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Royle TCA, Guiry EJ, Zhang H, Clark LT, Missal SM, Rabinow SA, James M, Yang DY. Documenting the short-tailed albatross ( Phoebastria albatrus) clades historically present in British Columbia, Canada, through ancient DNA analysis of archaeological specimens. Ecol Evol 2022; 12:e9116. [PMID: 35923939 PMCID: PMC9339763 DOI: 10.1002/ece3.9116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 06/11/2022] [Accepted: 06/23/2022] [Indexed: 11/18/2022] Open
Abstract
The short-tailed albatross (Phoebastria albatrus) is a threatened seabird whose present-day range encompasses much of the North Pacific. Within this species, there are two genetic clades (Clades 1 and 2) that have distinctive morphologies and foraging ecologies. Due to a global population collapse in the late 19th and early 20th centuries, the frequency of these clades among the short-tailed albatross population that historically foraged off British Columbia, Canada, is unclear. To document the species' historical genetic structure in British Columbia, we applied ancient DNA (aDNA) analysis to 51 archaeological short-tailed albatross specimens from the Yuquot site (Borden site number: DjSp-1) that span the past four millennia. We obtained a 141 bp cytochrome b sequence from 43 of the 51 (84.3%) analyzed specimens. Analyses of these sequences indicate 40 of the specimens belong to Clade 1, while 2 belong to Clade 2. We also identified a single specimen with a novel cytochrome b haplotype. Our results indicate that during the past four millennia most of the short-tailed albatrosses foraging near Yuquot belonged to Clade 1, while individuals from other lineages made more limited use of the area. Comparisons with the results of previous aDNA analyses of archaeological albatrosses from Japanese sites suggest the distribution of Clades 1 and 2 differed. While both albatross clades foraged extensively in the Northwest Pacific, Clade 1 albatrosses appear to have foraged along the west coast of Vancouver Island to a greater extent. Due to their differing distributions, these clades may be exposed to different threats.
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Affiliation(s)
- Thomas C. A. Royle
- Ancient DNA Laboratory, Department of ArchaeologySimon Fraser UniversityBurnabyBritish ColumbiaCanada
| | - Eric. J. Guiry
- School of Archaeology and Ancient HistoryUniversity of LeicesterLeicesterUK
- Department of AnthropologyTrent UniversityPeterboroughOntarioCanada
- Department of AnthropologyUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Hua Zhang
- Ancient DNA Laboratory, Department of ArchaeologySimon Fraser UniversityBurnabyBritish ColumbiaCanada
| | - Lauren T. Clark
- Ancient DNA Laboratory, Department of ArchaeologySimon Fraser UniversityBurnabyBritish ColumbiaCanada
| | - Shalegh M. Missal
- Ancient DNA Laboratory, Department of ArchaeologySimon Fraser UniversityBurnabyBritish ColumbiaCanada
| | - Sophie A. Rabinow
- Ancient DNA Laboratory, Department of ArchaeologySimon Fraser UniversityBurnabyBritish ColumbiaCanada
- Department of ArchaeologyUniversity of CambridgeCambridgeUK
| | - Margaretta James
- Land of Maquinna Cultural SocietyMowachaht/Muchalaht First NationTsaxana (Gold River)British ColumbiaCanada
| | - Dongya Y. Yang
- Ancient DNA Laboratory, Department of ArchaeologySimon Fraser UniversityBurnabyBritish ColumbiaCanada
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Lucas T, Vincent B, Eric P. Translocation of mitochondrial DNA into the nuclear genome blurs phylogeographic and conservation genetic studies in seabirds. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211888. [PMID: 35719890 PMCID: PMC9198517 DOI: 10.1098/rsos.211888] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 04/19/2022] [Indexed: 05/03/2023]
Abstract
Mitochondrial DNA (mtDNA) translocated into the nuclear genome (numt), when co-analysed with genuine mtDNA, could plague phylogeographic studies. To evaluate numt-related biases in population genetics parameters in birds, which are prone to accumulating numts, we targeted the mitochondrial mt-cytb gene. We looked at 13 populations of Audubon's shearwater (Puffinus lherminieri), including five mitochondrial lineages. mt-cytb homologue and paralogue (numt) sequences were determined by Sanger sequencing with and without prior exonuclease digestion of nuclear DNA. Numts formed monophyletic clades corresponding to three of the five mitochondrial lineages tested (the remaining two forming a paraphyletic group). Nineteen percent of numt alleles fell outside of their expected mitochondrial clade, a pattern consistent with multiple translocation events, incomplete lineage sorting (ILS), and/or introgression. When co-analysing mt-cytb paralogues and homologues, excluding individuals with ambiguities underestimates genetic diversity (4%) and differentiation (11%) among least-sampled populations. Removing ambiguous sites drops the proportion of inter-lineage genetic variance by 63%. While co-analysing numts with mitochondrial sequences can lead to severe bias and information loss in bird phylogeographic studies, the separate analysis of genuine mitochondrial loci and their nuclear paralogues can shed light on numt molecular evolution, as well as evolutionary processes such as ILS and introgression.
