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Aberle N, Volpe C, Østensen MA, Majaneva S. Long-term dynamics, population structure and connectivity of the helmet jellyfish Periphylla periphylla in a Norwegian fjord and adjacent waters. JOURNAL OF PLANKTON RESEARCH 2024; 46:59-71. [PMID: 38283690 PMCID: PMC10810686 DOI: 10.1093/plankt/fbad050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 10/11/2023] [Indexed: 01/30/2024]
Abstract
Mass occurrences of Periphylla periphylla in Norwegian fjords cause major concerns related to potential regime shifts that could affect ecosystem stability. 15 years of trawl data (2006-2015), complemented with comprehensive sampling in different areas and seasons (2018-2021) allowed new insights on the dynamics, structure and connectivity of P. periphylla populations within and beyond Trondheimsfjorden. Despite assumed population bursts, no clear trend on P. periphylla population size in Trondheimsfjorden were identified. Sampling frequency and population size suggest a local reproduction of P. periphylla, especially in the inner part of the fjord where young-of-the-year (YOY) individuals occur. Size variations occurred in relation to sampling month, thus pointing at seasonal patterns in growth and reproduction. No distinct population structure of P. periphylla populations within Trondheimsfjorden and over larger spatial scales (> 100 km) along the Norwegian coast was observed. Such poor geographic population structure provides evidence for a strong dispersal of P. periphylla, potentially triggered by frequent deep-water renewals of the fjords' basins that enable a high gene flow. Data on P. periphylla long-term dynamics, population structure and connectivity provide valuable information for ecosystem state assessments and enable the advancement of ecosystem management approaches, thus accounting for both stakeholder and ecosystem demands.
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Affiliation(s)
- Nicole Aberle
- Trondhjem Biological Station, Department of Biology Norwegian University of Science and Technology (NTNU), Trondheim 7012, Norway
- Institute of Marine Ecosystem and Fishery Science (IMF), Hamburg University, Hamburg 20148, Germany
| | - Charlotte Volpe
- Trondhjem Biological Station, Department of Biology Norwegian University of Science and Technology (NTNU), Trondheim 7012, Norway
- Fisheries and New Biomarine Industry, SINTEF Ocean, Trondheim 7465, Norway
| | - Mari-Ann Østensen
- Trondhjem Biological Station, Department of Biology Norwegian University of Science and Technology (NTNU), Trondheim 7012, Norway
| | - Sanna Majaneva
- Trondhjem Biological Station, Department of Biology Norwegian University of Science and Technology (NTNU), Trondheim 7012, Norway
- Ecosystems, Akvaplan Niva, Trondheim 7010, Norway
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Liu Y, Chan KN, Li X, Zhao X, Chu D, Yin Y, Liu Y, Chen A. The Genetic Diversity of White-Backed Planthoppers ( Sogatella furcifera) between Myanmar and Yunnan Province of China. Genes (Basel) 2023; 14:2164. [PMID: 38136986 PMCID: PMC10743027 DOI: 10.3390/genes14122164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/17/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023] Open
Abstract
In order to clarify the migration route and the source of white-backed planthopper (WBPH) (Sogatella furcifera) between Myanmar and Yunnan Province, China, we collected six populations throughout Myanmar and five populations around the border areas in Yunnan Province, China. A total of 790 base pairs in the mtDNA COI genes from 416 individuals were obtained. A total of 43 haplotypes were identified, among which 37 were unique haplotypes, and the remaining 6 were shared among different populations. Two common shared haplotypes (H_1 and H_2) had a widespread distribution in all populations and accounted for 88.8% of the total haplotype frequency, suggesting a high-level gene flow among the Myanmar and Yunnan populations. Bayesian skyline plot (BSP) analysis results indicated that the effective population size of WBPH expanded between about 10,000 and 7000 years ago, and S. furcifera might follow the post-LGM (Last Glacial Maximum) expansion pattern. Based on the total migrant (Nem) value, it can be deduced that north and northeast Myanmar were the primary migration sources for WBPH populations in the southwest and south Yunnan regions. This study aims to contribute to the sustainable regional management of this important rice pest and provide new insights into the genetic diversity of WBPH in Southeast Asia.
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Affiliation(s)
- Yue Liu
- Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests of Yunnan Province/Agricultural Environment and Resource Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China (Y.Y.)
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Khin Nyein Chan
- Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests of Yunnan Province/Agricultural Environment and Resource Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China (Y.Y.)
- Biotechnology Research Department, Ministry of Education, Mandalay 05151, Myanmar
| | - Xiangyong Li
- Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests of Yunnan Province/Agricultural Environment and Resource Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China (Y.Y.)
| | - Xueqing Zhao
- Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests of Yunnan Province/Agricultural Environment and Resource Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China (Y.Y.)
| | - Dong Chu
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao 266109, China
| | - Yanqiong Yin
- Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests of Yunnan Province/Agricultural Environment and Resource Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China (Y.Y.)
| | - Ying Liu
- Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests of Yunnan Province/Agricultural Environment and Resource Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China (Y.Y.)
| | - Aidong Chen
- Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests of Yunnan Province/Agricultural Environment and Resource Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China (Y.Y.)
