1
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Cruz CEF, Funkler GR, Zani ALS, Wagner PGC, Andretta I, Segura LN, Fagundes NJR. A Preliminary Assessment of the Potential Health and Genetic Impacts of Releasing Confiscated Passerines Into the Wild: A Reduced-Risk Approach. Front Vet Sci 2021; 8:679049. [PMID: 34708099 PMCID: PMC8542797 DOI: 10.3389/fvets.2021.679049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 09/13/2021] [Indexed: 11/13/2022] Open
Abstract
The illegal capture and trade of wild birds have long been threats to biodiversity. The rehabilitation and release of confiscated animals may be a useful conservation tool in species management. However, differences between populations regarding health (e.g., different pathogens) and adaptation (e.g., local adaptation) must be taken into account, since both can negatively impact the recipient population. In this pilot study, we used two of the most illegally trafficked Brazilian wild passerine species, namely the red-crested cardinal (Paroaria coronata) and green-winged saltator (Saltator similis) as case studies and assessed some of the health threats that the release of confiscated passerines may pose to free-living birds. We also investigated the level of difference in mitochondrial genetic structure among populations living in different ecoregions. Blood, feces, and oropharyngeal swabs from confiscated (n = 115) and free-living (n = 120) passerines from the release sites were tested for the Newcastle disease virus, Salmonella spp., and Mycoplasma gallisepticum. These are considered major avian diseases by the Brazilian National Avian Health Program. We analyzed mtDNA to study the difference in genetic structure between populations using samples from 127 free-living passerines. We found no evidence of the Newcastle disease virus or Salmonella spp. in confiscated or free-living passerines from either species. However, the levels of infection with M. galissepticum detected in our study for red-crested cardinals and green-winged saltators calls for a high degree of caution in captive release programs. The difference in genetic structure between populations occurring in different regions was low, and was not significant between those from the Pampa/Subtropical Grasslands region. These results suggest that it may be possible to establish a cost-effective and sensitive protocol for releasing confiscated songbirds, provided that further genome-wide studies indicate that the functional genetic diversity among (at least some of the) populations is also low.
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Affiliation(s)
- Cláudio E F Cruz
- Centro de Estudos em Manejo de Aves Silvestres, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Programa de Pós-Graduação em Ciências Veterinárias, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Gustavo R Funkler
- Programa de Pós-Graduação em Ciências Veterinárias, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Laboratório Porto Belo, Porto Alegre, Brazil
| | - André L S Zani
- Programa de Pós-Graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Paulo G C Wagner
- Centro de Triagem de Animais Silvestres, Instituto Brasileiro do Meio Ambiente e dos Recursos Naturais Renováveis, Porto Alegre, Brazil
| | - Inês Andretta
- Laboratório de Ensino Zootécnico, Faculdade de Agronomia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Luciano N Segura
- Museo de La Plata, Sección Ornitología, Universidad Nacional de La Plata, La Plata, Argentina
| | - Nelson J R Fagundes
- Programa de Pós-Graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Programa de Pós-Graduação em Biologia Animal, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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2
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Camacho-Sánchez FY, Aguirre AA, Narváez-Zapata JA, Zavala-Norzagaray AA, Ley-Quiñónez CP, Acosta-Sánchez HH, Rodriguez-González H, Delgado-Trejo C, Reyes-López MA. DNA barcode analysis of the endangered green turtle ( Chelonia mydas) in Mexico 1. Genome 2021; 64:879-891. [PMID: 33555972 DOI: 10.1139/gen-2019-0213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Technological and analytical advances to study evolutionary biology, ecology, and conservation of green turtles (Chelonia mydas) are realized through molecular approaches including DNA barcoding. We characterized the usefulness of COI DNA barcodes in green turtles in Mexico to better understand genetic divergence and other genetic parameters of this species. We analyzed 63 sequences, including 25 from green turtle field specimens collected from the Gulf of Mexico and from the Mexican Pacific and 38 already present in the Barcode of Life Data Systems (BOLD). A total of 13 haplotypes were identified with four novel haplotypes from the Pacific Ocean and three novel haplotypes from the Atlantic Ocean. Intraspecific distance values among COI gene sequences by two different models were 0.01, demonstrating that there is not a subdivision for green turtle species. Otherwise, the interspecific distance interval ranged from 0.07 to 0.13, supporting a clear subdivision among all sea turtle species. Haplotype and total nucleotide diversity values of the COI gene reflect a medium genetic diversity average. Green turtles of the Mexican Pacific showed common haplotypes to some Australian and Chinese turtles, but different from the haplotypes of the Mexican Atlantic. COI analysis revealed new haplotypes and confirmed that DNA barcodes were useful for evaluation of the population diversity of green turtles in Mexico.