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Affiliation(s)
- Torres Lucas
- Centre d'Etudes Biologiques de Chizé, UMR 7372, CNRS - La Rochelle Universite, Villiers en Bois, France
- Littoral, Environnement et Sociétés, UMR 7266 CNRS - La Rochelle Université, La Rochelle, France
| | - Bretagnolle Vincent
- Centre d'Etudes Biologiques de Chizé, UMR 7372, CNRS - La Rochelle Universite, Villiers en Bois, France
| | - Pante Eric
- Littoral, Environnement et Sociétés, UMR 7266 CNRS - La Rochelle Université, La Rochelle, France
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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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Kim JI, Do TD, Choi Y, Yeo Y, Kim CB. Characterization and Comparative Analysis of Complete Mitogenomes of Three Cacatua Parrots (Psittaciformes: Cacatuidae). Genes (Basel) 2021; 12:genes12020209. [PMID: 33572592 PMCID: PMC7910981 DOI: 10.3390/genes12020209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 01/26/2021] [Accepted: 01/28/2021] [Indexed: 12/11/2022] Open
Abstract
Cacatua alba, Cacatua galerita, and Cacatua goffiniana are parrots of the family Cacatuidae. Wild populations of these species are declining with C. alba listed by the International Union for the Conservation of Nature and Natural Resources (IUCN) as Endangered. In this study, complete mitogenomes were sequenced for a comparative analysis among the Cacatua species, and a detailed analysis of the control region. Mitogenome lengths of C. alba,C. galerita, and C. goffiniana were 18,894, 18,900, and 19,084 bp, respectively. They included 13 protein coding genes, two ribosomal RNA genes, 24 transfer RNA genes, three degenerated genes, and two control regions. Ten conserved motifs were found in three domains within each of the two control regions. For an evolution of duplicated control regions of Cacatua, domain I and the 3′ end of domain III experienced an independent evolution, while domain II and most of the regions of domain III was subjected to a concerted evolution. Based on a phylogenetic analysis of 37 mitochondrial genes, the genus Cacatua formed a well-supported, monophyletic, crown group within the Cacatuidae. Molecular dating results showed that Cacatua diverged from other genera of Cacatuinae in the middle of Miocene.
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Affiliation(s)
- Jung-Il Kim
- Department of Biotechnology, Sangmyung University, Seoul 03016, Korea; (J.-I.K.); (T.D.D.); (Y.C.)
| | - Thinh Dinh Do
- Department of Biotechnology, Sangmyung University, Seoul 03016, Korea; (J.-I.K.); (T.D.D.); (Y.C.)
| | - Yisoo Choi
- Department of Biotechnology, Sangmyung University, Seoul 03016, Korea; (J.-I.K.); (T.D.D.); (Y.C.)
| | - Yonggu Yeo
- Conservation and Health Center, Seoul Zoo, Gwacheon 13829, Korea;
| | - Chang-Bae Kim
- Department of Biotechnology, Sangmyung University, Seoul 03016, Korea; (J.-I.K.); (T.D.D.); (Y.C.)