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3
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A study of algorithms relating distributive lattices, median graphs, and Formal Concept Analysis. Int J Approx Reason 2022. [DOI: 10.1016/j.ijar.2021.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Qi J, Shi F, Zhang B, Chen X, Jie X, Furumitsu K, Corush JB, Yamaguchi A, Zhang J. Insights into genetic variation and demographic history of sharpnose rays: Examinations of three species of Telatrygon (Elasmobranchii, Dasyatidae) from the Indo-West Pacific. Integr Zool 2021; 17:1063-1077. [PMID: 34932875 DOI: 10.1111/1749-4877.12614] [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: 11/30/2022]
Abstract
Coastal and demersal chondrichthyans (sharks, rays, and skates) are expected to exhibit high levels of genetic differentiation in areas of complex geomorphology. Population genetic studies investigating the extent to which demographic history shapes the genetic structure of these fishes are rare. Here, we combination mitochondrial DNA (Cytb and ND2) and eight nuclear microsatellite loci from 244 individuals to examine the population genetic structure and demographic history of the three Indo-West Pacific species of sharpnose rays (Telatrygon zugei, Telatrygon biasa, and Trygon crozieri). High levels of genetic variation both within and between species was identified. Phylogenetic analysis partitioned haplotypes into two lineages supporting divergence of T. zugei from T. crozieri and T. biasa during the Pleistocene. Furthermore, microsatellite-based clustering analyses identified four genetic groups (i.e., T. zugei from Japan, T. zugei from coastal China, T. biasa from Gulf of Thailand, and T. crozieri from the Andaman Sea. Measurements of genetic differentiation also support these four groups. Additionally, Pleistocene demographic expansions were examined in all genetic groups. The climate oscillations and current hydrologic cycles in the Indo-West Pacific appear to be coincide with the hypothesis regarding speciation and the observed demographic history trends of the sharpnose rays. Considering the species group has, until recently, been thought to be one species, these results are critical for defining management units and guiding conservation efforts to preserve stingray biodiversity. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Jiwei Qi
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Fanglei Shi
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Baowei Zhang
- School of Life Science, Anhui University, Hefei, Anhui, China
| | - Xiao Chen
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Xing Jie
- East China Sea Centre of Standard and Metrology, SOA, Shanghai, China
| | | | - Joel B Corush
- Illinois Natural History Survey, University of Illinois Champaign-Urbana, Champaign, IL, 61820
| | | | - Jie Zhang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China
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5
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Motoki MT, Linton YM, Conn JE, Ruiz-Lopez F, Wilkerson RC. Phylogenetic Network of Mitochondrial COI Gene Sequences Distinguishes 10 Taxa Within the Neotropical Albitarsis Group (Diptera: Culicidae), Confirming the Separate Species Status of Anopheles albitarsis H (Diptera: Culicidae) and Revealing a Novel Lineage, Anopheles albitarsis J. JOURNAL OF MEDICAL ENTOMOLOGY 2021; 58:599-607. [PMID: 33033825 PMCID: PMC7954104 DOI: 10.1093/jme/tjaa211] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Indexed: 05/14/2023]
Abstract
The Neotropical Albitarsis Group is a complex assemblage of essentially isomorphic species which currently comprises eight recognized species-five formally described (Anopheles albitarsis Lynch-Arribalzaga, An. deaneorum Rosa-Freitas, An. janconnae Wilkerson and Sallum, An. marajoara Galvao and Damasceno, An. oryzalimnetes Wilkerson and Motoki) and three molecularly assigned (An. albitarsis F, G & I)-and one mitochondrial lineage (An. albitarsis H). To further explore species recognition within this important group, 658 base pairs of the mitochondrial DNA cytochrome oxidase subunit I (COI) were analyzed from 988 specimens from South America. We conducted statistical parsimony network analysis, generated estimates of haplotype, nucleotide, genetic differentiation, divergence time, and tested the effect of isolation by distance (IBD). Ten clusters were identified, which confirmed the validity of the eight previously determined species, and confirmed the specific status of the previous mitochondrial lineage An. albitarsis H. High levels of diversity were highlighted in two samples from Pará (= An. albitarsis J), which needs further exploration through additional sampling, but which may indicate another cryptic species. The highest intra-specific nucleotide diversity was observed in An. deaneorum, and the lowest in An. marajoara. Significant correlation between genetic and geographical distance was observed only in An. oryzalimnetes and An. albitarsis F. Divergence time within the Albitarsis Group was estimated at 0.58-2.25 Mya, during the Pleistocene. The COI barcode region was considered an effective marker for species recognition within the Albitarsis Group and a network approach was an analytical method to discriminate among species of this group.