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Affiliation(s)
- Fátima Yedith Camacho-Sánchez
- Conservation Medicine Lab, Centro de Biotecnología Genómica-Instituto Politécnico Nacional, Reynosa, Tamaulipas, Mexico.,Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, USA
| | - A Alonso Aguirre
- Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, USA
| | - José Alberto Narváez-Zapata
- Laboratorio de Biotecnología Industrial, Centro de Biotecnología Genómica-Instituto Politécnico Nacional, Reynosa, Tamaulipas, Mexico
| | - Alan A Zavala-Norzagaray
- Laboratorio de Vida Silvestre, Departamento de Medio Ambiente, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional, Unidad Sinaloa, Instituto Politécnico Nacional, Guasave, Sinaloa, Mexico
| | - Cesar P Ley-Quiñónez
- Laboratorio de Vida Silvestre, Departamento de Medio Ambiente, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional, Unidad Sinaloa, Instituto Politécnico Nacional, Guasave, Sinaloa, Mexico
| | - H Hugo Acosta-Sánchez
- United Nations Development Programme-Comisión Nacional de Áreas Naturales Protegidas, Ciudad Victoria, Tamaulipas, Mexico
| | - Hervey Rodriguez-González
- Laboratorio Nutrición Acuícola, Departamento de Acuacultura, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional, Unidad Sinaloa, Instituto Politécnico Nacional, Guasave, Sinaloa, Mexico
| | - Carlos Delgado-Trejo
- Departamento de Ecología Marina, Proyecto Tortuga Negra, Instituto de Investigaciones sobre los Recursos Naturales, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - Miguel Angel Reyes-López
- Conservation Medicine Lab, Centro de Biotecnología Genómica-Instituto Politécnico Nacional, Reynosa, Tamaulipas, Mexico
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Albrecht F, Hering J, Fuchs E, Illera JC, Ihlow F, Shannon TJ, Collinson JM, Wink M, Martens J, Päckert M. Phylogeny of the Eurasian Wren Nannus troglodytes (Aves: Passeriformes: Troglodytidae) reveals deep and complex diversification patterns of Ibero-Maghrebian and Cyrenaican populations. PLoS One 2020; 15:e0230151. [PMID: 32191719 PMCID: PMC7082076 DOI: 10.1371/journal.pone.0230151] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 02/22/2020] [Indexed: 11/19/2022] Open
Abstract
The Mediterranean Basin represents a Global Biodiversity Hotspot where many organisms show high inter- and intraspecific differentiation. Extant phylogeographic patterns of terrestrial circum-Mediterranean faunas were mainly shaped through Pleistocene range shifts and range fragmentations due to retreat into different glacial refugia. Thus, several extant Mediterranean bird species have diversified by surviving glaciations in different hospitable refugia and subsequently expanded their distribution ranges during the Holocene. Such a scenario was also suggested for the Eurasian Wren (Nannus troglodytes) despite the lack of genetic data for most Mediterranean subspecies. Our phylogenetic multi-locus analysis comprised 18 out of 28 currently accepted subspecies of N. troglodytes, including all but one subspecies which are present in the Mediterranean Basin. The resulting phylogenetic reconstruction dated the onset of the entire Holarctic radiation of three Nannus species to the early Pleistocene. In the Eurasian Wren, two North African subspecies represented separate basal lineages from the Maghreb (N. t. kabylorum) and from the Libyan Cyrenaica (N. t. juniperi), being only distantly related to other Mediterranean populations. Although N. troglodytes appeared to be paraphyletic with respect to the Nearctic Winter Wren (N. hiemalis), respective nodes did not receive strong statistical support. In contrast, paraphyly of the Ibero-Maghrebian taxon N. t. kabylorum was strongly supported. Southern Iberian populations of N. t. kabylorum did not clade with Maghrebian populations of the same subspecies but formed a sister clade to a highly diverse European clade (including nominate N. t. troglodytes and eight further taxa). In accordance with a pattern also found in other birds, Eurasian populations were split into a western clade (Europe, Caucasus) and an eastern clade (Central Asia, Sino-Himalayas, East Asia). This complex phylogeographic pattern revealed cryptic diversification in N. troglodytes, especially in the Iberio-Maghrebian region.