- Correspondence: ; Tel.: +82-2-2287-5288
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Urantówka AD, Kroczak A, Mackiewicz P. New view on the organization and evolution of Palaeognathae mitogenomes poses the question on the ancestral gene rearrangement in Aves. BMC Genomics 2020; 21:874. [PMID: 33287726 PMCID: PMC7720580 DOI: 10.1186/s12864-020-07284-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 11/26/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bird mitogenomes differ from other vertebrates in gene rearrangement. The most common avian gene order, identified first in Gallus gallus, is considered ancestral for all Aves. However, other rearrangements including a duplicated control region and neighboring genes have been reported in many representatives of avian orders. The repeated regions can be easily overlooked due to inappropriate DNA amplification or genome sequencing. This raises a question about the actual prevalence of mitogenomic duplications and the validity of the current view on the avian mitogenome evolution. In this context, Palaeognathae is especially interesting because is sister to all other living birds, i.e. Neognathae. So far, a unique duplicated region has been found in one palaeognath mitogenome, that of Eudromia elegans. RESULTS Therefore, we applied an appropriate PCR strategy to look for omitted duplications in other palaeognaths. The analyses revealed the duplicated control regions with adjacent genes in Crypturellus, Rhea and Struthio as well as ND6 pseudogene in three moas. The copies are very similar and were subjected to concerted evolution. Mapping the presence and absence of duplication onto the Palaeognathae phylogeny indicates that the duplication was an ancestral state for this avian group. This feature was inherited by early diverged lineages and lost two times in others. Comparison of incongruent phylogenetic trees based on mitochondrial and nuclear sequences showed that two variants of mitogenomes could exist in the evolution of palaeognaths. Data collected for other avian mitogenomes revealed that the last common ancestor of all birds and early diverging lineages of Neoaves could also possess the mitogenomic duplication. CONCLUSIONS The duplicated control regions with adjacent genes are more common in avian mitochondrial genomes than it was previously thought. These two regions could increase effectiveness of replication and transcription as well as the number of replicating mitogenomes per organelle. In consequence, energy production by mitochondria may be also more efficient. However, further physiological and molecular analyses are necessary to assess the potential selective advantages of the mitogenome duplications.
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Affiliation(s)
- Adam Dawid Urantówka
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, 7 Kozuchowska Street, 51-631 Wroclaw, Poland
| | - Aleksandra Kroczak
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, 7 Kozuchowska Street, 51-631 Wroclaw, Poland
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, 14a Fryderyka Joliot-Curie Street, 50-383 Wrocław, Poland
| | - Paweł Mackiewicz
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, 14a Fryderyka Joliot-Curie Street, 50-383 Wrocław, Poland
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Eda M, Yamasaki T, Izumi H, Tomita N, Konno S, Konno M, Murakami H, Sato F. Cryptic species in a Vulnerable seabird: shorttailed albatross consists of two species. ENDANGER SPECIES RES 2020. [DOI: 10.3354/esr01078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The occurrence of cryptic species within a threatened taxon is rare, but where they do occur, understanding species boundaries is essential for planning an effective conservation strategy. The short-tailed albatross Phoebastria albatrus is a Vulnerable seabird that mainly breeds on Torishima and the Senkaku Islands in the western North Pacific. Although it has been tacitly regarded as a single management unit with 2 breeding sites, the species is known to comprise 2 genetically separated populations (Senkaku-type and Torishima-type). However, morphological examination of birds from both populations has not been conducted owing to the difficulty in accessing the Senkaku Islands. In this study, we examined the morphological differences between immigrants from the Senkaku Islands to Torishima (Senkaku-type) and native birds on Torishima (Torishima-type) and found significant differences in morphological characteristics between the 2 bird types. In general, Torishima-type birds were larger than Senkaku-type birds, whereas Senkaku-type birds had relatively longer beaks. Based on the morphological differences found in this study as well as genetic and ecological differences revealed in previous studies, we believe that Senkaku- and Torishima-type birds should be classified as different cryptic species. To the best of our knowledge, this is the first case of cryptic species being identified in a threatened avian species.