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Affiliation(s)
- Maysa T Motoki
- Walter Reed Biosystematics Unit, Smithsonian Institution Museum Support Center, Suitland, MD
- Global Health Research, Vysnova Partners Inc., Landover, MD
- Corresponding author, e-mail:
| | - Yvonne-Marie Linton
- Walter Reed Biosystematics Unit, Smithsonian Institution Museum Support Center, Suitland, MD
- Department of Entomology, Smithsonian Institution—Natural Museum of Natural History, Washington, DC
- Walter Reed Army Institute of Research, Silver Spring, MD
| | - Jan E Conn
- Griffin Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY
- School of Public Health, Department of Biomedical Sciences, State University of New York, Albany, NY
| | - Fredy Ruiz-Lopez
- Walter Reed Biosystematics Unit, Smithsonian Institution Museum Support Center, Suitland, MD
- Programa de Estudio y Control de Enfermedades Tropicales (PECET), Facultad de Medicina, Universidad de Antioquia, Medellin, Colombia
| | - Richard C Wilkerson
- Walter Reed Biosystematics Unit, Smithsonian Institution Museum Support Center, Suitland, MD
- Department of Entomology, Smithsonian Institution—Natural Museum of Natural History, Washington, DC
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Raj P, Song R, Zhu H, Riediger L, Jun DJ, Liang C, Arana C, Zhang B, Gao Y, Wakeland BE, Dozmorov I, Zhou J, Kelly JA, Lauwerys BR, Guthridge JM, Olsen NJ, Nath SK, Pasare C, van Oers N, Gilkeson G, Tsao BP, Gaffney PM, Gregersen PK, James JA, Zuo X, Karp DR, Li QZ, Wakeland EK. Deep sequencing reveals a DAP1 regulatory haplotype that potentiates autoimmunity in systemic lupus erythematosus. Genome Biol 2020; 21:281. [PMID: 33213505 PMCID: PMC7677828 DOI: 10.1186/s13059-020-02184-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 10/19/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Systemic lupus erythematosus (SLE) is a clinically heterogeneous autoimmune disease characterized by the development of anti-nuclear antibodies. Susceptibility to SLE is multifactorial, with a combination of genetic and environmental risk factors contributing to disease development. Like other polygenic diseases, a significant proportion of estimated SLE heritability is not accounted for by common disease alleles analyzed by SNP array-based GWASs. Death-associated protein 1 (DAP1) was implicated as a candidate gene in a previous familial linkage study of SLE and rheumatoid arthritis, but the association has not been explored further. RESULTS We perform deep sequencing across the DAP1 genomic segment in 2032 SLE patients, and healthy controls, and discover a low-frequency functional haplotype strongly associated with SLE risk in multiple ethnicities. We find multiple cis-eQTLs embedded in a risk haplotype that progressively downregulates DAP1 transcription in immune cells. Decreased DAP1 transcription results in reduced DAP1 protein in peripheral blood mononuclear cells, monocytes, and lymphoblastoid cell lines, leading to enhanced autophagic flux in immune cells expressing the DAP1 risk haplotype. Patients with DAP1 risk allele exhibit significantly higher autoantibody titers and altered expression of the immune system, autophagy, and apoptosis pathway transcripts, indicating that the DAP1 risk allele mediates enhanced autophagy, leading to the survival of autoreactive lymphocytes and increased autoantibody. CONCLUSIONS We demonstrate how targeted sequencing captures low-frequency functional risk alleles that are missed by SNP array-based studies. SLE patients with the DAP1 genotype have distinct autoantibody and transcription profiles, supporting the dissection of SLE heterogeneity by genetic analysis.
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Affiliation(s)
- Prithvi Raj
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Ran Song
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Honglin Zhu
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Linley Riediger
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Dong-Jae Jun
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Chaoying Liang
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Carlos Arana
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Bo Zhang
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Yajing Gao
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Benjamin E Wakeland
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Igor Dozmorov
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jinchun Zhou
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jennifer A Kelly
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Bernard R Lauwerys
- Institut de Recherche Expérimentale et Clinique, Université catholique de Louvain, 1200, Bruxelles, Belgium
| | - Joel M Guthridge
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Nancy J Olsen
- Division of Rheumatology, Department of Medicine, Penn State Medical School, State College, PA, USA
| | - Swapan K Nath
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Chandrashekhar Pasare
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Nicolai van Oers
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Gary Gilkeson
- Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC, USA
| | - Betty P Tsao
- Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC, USA
| | - Patrick M Gaffney
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | | | - Judith A James
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Xiaoxia Zuo
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, 410008, China.