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Affiliation(s)
- Frederik Albrecht
- Museum of Zoology, Senckenberg Natural History Collections Dresden, Senckenberg|Leibniz Institution for Biodiversity and Earth System Research, Dresden, Saxony, Germany
- * E-mail:
| | - Jens Hering
- Verein Sächsischer Ornithologen e.V., Limbach-Oberfrohna, Saxony, Germany
| | - Elmar Fuchs
- Verein Sächsischer Ornithologen e.V., Weimar, Thuringia, Germany
| | - Juan Carlos Illera
- Research Unit of Biodiversity (UO-CSIC-PA), Oviedo University, Asturias, Spain
| | - Flora Ihlow
- Museum of Zoology, Senckenberg Natural History Collections Dresden, Senckenberg|Leibniz Institution for Biodiversity and Earth System Research, Dresden, Saxony, Germany
| | - Thomas J. Shannon
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, Scotland, United Kingdom
| | - J. Martin Collinson
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, Scotland, United Kingdom
| | - Michael Wink
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Baden-Württemberg, Germany
| | - Jochen Martens
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Rhineland-Palatinate, Germany
| | - Martin Päckert
- Museum of Zoology, Senckenberg Natural History Collections Dresden, Senckenberg|Leibniz Institution for Biodiversity and Earth System Research, Dresden, Saxony, Germany
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Yang S, Huo Y, Wang H, Ji J, Chen W, Huang Y. The spatio-temporal features of chicken mitochondrial ND2 gene heteroplasmy and the effects of nutrition factors on this gene. Sci Rep 2020; 10:2972. [PMID: 32075998 PMCID: PMC7031424 DOI: 10.1038/s41598-020-59703-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 01/17/2020] [Indexed: 11/25/2022] Open
Abstract
Mitochondrial heterogeneity is the presence of two or more types of mitochondrial (mt)DNA in the same individual/tissue/cell. It is closely related to animal health and disease. ND2 is a protein-coding gene in mtDNA, which participates in mitochondrial respiratory chain and oxidative phosphorylation. In previous studies, we observed that the mt.A5703T and mt.T5727G sites in the ND2 gene were the heteroplasmic variation sites. We used pyrophosphate sequencing technology to examine chicken mt.A5703T and mt.T5727G heteroplasmic sites in the ND2 gene, in different tissues and at different development stages in chickens. We also investigated whether nutritional factors could affect the mt.A5703T and mt.T5727G heteroplasmy. Our results showed that chicken mt.A5703T and mt.T5727G heteroplasmy had clear spatio-temporal specificities, which varied between tissues/development stages. The mtDNA heterogeneity was relatively stable upon nutrition intervention, 30% dietary energy restriction (from 18 to 48 days old) and different types of dietary fats (at 5% concentration, from 1 to 42 days old) did not change the breast muscle heteroplasmy of broilers at the mt.A5703T and mt.T5727G sites. In addition, multiple potential heteroplasmic sites were detected by clone sequencing in the ND2 region, which potentially reflected abundant heteroplasmy in the chicken mitochondrial genome. These results provide an important reference for further research on heteroplasmy in chicken mitochondria.
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Affiliation(s)
- Suliang Yang
- College of Livestock Husbandry and Veterinary Engineering, Henan Agricultural University, No. 15 Longzi Lake University Campus, Zhengzhou, 450046, P.R. China
| | - Yangyang Huo
- College of Livestock Husbandry and Veterinary Engineering, Henan Agricultural University, No. 15 Longzi Lake University Campus, Zhengzhou, 450046, P.R. China
| | - Huanjie Wang
- College of Livestock Husbandry and Veterinary Engineering, Henan Agricultural University, No. 15 Longzi Lake University Campus, Zhengzhou, 450046, P.R. China
| | - Jiefei Ji
- College of Livestock Husbandry and Veterinary Engineering, Henan Agricultural University, No. 15 Longzi Lake University Campus, Zhengzhou, 450046, P.R. China
| | - Wen Chen
- College of Livestock Husbandry and Veterinary Engineering, Henan Agricultural University, No. 15 Longzi Lake University Campus, Zhengzhou, 450046, P.R. China
| | - Yanqun Huang
- College of Livestock Husbandry and Veterinary Engineering, Henan Agricultural University, No. 15 Longzi Lake University Campus, Zhengzhou, 450046, P.R. China.
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5
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Jiang L, Peng L, Tang M, You Z, Zhang M, West A, Ruan Q, Chen W, Merilä J. Complete mitochondrial genome sequence of the Himalayan Griffon, Gyps himalayensis (Accipitriformes: Accipitridae): Sequence, structure, and phylogenetic analyses. Ecol Evol 2019; 9:8813-8828. [PMID: 31410282 PMCID: PMC6686361 DOI: 10.1002/ece3.5433] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/12/2019] [Accepted: 06/17/2019] [Indexed: 11/12/2022] Open
Abstract
This is the first study to describe the mitochondrial genome of the Himalayan Griffon, Gyps himalayensis, which is an Old World vulture belonging to the family Accipitridae and occurring along the Himalayas and the adjoining Tibetan Plateau. Its mitogenome is a closed circular molecule 17,381 bp in size containing 13 protein-coding genes, 22 tRNA coding genes, two rRNA-coding genes, a control region (CR), and an extra pseudo-control region (CCR) that are conserved in most Accipitridae mitogenomes. The overall base composition of the G. himalayensis mitogenome is 24.55% A, 29.49% T, 31.59% C, and 14.37% G, which is typical for bird mitochondrial genomes. The alignment of the Accipitridae species control regions showed high levels of genetic variation and abundant AT content. At the 5' end of the domain I region, a long continuous poly-C sequence was found. Two tandem repeats were found in the pseudo-control regions. Phylogenetic analysis with Bayesian inference and maximum likelihood based on 13 protein-coding genes indicated that the relationships at the family level were (Falconidae + (Cathartidae + (Sagittariidae + (Accipitridae + Pandionidae))). In the Accipitridae clade, G. himalayensis is more closely related to Aegypius monachus than to Spilornis cheela. The complete mitogenome of G. himalayensis provides a potentially useful resource for further exploration of the taxonomic status and phylogenetic history of Gyps species.