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Affiliation(s)
- M Eda
- Hokkaido University Museum, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0810, Japan
| | - T Yamasaki
- Division of Natural History, Yamashina Institute for Ornithology, Konoyama 115, Abiko 270-1145, Japan
| | - H Izumi
- Hokkaido University Museum, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0810, Japan
| | - N Tomita
- Division of Avian Conservation, Yamashina Institute for Ornithology, Konoyama 115, Abiko 270-1145, Japan
| | - S Konno
- Division of Avian Conservation, Yamashina Institute for Ornithology, Konoyama 115, Abiko 270-1145, Japan
| | - M Konno
- Division of Avian Conservation, Yamashina Institute for Ornithology, Konoyama 115, Abiko 270-1145, Japan
| | - H Murakami
- Division of Avian Conservation, Yamashina Institute for Ornithology, Konoyama 115, Abiko 270-1145, Japan
| | - F Sato
- Division of Avian Conservation, Yamashina Institute for Ornithology, Konoyama 115, Abiko 270-1145, Japan
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Mackiewicz P, Urantówka AD, Kroczak A, Mackiewicz D. Resolving Phylogenetic Relationships within Passeriformes Based on Mitochondrial Genes and Inferring the Evolution of Their Mitogenomes in Terms of Duplications. Genome Biol Evol 2019; 11:2824-2849. [PMID: 31580435 PMCID: PMC6795242 DOI: 10.1093/gbe/evz209] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/30/2019] [Indexed: 12/29/2022] Open
Abstract
Mitochondrial genes are placed on one molecule, which implies that they should carry consistent phylogenetic information. Following this advantage, we present a well-supported phylogeny based on mitochondrial genomes from almost 300 representatives of Passeriformes, the most numerous and differentiated Aves order. The analyses resolved the phylogenetic position of paraphyletic Basal and Transitional Oscines. Passerida occurred divided into two groups, one containing Paroidea and Sylvioidea, whereas the other, Passeroidea and Muscicapoidea. Analyses of mitogenomes showed four types of rearrangements including a duplicated control region (CR) with adjacent genes. Mapping the presence and absence of duplications onto the phylogenetic tree revealed that the duplication was the ancestral state for passerines and was maintained in early diverged lineages. Next, the duplication could be lost and occurred independently at least four times according to the most parsimonious scenario. In some lineages, two CR copies have been inherited from an ancient duplication and highly diverged, whereas in others, the second copy became similar to the first one due to concerted evolution. The second CR copies accumulated over twice as many substitutions as the first ones. However, the second CRs were not completely eliminated and were retained for a long time, which suggests that both regions can fulfill an important role in mitogenomes. Phylogenetic analyses based on CR sequences subjected to the complex evolution can produce tree topologies inconsistent with real evolutionary relationships between species. Passerines with two CRs showed a higher metabolic rate in relation to their body mass.