| | - David R Karp
- Rheumatic Diseases Division, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Quan-Zhen Li
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Edward K Wakeland
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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Rito T, Richards MB, Pala M, Correia-Neves M, Soares PA. Phylogeography of 27,000 SARS-CoV-2 Genomes: Europe as the Major Source of the COVID-19 Pandemic. Microorganisms 2020; 8:E1678. [PMID: 33137892 PMCID: PMC7693378 DOI: 10.3390/microorganisms8111678] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 10/26/2020] [Accepted: 10/27/2020] [Indexed: 12/13/2022] Open
Abstract
The novel coronavirus SARS-CoV-2 emerged from a zoonotic transmission in China towards the end of 2019, rapidly leading to a global pandemic on a scale not seen for a century. In order to cast fresh light on the spread of the virus and on the effectiveness of the containment measures adopted globally, we used 26,869 SARS-CoV-2 genomes to build a phylogeny with 20,247 mutation events and adopted a phylogeographic approach. We confirmed that the phylogeny pinpoints China as the origin of the pandemic with major founders worldwide, mainly during January 2020. However, a single specific East Asian founder underwent massive radiation in Europe and became the main actor of the subsequent spread worldwide during March 2020. This lineage accounts for the great majority of cases detected globally and even spread back to the source in East Asia. Despite an East Asian source, therefore, the global pandemic was mainly fueled by its expansion across and out of Europe. It seems likely that travel bans established throughout the world in the second half of March helped to decrease the number of intercontinental exchanges, particularly from mainland China, but were less effective between Europe and North America where exchanges in both directions are visible up to April, long after bans were imposed.
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Affiliation(s)
- Teresa Rito
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal; (T.R.); (M.C.-N.)
- ICVS/3B’s, PT Government Associate Laboratory, University of Minho, 4710-057 Braga, Portugal
| | - Martin B. Richards
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield HD1 3DH, UK; (M.B.R.); (M.P.)
| | - Maria Pala
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield HD1 3DH, UK; (M.B.R.); (M.P.)
| | - Margarida Correia-Neves
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal; (T.R.); (M.C.-N.)
- ICVS/3B’s, PT Government Associate Laboratory, University of Minho, 4710-057 Braga, Portugal
| | - Pedro A. Soares
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, 4710-057 Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
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8
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Power JM, Grimm GW, List JM. Evolutionary dynamics in the dispersal of sign languages. ROYAL SOCIETY OPEN SCIENCE 2020; 7:191100. [PMID: 32218940 PMCID: PMC7029929 DOI: 10.1098/rsos.191100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 12/13/2019] [Indexed: 06/10/2023]
Abstract
The evolution of spoken languages has been studied since the mid-nineteenth century using traditional historical comparative methods and, more recently, computational phylogenetic methods. By contrast, evolutionary processes resulting in the diversity of contemporary sign languages (SLs) have received much less attention, and scholars have been largely unsuccessful in grouping SLs into monophyletic language families using traditional methods. To date, no published studies have attempted to use language data to infer relationships among SLs on a large scale. Here, we report the results of a phylogenetic analysis of 40 contemporary and 36 historical SL manual alphabets coded for morphological similarity. Our results support grouping SLs in the sample into six main European lineages, with three larger groups of Austrian, British and French origin, as well as three smaller groups centring around Russian, Spanish and Swedish. The British and Swedish lineages support current knowledge of relationships among SLs based on extra-linguistic historical sources. With respect to other lineages, our results diverge from current hypotheses by indicating (i) independent evolution of Austrian, French and Spanish from Spanish sources; (ii) an internal Danish subgroup within the Austrian lineage; and (iii) evolution of Russian from Austrian sources.
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Affiliation(s)
- Justin M. Power
- Department of Linguistics, University of Texas at Austin, Austin, TX, USA
| | | | - Johann-Mattis List
- Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Jena, Germany
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Comparative phylogeography of two hemipteran species (Geisha distinctissima and Megacopta cribraria) in the Zhoushan Archipelago of China reveals contrasting genetic structures despite concordant historical demographies. Heredity (Edinb) 2019; 124:207-222. [PMID: 31501533 DOI: 10.1038/s41437-019-0265-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 08/06/2019] [Accepted: 08/22/2019] [Indexed: 11/08/2022] Open
Abstract
Continental islands are useful models to explore the roles of shared historical factors in the evolution of sympatric species. However, China's largest continental group of islands, the Zhoushan Archipelago, was neglected by most studies focusing on biodiversity hotspots. Here we investigated the phylogeographic patterns and the historical demography of two sympatric hemipteran insects (Geisha distinctissima and Megacopta cribraria), which shared historical factors in the Zhoushan Archipelago. The results based on mtDNA (COX1, COX2-COX3, and CYTB) and nDNA (28S and ITS2) showed that G. distinctissima diverged into three genetic lineages (L1-L3) ~8.9-13.7 thousand years ago (kya), which coincided with the period of island isolation. However, the three lineages exhibit no clear phylogeographic patterns for frequent asymmetrical gene flow (starting around 5 kya) from the mainland and adjacent islands to other distant islands due to subsequent human activities. In contrast, only one genetic lineage exists for M. cribraria, without any phylogeographic structures. The ancestral range in the mainland as well as in neighboring islands, together with the frequent asymmetrical gene flow of M. cribraria (from the mainland and neighboring islands to more distant islands) within the last 5000 years suggests that human activities may have lead to the colonization of this species in the Zhoushan Archipelago. The contrasting genetic structures indicate shared historical factors but independent evolutionary histories for the two sympatric species in the Zhoushan Archipelago. Our demographic analysis clearly showed that both species underwent population expansion before 5 kya during the post-LGM (Last Glacial Maximum), which indicates that the two species shared concordant historical demographies. This result suggests that the population size of the two species was affected similarly by the climatic oscillations of post-LGM in Eastern China. Together, our findings reveal that the two insect species in the Zhoushan Archipelago exhibit contrasting genetic structures despite concordant historical demographies, which provides an important framework for the exploration of the evolution patterns of sympatric species in the continental island.