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Affiliation(s)
- Lichun Jiang
- Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and TechnologyMianyang Normal UniversityMianyangSichuanChina
- Ecological Security and Protection Key Laboratory of Sichuan ProvinceMianyang Normal UniversityMianyangSichuanChina
| | - Liqing Peng
- Ecological Security and Protection Key Laboratory of Sichuan ProvinceMianyang Normal UniversityMianyangSichuanChina
| | - Min Tang
- Ecological Security and Protection Key Laboratory of Sichuan ProvinceMianyang Normal UniversityMianyangSichuanChina
| | - Zhangqiang You
- Ecological Security and Protection Key Laboratory of Sichuan ProvinceMianyang Normal UniversityMianyangSichuanChina
| | - Min Zhang
- Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and TechnologyMianyang Normal UniversityMianyangSichuanChina
| | - Andrea West
- Centre for Integrative Ecology, School of Life and Environmental SciencesDeakin UniversityGeelongVicAustralia
| | - Qiping Ruan
- Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and TechnologyMianyang Normal UniversityMianyangSichuanChina
| | - Wei Chen
- Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and TechnologyMianyang Normal UniversityMianyangSichuanChina
- Ecological Security and Protection Key Laboratory of Sichuan ProvinceMianyang Normal UniversityMianyangSichuanChina
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty Biological & Environmental SciencesUniversity of HelsinkiHelsinkiFinland
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Bronstein O, Kroh A, Haring E. Mind the gap! The mitochondrial control region and its power as a phylogenetic marker in echinoids. BMC Evol Biol 2018; 18:80. [PMID: 29848319 PMCID: PMC5977486 DOI: 10.1186/s12862-018-1198-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 05/18/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND In Metazoa, mitochondrial markers are the most commonly used targets for inferring species-level molecular phylogenies due to their extremely low rate of recombination, maternal inheritance, ease of use and fast substitution rate in comparison to nuclear DNA. The mitochondrial control region (CR) is the main non-coding area of the mitochondrial genome and contains the mitochondrial origin of replication and transcription. While sequences of the cytochrome oxidase subunit 1 (COI) and 16S rRNA genes are the prime mitochondrial markers in phylogenetic studies, the highly variable CR is typically ignored and not targeted in such analyses. However, the higher substitution rate of the CR can be harnessed to infer the phylogeny of closely related species, and the use of a non-coding region alleviates biases resulting from both directional and purifying selection. Additionally, complete mitochondrial genome assemblies utilizing next generation sequencing (NGS) data often show exceptionally low coverage at specific regions, including the CR. This can only be resolved by targeted sequencing of this region. RESULTS Here we provide novel sequence data for the echinoid mitochondrial control region in over 40 species across the echinoid phylogenetic tree. We demonstrate the advantages of directly targeting the CR and adjacent tRNAs to facilitate complementing low coverage NGS data from complete mitochondrial genome assemblies. Finally, we test the performance of this region as a phylogenetic marker both in the lab and in phylogenetic analyses, and demonstrate its superior performance over the other available mitochondrial markers in echinoids. CONCLUSIONS Our target region of the mitochondrial CR (1) facilitates the first thorough investigation of this region across a wide range of echinoid taxa, (2) provides a tool for complementing missing data in NGS experiments, and (3) identifies the CR as a powerful, novel marker for phylogenetic inference in echinoids due to its high variability, lack of selection, and high compatibility across the entire class, outperforming conventional mitochondrial markers.