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Affiliation(s)
- Paweł Mackiewicz
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, Poland
| | - Adam Dawid Urantówka
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, Poland
| | - Aleksandra Kroczak
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, Poland
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, Poland
| | - Dorota Mackiewicz
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, Poland
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Urantówka AD, Kroczak A, Silva T, Padrón RZ, Gallardo NF, Blanch J, Blanch B, Mackiewicz P. New Insight into Parrots' Mitogenomes Indicates That Their Ancestor Contained a Duplicated Region. Mol Biol Evol 2018; 35:2989-3009. [PMID: 30304531 PMCID: PMC6278868 DOI: 10.1093/molbev/msy189] [Citation(s) in RCA: 15] [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] [Indexed: 02/07/2023] Open
Abstract
Mitochondrial genomes of vertebrates are generally thought to evolve under strong selection for size reduction and gene order conservation. Therefore, a growing number of mitogenomes with duplicated regions changes our view on the genome evolution. Among Aves, order Psittaciformes (parrots) is especially noteworthy because of its large morphological, ecological, and taxonomical diversity, which offers an opportunity to study genome evolution in various aspects. Former analyses showed that tandem duplications comprising the control region with adjacent genes are restricted to several lineages in which the duplication occurred independently. However, using an appropriate polymerase chain reaction strategy, we demonstrate that early diverged parrot groups contain mitogenomes with the duplicated region. These findings together with mapping duplication data from other mitogenomes onto parrot phylogeny indicate that the duplication was an ancestral state for Psittaciformes. The state was inherited by main parrot groups and was lost several times in some lineages. The duplicated regions were subjected to concerted evolution with a frequency higher than the rate of speciation. The duplicated control regions may provide a selective advantage due to a more efficient initiation of replication or transcription and a larger number of replicating genomes per organelle, which may lead to a more effective energy production by mitochondria. The mitogenomic duplications were associated with phenotypic features and parrots with the duplicated region can live longer, show larger body mass as well as predispositions to a more active flight. The results have wider implications on the presence of duplications and their evolution in mitogenomes of other avian groups.
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Affiliation(s)
- Adam Dawid Urantówka
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, Wroclaw, Poland
| | - Aleksandra Kroczak
- Department of Genomics, Faculty of Biotechnology, Wrocław University, Wrocław, Poland
| | | | | | | | - Julie Blanch
- Rosewood Bird Gardens & Breeding Farm, Rosewood, QLD, Australia
| | - Barry Blanch
- Rosewood Bird Gardens & Breeding Farm, Rosewood, QLD, Australia
| | - Paweł Mackiewicz
- Department of Genomics, Faculty of Biotechnology, Wrocław University, Wrocław, Poland
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Torres L, Welch AJ, Zanchetta C, Chesser RT, Manno M, Donnadieu C, Bretagnolle V, Pante E. Evidence for a duplicated mitochondrial region in Audubon's shearwater based on MinION sequencing. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 30:256-263. [PMID: 30043666 DOI: 10.1080/24701394.2018.1484116] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Mitochondrial genetic markers have been extensively used to study the phylogenetics and phylogeography of many birds, including seabirds of the order Procellariiformes. Evidence suggests that part of the mitochondrial genome of Procellariiformes, especially albatrosses, is duplicated, but no DNA fragment covering the entire duplication has been sequenced. We sequenced the complete mitochondrial genome of a non-albatross species of Procellariiformes, Puffinus lherminieri (Audubon's shearwater) using the long-read MinION (ONT) technology. Two mitogenomes were assembled from the same individual, differing by 52 SNPs and in length. The shorter was 19 kb long while the longer was 21 kb, due to the presence of two identical copies of nad6, three tRNA, and two dissimilar copies of the control region (CR). Contrary to albatrosses, cob was not duplicated. We further detected a complex repeated region of undetermined length between the CR and 12S. Long-read sequencing suggests heteroplasmy and a novel arrangement within the duplicated region, indicating a complex evolution of the mitogenome in Procellariiformes.
