20,030 bp for C. nippona, which was the largest among seven Crassostrea mitogenomes. Among six Asian oysters, the gene order of mitochondrial DNA was identical except for C. nippona with a transposition of trnG. While the American oyster C. virginica and Asian oysters showed broad differences in gene order with relocation of most tRNA genes and indels of duplicated tRNAs and rrnS, indicating the relatively distant relationships between the American oyster and Asian oysters. Different from other six Crassostrea oysters, C. nippona had two repeats of 66 bp in non-coding regions. Pairwise divergence among the seven Crassostrea oysters based on DNA sequences of 12 protein-coding genes ranged from 3.1 to 44.4% (Kimura two-parameter distance, K2P). The close relationship between C. nippona and C. hongkongensis was revealed by K2P of 18.9%. Phylogenetic analyses robustly revealed Crassostrea monophyly, with C. virginica at the basal position. The results of phylogenetic analyses strongly supported C. gigas and C. angulata had the closest relationship, with C. sikamea being the sister taxon. These findings presented here provide a better insight into the relationships within Crassostrea and will be useful for further evolution studies of oysters.
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Affiliation(s)
- Hong Yu
- Fisheries College, Ocean University of China, Yushan Road 5, Qingdao 266003, China
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50
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Kaur T, Ong AHK. Heteroplasmy, Length, and Sequence Characterization of the Mitochondrial Control Region in Tomistoma schlegelii. Biochem Genet 2011; 49:562-75. [DOI: 10.1007/s10528-011-9431-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Accepted: 10/28/2010] [Indexed: 11/28/2022]
Affiliation(s)
- Taranjeet Kaur
- Universiti Tunku Abdul Rahman, Kuala Lumpur, Wilayah Persekutuan, Malaysia
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