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Affiliation(s)
- Omri Bronstein
- Natural History Museum Vienna, Geological-Palaeontological Department, 1010 Vienna, Austria
- Natural History Museum Vienna, Central Research Laboratories, 1010 Vienna, Austria
| | - Andreas Kroh
- Natural History Museum Vienna, Geological-Palaeontological Department, 1010 Vienna, Austria
| | - Elisabeth Haring
- Natural History Museum Vienna, Central Research Laboratories, 1010 Vienna, Austria
- Department of Integrative Zoology, University of Vienna, Vienna, Austria
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7
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Dohms KM, Graham BA, Burg TM. Multilocus genetic analyses and spatial modeling reveal complex population structure and history in a widespread resident North American passerine ( Perisoreus canadensis). Ecol Evol 2017; 7:9869-9889. [PMID: 29238522 PMCID: PMC5723591 DOI: 10.1002/ece3.3478] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 08/08/2017] [Accepted: 08/19/2017] [Indexed: 11/29/2022] Open
Abstract
An increasing body of studies of widely distributed, high latitude species shows a variety of refugial locations and population genetic patterns. We examined the effects of glaciations and dispersal barriers on the population genetic patterns of a widely distributed, high latitude, resident corvid, the gray jay (Perisoreus canadensis), using the highly variable mitochondrial DNA (mtDNA) control region and microsatellite markers combined with species distribution modeling. We sequenced 914 bp of mtDNA control region for 375 individuals from 37 populations and screened seven loci for 402 individuals from 27 populations across the gray jay range. We used species distribution modeling and a range of phylogeographic analyses (haplotype diversity, ΦST, SAMOVA, FST, Bayesian clustering analyses) to examine evolutionary history and population genetic structure. MtDNA and microsatellite markers revealed significant genetic differentiation among populations with high concordance between markers. Paleodistribution models supported at least five potential areas of suitable gray jay habitat during the last glacial maximum and revealed distributions similar to the gray jay's contemporary during the last interglacial. Colonization from and prolonged isolation in multiple refugia is evident. Historical climatic fluctuations, the presence of multiple dispersal barriers, and highly restricted gene flow appear to be responsible for strong genetic diversification and differentiation in gray jays.
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Affiliation(s)
- Kimberly M Dohms
- Department of Biological Sciences University of Lethbridge Lethbridge AB Canada.,Present address: Canadian Wildlife Service, Environment and Climate Change Canada Delta BC Canada
| | - Brendan A Graham
- Department of Biological Sciences University of Windsor Windsor ON Canada
| | - Theresa M Burg
- Department of Biological Sciences University of Lethbridge Lethbridge AB Canada
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Suntrarachun S, Chanhome L, Sumontha M. Phylogenetic analysis of the king cobra, Ophiophagus hannah in Thailand based on mitochondrial DNA sequences. ASIAN BIOMED 2017. [DOI: 10.5372/1905-7415.0802.289] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Abstract
Background: Snakes possess adaptive characteristics of morphology that may result in incorrect reconstruction of phylogeny. Molecular approaches have become the major source of new information for advancing our understanding of evolutionary, genetic relationships, and species identification.
Objective: We studied DNA sequences of Ophiophagus hannah in different parts of Thailand and compared them with those of O. hannah from other countries.
Materials and Methods: We studied the mitochondrial NADH dehydrogenase subunit 2 (ND2) and control region (CR) sequences of 12 individuals O. hannah from different localities across Thailand. Phylogenetic analysis of DNA sequences were compared to the published sequences of O. hannah deposited in NCBI GenBank database from other countries.
Results: O. hannah could be categorized into 2 Clades, 5 haplotypes, and 4 localities based on 43 different nucleotide positions from the 736 bp of ND2 and 673 bp of CR. Clade A was haplotype A from southern Thailand. Clade B consisted of haplotypes B, C, D, and E. Haplotype B and C came from northern Thailand. Haplotype D came from western Thailand, while haplotype E was O. hannah from central Thailand. The DNA sequences of Clade B were similar to the sequences of O. hannah in Myanmar and southern China that are already deposited in NCBI GenBank database.
Conclusion: We found a different genotype of O. hannah from southern Thailand and suggest that this may be a new species of O. hannah.
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Affiliation(s)
- Sunutcha Suntrarachun
- Queen Saovabha Memorial Institute, The Thai Red Cross Society, Bangkok 10330, Thailand
| | - Lawan Chanhome
- Queen Saovabha Memorial Institute, The Thai Red Cross Society, Bangkok 10330, Thailand
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9
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Delmore KE, Kenyon HL, Germain RR, Irwin DE. Phenotypic divergence during speciation is inversely associated with differences in seasonal migration. Proc Biol Sci 2016; 282:rspb.2015.1921. [PMID: 26559951 DOI: 10.1098/rspb.2015.1921] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Differences in seasonal migration might promote reproductive isolation and differentiation by causing populations in migratory divides to arrive on the breeding grounds at different times and/or produce hybrids that take inferior migratory routes. We examined this question by quantifying divergence in song, colour, and morphology between sister pairs of North American migratory birds. We predicted that apparent rates of phenotypic differentiation would differ between pairs that do and do not form migratory divides. Consistent with this prediction, results from mixed effects models and Ornstein-Uhlenbeck models of evolution showed different rates of divergence between these groups; surprisingly, differentiation was greater among non-divide pairs. We interpret this finding as a result of variable rates of population blending and fusion between partially diverged forms. Ancient pairs of populations that subsequently fused are now observed as a single form, whereas those that did not fuse are observable as pairs and included in our study. We propose that fusion of two populations is more likely to occur when they have similar migratory routes and little other phenotypic differentiation that would cause reproductive isolation. By contrast, pairs with migratory divides are more likely to remain reproductively isolated, even when differing little in other phenotypic traits. These findings suggest that migratory differences may be one among several isolating barriers that prevent divergent populations from fusing and thereby increase the likelihood that they will continue differentiating as distinct species.