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Affiliation(s)
- Lucas Torres
- a Centre d'Etudes Biologiques de Chizé, UMR 7372, CNRS , Université de La Rochelle , Villiers en Bois , France.,b Littoral, Environnement et Sociétés, UMR 7266 CNRS , Université de La Rochelle , La Rochelle , France
| | | | - Catherine Zanchetta
- d Centre INRA de Toulouse Midi-Pyrénées , US1426 Get-PlaGe , Castanet-Tolosan , France
| | - R Terry Chesser
- e USGS Patuxent Wildlife Research Center , National Museum of Natural History, Smithsonian Institution , Washington , DC , USA
| | - Maxime Manno
- d Centre INRA de Toulouse Midi-Pyrénées , US1426 Get-PlaGe , Castanet-Tolosan , France
| | - Cécile Donnadieu
- d Centre INRA de Toulouse Midi-Pyrénées , US1426 Get-PlaGe , Castanet-Tolosan , France
| | - Vincent Bretagnolle
- a Centre d'Etudes Biologiques de Chizé, UMR 7372, CNRS , Université de La Rochelle , Villiers en Bois , France
| | - Eric Pante
- b Littoral, Environnement et Sociétés, UMR 7266 CNRS , Université de La Rochelle , La Rochelle , France
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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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Deguchi T, Sato F, Eda M, Izumi H, Suzuki H, Suryan RM, Lance EW, Hasegawa H, Ozaki K. Translocation and hand-rearing result in short-tailed albatrosses returning to breed in the Ogasawara Islands 80 years after extirpation. Anim Conserv 2016. [DOI: 10.1111/acv.12322] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- T. Deguchi
- Division of Avian Conservation; Yamashina Institute for Ornithology; Abiko Japan
| | - F. Sato
- Division of Avian Conservation; Yamashina Institute for Ornithology; Abiko Japan
| | - M. Eda
- Hokkaido University Museum; Hokkaido University; Sapporo Japan
| | - H. Izumi
- Hokkaido University Museum; Hokkaido University; Sapporo Japan
| | - H. Suzuki
- Institute of Boninology; Ogasawara Japan
| | - R. M. Suryan
- Department of Fisheries and Wildlife; Hatfield Marine Science Center; Oregon State University; Newport OR USA
| | - E. W. Lance
- Endangered Species Branch; Anchorage Fish and Wildlife Field Office; Anchorage AK USA
| | - H. Hasegawa
- Department of Biology; Toho University; Funabashi Japan
| | - K. Ozaki
- Division of Avian Conservation; Yamashina Institute for Ornithology; Abiko Japan
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Akiyama T, Nishida C, Momose K, Onuma M, Takami K, Masuda R. Gene duplication and concerted evolution of mitochondrial DNA in crane species. Mol Phylogenet Evol 2016; 106:158-163. [PMID: 27693570 DOI: 10.1016/j.ympev.2016.09.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 06/10/2016] [Accepted: 09/28/2016] [Indexed: 11/25/2022]
Abstract
The gene duplication in mitochondrial DNA (mtDNA) has been reported in diverse bird taxa so far. Although many phylogenetic and population genetic analyses of cranes were carried out based on mtDNA diversity, whether mtDNA contains duplicated regions is unknown. To address the presence or absence of gene duplication in cranes and investigate the molecular evolutionary features of crane mtDNA, we analyzed the gene organization and the molecular phylogeny of mtDNA from 13 crane species. We found that the mtDNA in 13 crane species shared a tandem duplicated region, which consists of duplicated sequence sets including cytochrome b (Cytb), NADH6, control region (CR) and three genes of tRNA. The gene order in the duplicated region was identical among all the 13 crane species, and the nucleotide sequences found within each individual showed high similarities. In addition, phylogenetic trees based on homologous sequences of CR and Cytb indicated the possibility of concerted evolution among the duplicated genes. The results suggested that the duplication event occurred in the common ancestor of crane species or some older ancestors.
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Affiliation(s)
- Takuya Akiyama
- Department of Natural History Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Chizuko Nishida
- Department of Natural History Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan; Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | | | - Manabu Onuma
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Tsukuba 305-8506, Japan
| | - Kazutoshi Takami
- Osaka Municipal Tennoji Zoological Gardens, Osaka 543-0063, Japan
| | - Ryuichi Masuda
- Department of Natural History Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan; Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan.