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10
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Ginja C, Gama LT, Cortés O, Burriel IM, Vega-Pla JL, Penedo C, Sponenberg P, Cañón J, Sanz A, do Egito AA, Alvarez LA, Giovambattista G, Agha S, Rogberg-Muñoz A, Lara MAC, Delgado JV, Martinez A. The genetic ancestry of American Creole cattle inferred from uniparental and autosomal genetic markers. Sci Rep 2019; 9:11486. [PMID: 31391486 PMCID: PMC6685949 DOI: 10.1038/s41598-019-47636-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 07/16/2019] [Indexed: 12/31/2022] Open
Abstract
Cattle imported from the Iberian Peninsula spread throughout America in the early years of discovery and colonization to originate Creole breeds, which adapted to a wide diversity of environments and later received influences from other origins, including zebu cattle in more recent years. We analyzed uniparental genetic markers and autosomal microsatellites in DNA samples from 114 cattle breeds distributed worldwide, including 40 Creole breeds representing the whole American continent, and samples from the Iberian Peninsula, British islands, Continental Europe, Africa and American zebu. We show that Creole breeds differ considerably from each other, and most have their own identity or group with others from neighboring regions. Results with mtDNA indicate that T1c-lineages are rare in Iberia but common in Africa and are well represented in Creoles from Brazil and Colombia, lending support to a direct African influence on Creoles. This is reinforced by the sharing of a unique Y-haplotype between cattle from Mozambique and Creoles from Argentina. Autosomal microsatellites indicate that Creoles occupy an intermediate position between African and European breeds, and some Creoles show a clear Iberian signature. Our results confirm the mixed ancestry of American Creole cattle and the role that African cattle have played in their development.
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Affiliation(s)
- Catarina Ginja
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Porto, Portugal
| | - Luis Telo Gama
- CIISA.Faculdade de Medicina Veterinaria, Universidade de Lisboa, Lisbon, Portugal
| | - Oscar Cortés
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain.
| | - Inmaculada Martin Burriel
- Laboratorio de Genética Bioquímica, Facultad de Veterinaria, Universidad de Zaragoza, Zaragoza, Spain
| | - Jose Luis Vega-Pla
- Laboratorio de Investigación Aplicada, Servicio de Cría Caballar de las Fuerzas Armadas, Córdoba, Spain
| | - Cecilia Penedo
- Veterinary Genetics Laboratory, University of California, Davis, California, USA
| | - Phil Sponenberg
- Virginia-Maryland Regional College of Veterinary Medicine. Virginia Tech, Virginia, USA
| | - Javier Cañón
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Arianne Sanz
- Laboratorio de Genética Bioquímica, Facultad de Veterinaria, Universidad de Zaragoza, Zaragoza, Spain
| | | | | | | | - Saif Agha
- Animal Production Department, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | | | | | | | - Juan Vicente Delgado
- Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain
| | - Amparo Martinez
- Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain.,Animal Beeding Consulting S.L. Universidad de Córdoba, Córdoba, Spain
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11
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Du Z, Ishikawa T, Liu H, Kamitani S, Tadauchi O, Cai W, Li H. Phylogeography of the Assassin Bug Sphedanolestes impressicollis in East Asia Inferred From Mitochondrial and Nuclear Gene Sequences. Int J Mol Sci 2019; 20:ijms20051234. [PMID: 30870981 PMCID: PMC6429140 DOI: 10.3390/ijms20051234] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 03/05/2019] [Accepted: 03/06/2019] [Indexed: 11/29/2022] Open
Abstract
The assassin bug, Sphedanolestes impressicollis (Hemiptera: Reduviidae), is widely distributed in East Asia. It is an ideal model for evaluating the effects of climatic fluctuation and geographical events on the distribution patterns of East Asian reduviids. Here, we used two mitochondrial genes and one nuclear gene to investigate the phylogeographic pattern of the assassin bug based on comprehensive sampling in China, Japan, South Korea, Vietnam, and Laos. High levels of genetic differentiation were detected among the geographic populations classified into the northern and southern groups. A significant correlation was detected between genetic and geographical distances. The East China Sea land bridge served as a “dispersal corridor” during Pleistocene glaciation. The estimated divergence time indicated that the northern group may have separated from the eastern Chinese populations when the sea level rapidly rose during the “Ryukyu Coral Sea Stage” and the East China Sea land bridge was completely submerged. Demographic history and ecological niche modeling suggested that appropriate climatic conditions may have accounted for the rapid spread across the Korean Peninsula and Japan during the late Pleistocene. Our study underscores the pivotal roles of the Pleistocene sea level changes and climatic fluctuations in determining the distribution patterns of East Asian reduviids.