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Affiliation(s)
- Kira E Delmore
- Department of Zoology, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, Canada V6T1Z4
| | - Haley L Kenyon
- Department of Zoology, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, Canada V6T1Z4
| | - Ryan R Germain
- Department of Forest and Conservation Sciences, University of British Columbia, 2424 Main Mall, Vancouver, British Columbia, Canada V6T1Z4
| | - Darren E Irwin
- Department of Zoology, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, Canada V6T1Z4
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10
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Meng S, Pan T, Sun Z, Bei Y, Meng T, Li G, Wu D, Zhang B. Extremely low genetic diversity of mtDNA control region and remarkable population differentiation of Ichthyophis bannanicus (Amphibia: Gymnophiona). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 28:98-103. [PMID: 26678840 DOI: 10.3109/19401736.2015.1110816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
It is widely accepted that the mitochondrial DNA (mtDNA) control region (CR) gene evolves more quickly than protein-encoding genes, such as ND2 and Cyt b, with few exceptions. However, some species have a different evolution pattern. In the present study, we sequenced the mtDNA CR partial sequences (454 base pairs) of 142 individuals from five sampling sites of Ichthyophis bannanicus and compared the genetic diversity and structure with the information from the NADH dehydrogenase subunit 2 (ND2) and Cytochrome b (Cyt b) genes within this species. Extremely low genetic diversity was found in the mtDNA CR compared with those of the ND2 and Cyt b genes. These results showed that the relatively mean clock rate of the CR was broadly lower than those of the ND2 (about 2.55 times) and Cyt b (about 3.14 times) genes. Despite the extremely low genetic diversity of CR, the population structure analysis identified two groups, Xishuangbanna and Northern Vietnam-Yulin-Yangchun-Deqing, which indicated that the Red River systems may have acted as gene-flow barriers for I. bannanicus.
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Affiliation(s)
- Shaoquan Meng
- a College of Life Sciences, Fujian Agriculture and Forest University , Fuzhou , Fujian , China.,b College of Life Science & Technology, Yulin Normal University , Yulin , Guangxi , China
| | - Tao Pan
- c School of Life Science, Anhui University , Hefei , Anhui , China , and
| | - Zhonglou Sun
- c School of Life Science, Anhui University , Hefei , Anhui , China , and
| | - Yongjian Bei
- b College of Life Science & Technology, Yulin Normal University , Yulin , Guangxi , China
| | - Tao Meng
- d Guangxi Forest Inventory and Planning Institute , Nanning , Guangxi , China
| | - Guifen Li
- b College of Life Science & Technology, Yulin Normal University , Yulin , Guangxi , China
| | - Defeng Wu
- a College of Life Sciences, Fujian Agriculture and Forest University , Fuzhou , Fujian , China
| | - Baowei Zhang
- c School of Life Science, Anhui University , Hefei , Anhui , China , and
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11
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Newhouse DJ, Balakrishnan CN. High major histocompatibility complex class I polymorphism despite bottlenecks in wild and domesticated populations of the zebra finch (Taeniopygia guttata). BMC Evol Biol 2015; 15:265. [PMID: 26627847 PMCID: PMC4667478 DOI: 10.1186/s12862-015-0546-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 11/20/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Two subspecies of zebra finch, Taeniopygia guttata castanotis and T. g. guttata are native to Australia and the Lesser Sunda Islands, respectively. The Australian subspecies has been domesticated and is now an important model system for research. Both the Lesser Sundan subspecies and domesticated Australian zebra finches have undergone population bottlenecks in their history, and previous analyses using neutral markers have reported reduced neutral genetic diversity in these populations. Here we characterize patterns of variation in the third exon of the highly variable major histocompatibility complex (MHC) class I α chain. As a benchmark for neutral divergence, we also report the first mitochondrial NADH dehydrogenase 2 (ND2) sequences in this important model system. RESULTS Despite natural and human-mediated population bottlenecks, we find that high MHC class I polymorphism persists across all populations. As expected, we find higher levels of nucleotide diversity in the MHC locus relative to neutral loci, and strong evidence of positive selection acting on important residues forming the peptide-binding region (PBR). Clear population differentiation of MHC allele frequencies is also evident, and this may be due to adaptation to new habitats and associated pathogens and/or genetic drift. Whereas the MHC Class I locus shows broad haplotype sharing across populations, ND2 is the first locus surveyed to date to show reciprocal monophyly of the two subspecies. CONCLUSIONS Despite genetic bottlenecks and genetic drift, all surveyed zebra finch populations have maintained high MHC Class I diversity. The diversity at the MHC Class I locus in the Lesser Sundan subspecies contrasts sharply with the lack of diversity in previously examined neutral loci, and may thus be a result of selection acting to maintain polymorphism. Given uncertainty in historical population demography, however, it is difficult to rule out neutral processes in maintaining the observed diversity. The surveyed populations also differ in MHC Class I allele frequencies, and future studies are needed to assess whether these changes result in functional immune differences.