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Lounsberry ZT, Brown SK, Collins PW, Henry RW, Newsome SD, Sacks BN. Next-generation sequencing workflow for assembly of nonmodel mitogenomes exemplified with North Pacific albatrosses (Phoebastriaspp.). Mol Ecol Resour 2015; 15:893-902. [DOI: 10.1111/1755-0998.12365] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 12/12/2014] [Accepted: 12/18/2014] [Indexed: 01/23/2023]
Affiliation(s)
- Z. T. Lounsberry
- Mammalian Ecology and Conservation Unit; Veterinary Genetics Laboratory; School of Veterinary Medicine; University of California, Davis; One Shields Avenue/Old Davis Rd. Davis CA 95616 USA
| | - S. K. Brown
- Mammalian Ecology and Conservation Unit; Veterinary Genetics Laboratory; School of Veterinary Medicine; University of California, Davis; One Shields Avenue/Old Davis Rd. Davis CA 95616 USA
| | - P. W. Collins
- Santa Barbara Museum of Natural History; 2559 Puesta Del Sol Santa Barbara CA 93105 USA
| | - R. W. Henry
- Institute for Marine Sciences; Center for Ocean Health; Long Marine Lab; University of California, Santa Cruz; 100 Shaffer Road Santa Cruz CA 95060 USA
| | - S. D. Newsome
- Department of Biology; University of New Mexico; 167 Castetter Hall, MSC03 2020 Albuquerque NM 87131 USA
| | - B. N. Sacks
- Mammalian Ecology and Conservation Unit; Veterinary Genetics Laboratory; School of Veterinary Medicine; University of California, Davis; One Shields Avenue/Old Davis Rd. Davis CA 95616 USA
- Department of Population Health and Reproduction; School of Veterinary Medicine; University of California, Davis; One Shields Avenue/Old Davis Rd. Davis CA 95616 USA
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The Present Status of Available Genetic Information for Avian Species Distributing in Japan and on the List of “Nationally Endangered Species of Wild Fauna and Flora”. J Poult Sci 2015. [DOI: 10.2141/jpsa.0150015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Zhou X, Lin Q, Fang W, Chen X. The complete mitochondrial genomes of sixteen ardeid birds revealing the evolutionary process of the gene rearrangements. BMC Genomics 2014; 15:573. [PMID: 25001581 PMCID: PMC4111848 DOI: 10.1186/1471-2164-15-573] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Accepted: 07/03/2014] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND The animal mitochondrial genome is generally considered to be under selection for both compactness and gene order conservation. As more mitochondrial genomes are sequenced, mitochondrial duplications and gene rearrangements have been frequently identified among diverse animal groups. Although several mechanisms of gene rearrangement have been proposed thus far, more observational evidence from major taxa is needed to validate specific mechanisms. In the current study, the complete mitochondrial DNA of sixteen bird species from the family Ardeidae was sequenced and the evolution of mitochondrial gene rearrangements was investigated. The mitochondrial genomes were then used to review the phylogenies of these ardeid birds. RESULTS The complete mitochondrial genome sequences of the sixteen ardeid birds exhibited four distinct mitochondrial gene orders in which two of them, named as "duplicate tRNA(Glu)-CR" and "duplicate tRNAThr-tRNA(Pro) and CR", were newly discovered. These gene rearrangements arose from an evolutionary process consistent with the tandem duplication--random loss model (TDRL). Additionally, duplications in these gene orders were near identical in nucleotide sequences within each individual, suggesting that they evolved in concert. Phylogenetic analyses of the sixteen ardeid species supported the idea that Ardea ibis, Ardea modesta and Ardea intermedia should be classified as genus Ardea, and Ixobrychus flavicollis as genus Ixobrychus, and indicated that within the subfamily Ardeinae, Nycticorax nycticorax is closely related to genus Egretta and that Ardeola bacchus and Butorides striatus are closely related to the genus Ardea. CONCLUSIONS The duplicate tRNAThr-CR gene order is found in most ardeid lineages, suggesting this gene order is the ancestral pattern within these birds and persisted in most lineages via concerted evolution. In two independent lineages, when the concerted evolution stopped in some subsections due to the accumulation of numerous substitutions and deletions, the duplicate tRNAThr-CR gene order was transformed into three other gene orders. The phylogenetic trees produced from concatenated rRNA and protein coding genes have high support values in most nodes, indicating that the mitochondrial genome sequences are promising markers for resolving the phylogenetic issues of ardeid birds when more taxa are added.