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Affiliation(s)
- Zhenyong Du
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China.
| | - Tadashi Ishikawa
- Laboratory of Entomology, Faculty of Agriculture, Tokyo University of Agriculture, Atsugi, Kanagawa 243-0034, Japan.
| | - Hui Liu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China.
- Entomological Laboratory, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 812-8581, Japan.
| | - Satoshi Kamitani
- Entomological Laboratory, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 812-8581, Japan.
| | - Osamu Tadauchi
- Entomological Laboratory, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 812-8581, Japan.
| | - Wanzhi Cai
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China.
| | - Hu Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China.
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12
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Schnitzler A, Granado J, Putelat O, Arbogast RM, Drucker D, Eberhard A, Schmutz A, Klaefiger Y, Lang G, Salzburger W, Schibler J, Schlumbaum A, Bocherens H. Genetic diversity, genetic structure and diet of ancient and contemporary red deer (Cervus elaphus L.) from north-eastern France. PLoS One 2018; 13:e0189278. [PMID: 29304165 PMCID: PMC5755736 DOI: 10.1371/journal.pone.0189278] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Accepted: 11/23/2017] [Indexed: 11/18/2022] Open
Abstract
In north-eastern France, red deer (Cervus elaphus L.) populations were rebuilt from a few hundred individuals, which have subsisted in remote valleys of the Vosges mountains, and to a lesser extent from individuals escaped from private enclosures; at present times, this species occupies large areas, mainly in the Vosges Mountains. In this study, we examined the population dynamics of red deer in the Vosges Mountains using ancient and contemporary mitochondrial DNA (mtDNA) from 140 samples (23 ancient + 117 modern) spanning the last 7'000 years. In addition, we reconstructed the feeding habits and the habitat of red deer since the beginning of agriculture applying isotopic analyses in order to establish a basis for current environmental management strategies. We show that past and present red deer in the Vosges Mountains belong to mtDNA haplogroup A, suggesting that they originated from the Iberian refugium after the last glacial maximum (LGM). Palaeogenetic analysis of ancient bone material revealed the presence of two distinct haplotypes with different temporal distributions. Individuals belonging to the two haplotype groups apparently occupied two different habitats over at least 7'000 years. AM6 correlates with an ecological type that feeds in densely forested mountain landscapes, while AM235 correlates with feeding in lowland landscapes, composed of a mixture of meadows and riverine, herb-rich woodlands. Our results suggest that red deer of north-eastern France was able to adapt, over the long term, to these different habitat types, possibly due to efficient ethological barriers. Modern haplotype patterns support the historical record that red deer has been exposed to strong anthropogenic influences as a major game species.
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Affiliation(s)
- Annik Schnitzler
- LIEC UMR 7360, University of Lorraine - UFR Sci FA, Campus Bridoux, Metz, France
- * E-mail:
| | - José Granado
- Integrative Prehistoric and Archaeological Science (IPAS), University of Basel, Basel, Switzerland
| | - Olivier Putelat
- Archéologie Alsace, Sélestat & UMR 7041 ArScan - Archéologies environnementales - Maison de l’Archéologie et de l’Ethnologie, Nanterre, France
| | | | - Dorothée Drucker
- Senckenberg Center for Human Evolution and Palaeoenvironment (HEP), University of Tübingen, Tübingen, Germany
| | - Anna Eberhard
- Zoological Institute, University of Basel, Basel, Switzerland
| | - Anja Schmutz
- Zoological Institute, University of Basel, Basel, Switzerland
| | - Yuri Klaefiger
- Zoological Institute, University of Basel, Basel, Switzerland
| | | | | | - Joerg Schibler
- Integrative Prehistoric and Archaeological Science (IPAS), University of Basel, Basel, Switzerland
| | - Angela Schlumbaum
- Integrative Prehistoric and Archaeological Science (IPAS), University of Basel, Basel, Switzerland
| | - Hervé Bocherens
- Senckenberg Center for Human Evolution and Palaeoenvironment (HEP), University of Tübingen, Tübingen, Germany
- Dept of Geosciences (Biogeology), University of Tübingen, Tübingen, Germany
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13
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Population genetic structure of the land snail Camaena cicatricosa (Stylommatophora, Camaenidae) in China inferred from mitochondrial genes and ITS2 sequences. Sci Rep 2017; 7:15590. [PMID: 29142227 PMCID: PMC5688059 DOI: 10.1038/s41598-017-15758-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 11/01/2017] [Indexed: 02/01/2023] Open
Abstract
The phylogeographic structure of the land snail Camaena cicatricosa was analyzed in this study based on mitochondrial gene (COI and 16srRNA, mt DNA) and internal transcribed spacer (ITS2) sequences in 347 individuals. This snail is the vector of the zoonotic food-borne parasite Angiostrongylus cantonensis and one of the main harmful snails distributed exclusively in China. The results revealed significant fixation indices of genetic differentiation and high gene flow between most populations except several populations. An isolation-by-distance test showed no significant correlation between genetic distance and geographical distance among C. cicatricosa populations, which suggested that gene flow was not restricted by distance. The levels of haplotype and nucleotide diversity of C. cicatricosa were generally high, except those in some special populations, according to the mt DNA and ITS2 data. Furthermore, the phylogenetic trees and asteroid networks of haplotypes indicated nonobvious genetic structure, the same as results got based on the synonymous and non synonymous sites of 347 sequences of the COI gene. All lines of evidence indicated that climatic changes and geographical and human barriers do not substantially affect the current population structure and distribution of the investigated snails.