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Affiliation(s)
- Daniel J Newhouse
- Howell Science Complex, East Carolina University, Greenville, NC, 27858, USA.
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Norman JA, Blackmore CJ, Rourke M, Christidis L. Effects of mitochondrial DNA rate variation on reconstruction of Pleistocene demographic history in a social avian species, Pomatostomus superciliosus. PLoS One 2014; 9:e106267. [PMID: 25181547 PMCID: PMC4152169 DOI: 10.1371/journal.pone.0106267] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 08/04/2014] [Indexed: 11/18/2022] Open
Abstract
Mitochondrial sequence data is often used to reconstruct the demographic history of Pleistocene populations in an effort to understand how species have responded to past climate change events. However, departures from neutral equilibrium conditions can confound evolutionary inference in species with structured populations or those that have experienced periods of population expansion or decline. Selection can affect patterns of mitochondrial DNA variation and variable mutation rates among mitochondrial genes can compromise inferences drawn from single markers. We investigated the contribution of these factors to patterns of mitochondrial variation and estimates of time to most recent common ancestor (TMRCA) for two clades in a co-operatively breeding avian species, the white-browed babbler Pomatostomus superciliosus. Both the protein-coding ND3 gene and hypervariable domain I control region sequences showed departures from neutral expectations within the superciliosus clade, and a two-fold difference in TMRCA estimates. Bayesian phylogenetic analysis provided evidence of departure from a strict clock model of molecular evolution in domain I, leading to an over-estimation of TMRCA for the superciliosus clade at this marker. Our results suggest mitochondrial studies that attempt to reconstruct Pleistocene demographic histories should rigorously evaluate data for departures from neutral equilibrium expectations, including variation in evolutionary rates across multiple markers. Failure to do so can lead to serious errors in the estimation of evolutionary parameters and subsequent demographic inferences concerning the role of climate as a driver of evolutionary change. These effects may be especially pronounced in species with complex social structures occupying heterogeneous environments. We propose that environmentally driven differences in social structure may explain observed differences in evolutionary rate of domain I sequences, resulting from longer than expected retention times for matriarchal lineages in the superciliosus clade.
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Affiliation(s)
- Janette A. Norman
- National Marine Science Centre, Southern Cross University, Coffs Harbour, New South Wales, Australia
- Department of Genetics, University of Melbourne, Parkville, Victoria, Australia
- Museum Victoria, Melbourne, Victoria, Australia
| | - Caroline J. Blackmore
- National Marine Science Centre, Southern Cross University, Coffs Harbour, New South Wales, Australia
| | - Meaghan Rourke
- Museum Victoria, Melbourne, Victoria, Australia
- School of Science and Engineering, Deakin University, Geelong, Victoria, Australia
- New South Wales Department of Primary Industries, Narrandera Fisheries Centre, Narrandera, New South Wales, Australia
| | - Les Christidis
- National Marine Science Centre, Southern Cross University, Coffs Harbour, New South Wales, Australia
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DNA barcoding works in practice but not in (neutral) theory. PLoS One 2014; 9:e100755. [PMID: 24988408 PMCID: PMC4079456 DOI: 10.1371/journal.pone.0100755] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 05/30/2014] [Indexed: 11/19/2022] Open
Abstract
Background DNA barcode differences within animal species are usually much less than differences among species, making it generally straightforward to match unknowns to a reference library. Here we aim to better understand the evolutionary mechanisms underlying this usual “barcode gap” pattern. We employ avian barcode libraries to test a central prediction of neutral theory, namely, intraspecific variation equals 2 Nµ, where N is population size and µ is mutations per site per generation. Birds are uniquely suited for this task: they have the best-known species limits, are well represented in barcode libraries, and, most critically, are the only large group with documented census population sizes. In addition, we ask if mitochondrial molecular clock measurements conform to neutral theory prediction of clock rate equals µ. Results Intraspecific COI barcode variation was uniformly low regardless of census population size (n = 142 species in 15 families). Apparent outliers reflected lumping of reproductively isolated populations or hybrid lineages. Re-analysis of a published survey of cytochrome b variation in diverse birds (n = 93 species in 39 families) further confirmed uniformly low intraspecific variation. Hybridization/gene flow among species/populations was the main limitation to DNA barcode identification. Conclusions/Significance To our knowledge, this is the first large study of animal mitochondrial diversity using actual census population sizes and the first to test outliers for population structure. Our finding of universally low intraspecific variation contradicts a central prediction of neutral theory and is not readily accounted for by commonly proposed ad hoc modifications. We argue that the weight of evidence–low intraspecific variation and the molecular clock–indicates neutral evolution plays a minor role in mitochondrial sequence evolution. As an alternate paradigm consistent with empirical data, we propose extreme purifying selection, including at synonymous sites, limits variation within species and continuous adaptive selection drives the molecular clock.