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Affiliation(s)
- Xiaoping Zhou
- Key Laboratory of Ministry of Education for Coast and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102 People’s Republic of China
| | - Qingxian Lin
- Key Laboratory of Ministry of Education for Coast and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102 People’s Republic of China
| | - Wenzhen Fang
- Key Laboratory of Ministry of Education for Coast and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102 People’s Republic of China
| | - Xiaolin Chen
- Key Laboratory of Ministry of Education for Coast and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102 People’s Republic of China
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Kawashima Y, Nishihara H, Akasaki T, Nikaido M, Tsuchiya K, Segawa S, Okada N. The complete mitochondrial genomes of deep-sea squid (Bathyteuthis abyssicola), bob-tail squid (Semirossia patagonica) and four giant cuttlefish (Sepia apama, S. latimanus, S. lycidas and S. pharaonis), and their application to the phylogenetic analysis of Decapodiformes. Mol Phylogenet Evol 2013; 69:980-93. [PMID: 23811434 DOI: 10.1016/j.ympev.2013.06.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Revised: 06/01/2013] [Accepted: 06/13/2013] [Indexed: 11/18/2022]
Abstract
We determined the complete mitochondrial (mt) genomes of the deep-sea squid (Bathyteuthis abyssicola; supperfamily Bathyteuthoidea), the bob-tail squid (Semirossia patagonica; order Sepiolida) and four giant cuttlefish (Sepia apama, S. latimanus, S. lycidas and S. pharaonis; order Sepiida). The unique structures of the mt genomes of Bathyteuthis and Semirossia provide new information about the evolution of decapodiform mt genomes. We show that the mt genome of B. abyssicola, like those of other oegopsids studied so far, has two long duplicated regions that include seven genes (COX1-3, ATP6 and ATP8, tRNA(Asn), and either ND2 or ND3) and that one of the duplicated COX3 genes has lost its function. The mt genome of S. patagonica is unlike any other decapodiforms and, like Nautilus, its ATP6 and ATP8 genes are not adjacent to each other. The four giant cuttlefish have identical mt gene order to other cuttlefish determined to date. Molecular phylogenetic analyses using maximum likelihood and Bayesian methods suggest that traditional order Sepioidea (Sepiolida+Sepiida) is paraphyletic and Sepia (cuttlefish) has the sister-relationship with all other decapodiforms. Taking both the phylogenetic analyses and the mt gene order analyses into account, it is likely that the octopus-type mt genome is an ancestral state and that it had maintained from at least the Cephalopoda ancestor to the common ancestor of Oegopsida, Myopsida and Sepiolida.
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Affiliation(s)
- Yuumi Kawashima
- Central Customs Laboratory, 6-3-5, Kashiwanoha, Kashiwa-shi, Chiba 277-0082, Japan
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Effects of long-term isolation on genetic variation and within-island population genetic structure in Christmas Island (Indian Ocean) seabirds. CONSERV GENET 2012. [DOI: 10.1007/s10592-012-0390-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Eda M, Koike H, Kuro-o M, Mihara S, Hasegawa H, Higuchi H. Inferring the ancient population structure of the vulnerable albatross Phoebastria albatrus, combining ancient DNA, stable isotope, and morphometric analyses of archaeological samples. CONSERV GENET 2011. [DOI: 10.1007/s10592-011-0270-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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The Rate and Tract Length of Gene Conversion between Duplicated Genes. Genes (Basel) 2011; 2:313-31. [PMID: 24710193 PMCID: PMC3924818 DOI: 10.3390/genes2020313] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Revised: 03/11/2011] [Accepted: 03/17/2011] [Indexed: 11/26/2022] Open
Abstract
Interlocus gene conversion occurs such that a certain length of DNA fragment is non-reciprocally transferred (copied and pasted) between paralogous regions. To understand the rate and tract length of gene conversion, there are two major approaches. One is based on mutation-accumulation experiments, and the other uses natural DNA sequence variation. In this review, we overview the two major approaches and discuss their advantages and disadvantages. In addition, to demonstrate the importance of statistical analysis of empirical and evolutionary data for estimating tract length, we apply a maximum likelihood method to several data sets.
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