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Smouse PE, Banks SC, Peakall R. Converting quadratic entropy to diversity: Both animals and alleles are diverse, but some are more diverse than others. PLoS One 2017; 12:e0185499. [PMID: 29088229 PMCID: PMC5663342 DOI: 10.1371/journal.pone.0185499] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 09/13/2017] [Indexed: 12/14/2022] Open
Abstract
The use of diversity metrics has a long history in population ecology, while population genetic work has been dominated by variance-derived metrics instead, a technical gap that has slowed cross-communication between the fields. Interestingly, Rao’s Quadratic Entropy (RQE), comparing elements for ‘degrees of divergence’, was originally developed for population ecology, but has recently been deployed for evolutionary studies. We here translate RQE into a continuous diversity analogue, and then construct a multiply nested diversity partition for alleles, individuals, populations, and species, each component of which exhibits the behavior of proper diversity metrics, and then translate these components into [0,1]—scaled form. We also deploy non-parametric statistical tests of the among-stratum components and novel tests of the homogeneity of within-stratum diversity components at any hierarchical level. We then illustrate this new analysis with eight nSSR loci and a pair of close Australian marsupial (Antechinus) congeners, using both ‘different is different’ and ‘degree of difference’ distance metrics. The total diversity in the collection is larger than that within either species, but most of the within-species diversity is resident within single populations. The combined A. agilis collection exhibits more diversity than does the combined A. stuartii collection, possibly attributable to localized differences in either local ecological disturbance regimes or differential levels of population isolation. Beyond exhibiting different allelic compositions, the two congeners are becoming more divergent for the arrays of allele sizes they possess.
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Affiliation(s)
- Peter E. Smouse
- Department of Ecology, Evolution & Natural Resources, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Sam C. Banks
- The Fenner School of Environment and Society, The Australian National University, Acton, ACT, Australia
- * E-mail:
| | - Rod Peakall
- Research School of Biology, The Australian National University, Acton, ACT, Australia
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15
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Biedrzycka A, O'Connor E, Sebastian A, Migalska M, Radwan J, Zając T, Bielański W, Solarz W, Ćmiel A, Westerdahl H. Extreme MHC class I diversity in the sedge warbler (Acrocephalus schoenobaenus); selection patterns and allelic divergence suggest that different genes have different functions. BMC Evol Biol 2017; 17:159. [PMID: 28679358 PMCID: PMC5497381 DOI: 10.1186/s12862-017-0997-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 06/14/2017] [Indexed: 11/23/2022] Open
Abstract
Background Recent work suggests that gene duplications may play an important role in the evolution of immunity genes. Passerine birds, and in particular Sylvioidea warblers, have highly duplicated major histocompatibility complex (MHC) genes, which are key in immunity, compared to other vertebrates. However, reasons for this high MHC gene copy number are yet unclear. High-throughput sequencing (HTS) allows MHC genotyping even in individuals with extremely duplicated genes. This HTS data can reveal evidence of selection, which may help to unravel the putative functions of different gene copies, i.e. neofunctionalization. We performed exhaustive genotyping of MHC class I in a Sylvioidea warbler, the sedge warbler, Acrocephalus schoenobaenus, using the Illumina MiSeq technique on individuals from a wild study population. Results The MHC diversity in 863 genotyped individuals by far exceeds that of any other bird species described to date. A single individual could carry up to 65 different alleles, a large proportion of which are expressed (transcribed). The MHC alleles were of three different lengths differing in evidence of selection, diversity and divergence within our study population. Alleles without any deletions and alleles containing a 6 bp deletion showed characteristics of classical MHC genes, with evidence of multiple sites subject to positive selection and high sequence divergence. In contrast, alleles containing a 3 bp deletion had no sites subject to positive selection and had low divergence. Conclusions Our results suggest that sedge warbler MHC alleles that either have no deletion, or contain a 6 bp deletion, encode classical antigen presenting MHC molecules. In contrast, MHC alleles containing a 3 bp deletion may encode molecules with a different function. This study demonstrates that highly duplicated MHC genes can be characterised with HTS and that selection patterns can be useful for revealing neofunctionalization. Importantly, our results highlight the need to consider the putative function of different MHC genes in future studies of MHC in relation to disease resistance and fitness. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0997-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aleksandra Biedrzycka
- Institute of Nature Conservation, Polish Academy of Sciences, Al. Mickiewicza 33, 31-120, Kraków, Poland.