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Using ancient DNA to study the origins and dispersal of ancestral Polynesian chickens across the Pacific. Proc Natl Acad Sci U S A 2014; 111:4826-31. [PMID: 24639505 DOI: 10.1073/pnas.1320412111] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The human colonization of Remote Oceania remains one of the great feats of exploration in history, proceeding east from Asia across the vast expanse of the Pacific Ocean. Human commensal and domesticated species were widely transported as part of this diaspora, possibly as far as South America. We sequenced mitochondrial control region DNA from 122 modern and 22 ancient chicken specimens from Polynesia and Island Southeast Asia and used these together with Bayesian modeling methods to examine the human dispersal of chickens across this area. We show that specific techniques are essential to remove contaminating modern DNA from experiments, which appear to have impacted previous studies of Pacific chickens. In contrast to previous reports, we find that all ancient specimens and a high proportion of the modern chickens possess a group of unique, closely related haplotypes found only in the Pacific. This group of haplotypes appears to represent the authentic founding mitochondrial DNA chicken lineages transported across the Pacific, and allows the early dispersal of chickens across Micronesia and Polynesia to be modeled. Importantly, chickens carrying this genetic signature persist on several Pacific islands at high frequencies, suggesting that the original Polynesian chicken lineages may still survive. No early South American chicken samples have been detected with the diagnostic Polynesian mtDNA haplotypes, arguing against reports that chickens provide evidence of Polynesian contact with pre-European South America. Two modern specimens from the Philippines carry haplotypes similar to the ancient Pacific samples, providing clues about a potential homeland for the Polynesian chicken.
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Dufort MJ, Keith Barker F. Range dynamics, rather than convergent selection, explain the mosaic distribution of red-winged blackbird phenotypes. Ecol Evol 2013; 3:4910-24. [PMID: 24455125 PMCID: PMC3892357 DOI: 10.1002/ece3.859] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 09/26/2013] [Accepted: 09/30/2013] [Indexed: 11/24/2022] Open
Abstract
Geographic distributions of genetic and phenotypic characters can illuminate historical evolutionary processes. In particular, mosaic distributions of phenotypically similar populations can arise from parallel evolution or from irregular patterns of dispersal and colonization by divergent forms. Two phenotypically divergent forms of the red-winged blackbird (Agelaius phoeniceus) show a mosaic phenotypic distribution, with a "bicolored" form occurring disjunctly in California and Mexico. We analyzed the relationships among these bicolored populations and neighboring typical populations, using ∼600 bp of mitochondrial DNA sequence data and 10 nuclear short tandem repeat loci. We find that bicolored populations, although separated by ∼3000 km, are genetically more similar to one other than they are to typical populations separated by ∼400 km. We also find evidence of ongoing gene flow among populations, including some evidence of asymmetric gene flow. We conclude that the current distribution of bicolored forms represents incomplete speciation, where recent asymmetric hybridization with typical A. phoeniceus is dividing the range of a formerly widespread bicolored form. This hypothesis predicts that bicolored forms may suffer extinction by hybridization. Future work will use fine-scaled geographical sampling and nuclear sequence data to test for hybrid origins of currently typical populations and to more precisely quantify the directionality of gene flow.
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Affiliation(s)
- Matthew J Dufort
- Department of Ecology, Evolution and Behavior, University of Minnesota 100 Ecology Building, 1987 Upper Buford Circle, Saint Paul, Minnesota, 55108
| | - F Keith Barker
- Department of Ecology, Evolution and Behavior, University of Minnesota 100 Ecology Building, 1987 Upper Buford Circle, Saint Paul, Minnesota, 55108 ; Bell Museum of Natural History, University of Minnesota 100 Ecology Building, 1987 Upper Buford Circle, Saint Paul, Minnesota, 55108
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