| | - Emily O'Connor
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Ecology Building, Sölvegatan 37, 223 62, Lund, Sweden
| | - Alvaro Sebastian
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University in Poznań, ul. Umultowska 89, 61-614, Poznań, Poland
| | - Magdalena Migalska
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University in Poznań, ul. Umultowska 89, 61-614, Poznań, Poland
| | - Jacek Radwan
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University in Poznań, ul. Umultowska 89, 61-614, Poznań, Poland
| | - Tadeusz Zając
- Institute of Nature Conservation, Polish Academy of Sciences, Al. Mickiewicza 33, 31-120, Kraków, Poland
| | - Wojciech Bielański
- Institute of Nature Conservation, Polish Academy of Sciences, Al. Mickiewicza 33, 31-120, Kraków, Poland
| | - Wojciech Solarz
- Institute of Nature Conservation, Polish Academy of Sciences, Al. Mickiewicza 33, 31-120, Kraków, Poland
| | - Adam Ćmiel
- Institute of Nature Conservation, Polish Academy of Sciences, Al. Mickiewicza 33, 31-120, Kraków, Poland
| | - Helena Westerdahl
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Ecology Building, Sölvegatan 37, 223 62, Lund, Sweden
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16
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Zhang LJ, Cai WZ, Luo JY, Zhang S, Wang CY, Lv LM, Zhu XZ, Wang L, Cui JJ. Phylogeographic patterns of Lygus pratensis (Hemiptera: Miridae): Evidence for weak genetic structure and recent expansion in northwest China. PLoS One 2017; 12:e0174712. [PMID: 28369108 PMCID: PMC5378377 DOI: 10.1371/journal.pone.0174712] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 03/14/2017] [Indexed: 12/02/2022] Open
Abstract
Lygus pratensis (L.) is an important cotton pest in China, especially in the northwest region. Nymphs and adults cause serious quality and yield losses. However, the genetic structure and geographic distribution of L. pratensis is not well known. We analyzed genetic diversity, geographical structure, gene flow, and population dynamics of L. pratensis in northwest China using mitochondrial and nuclear sequence datasets to study phylogeographical patterns and demographic history. L. pratensis (n = 286) were collected at sites across an area spanning 2,180,000 km2, including the Xinjiang and Gansu-Ningxia regions. Populations in the two regions could be distinguished based on mitochondrial criteria but the overall genetic structure was weak. The nuclear dataset revealed a lack of diagnostic genetic structure across sample areas. Phylogenetic analysis indicated a lack of population level monophyly that may have been caused by incomplete lineage sorting. The Mantel test showed a significant correlation between genetic and geographic distances among the populations based on the mtDNA data. However the nuclear dataset did not show significant correlation. A high level of gene flow among populations was indicated by migration analysis; human activities may have also facilitated insect movement. The availability of irrigation water and ample cotton hosts makes the Xinjiang region well suited for L. pratensis reproduction. Bayesian skyline plot analysis, star-shaped network, and neutrality tests all indicated that L. pratensis has experienced recent population expansion. Climatic changes and extensive areas occupied by host plants have led to population expansion of L. pratensis. In conclusion, the present distribution and phylogeographic pattern of L. pratensis was influenced by climate, human activities, and availability of plant hosts.
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Affiliation(s)
- Li-Juan Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, China
| | - Wan-Zhi Cai
- Department of Entomology, China Agricultural University, Beijing, China
| | - Jun-Yu Luo
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, China
| | - Shuai Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, China
| | - Chun-Yi Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, China
| | - Li-Min Lv
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, China
| | - Xiang-Zhen Zhu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, China
| | - Li Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, China
| | - Jin-Jie Cui
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, China
- * E-mail:
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17
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Inference of Ancestral Recombination Graphs through Topological Data Analysis. PLoS Comput Biol 2016; 12:e1005071. [PMID: 27532298 PMCID: PMC4988722 DOI: 10.1371/journal.pcbi.1005071] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 07/20/2016] [Indexed: 12/30/2022] Open
Abstract
The recent explosion of genomic data has underscored the need for interpretable and comprehensive analyses that can capture complex phylogenetic relationships within and across species. Recombination, reassortment and horizontal gene transfer constitute examples of pervasive biological phenomena that cannot be captured by tree-like representations. Starting from hundreds of genomes, we are interested in the reconstruction of potential evolutionary histories leading to the observed data. Ancestral recombination graphs represent potential histories that explicitly accommodate recombination and mutation events across orthologous genomes. However, they are computationally costly to reconstruct, usually being infeasible for more than few tens of genomes. Recently, Topological Data Analysis (TDA) methods have been proposed as robust and scalable methods that can capture the genetic scale and frequency of recombination. We build upon previous TDA developments for detecting and quantifying recombination, and present a novel framework that can be applied to hundreds of genomes and can be interpreted in terms of minimal histories of mutation and recombination events, quantifying the scales and identifying the genomic locations of recombinations. We implement this framework in a software package, called TARGet, and apply it to several examples, including small migration between different populations, human recombination, and horizontal evolution in finches inhabiting the Galápagos Islands.
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18
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Cheng Y, Zhou K, Humphreys MW, Harper JA, Ma X, Zhang X, Yan H, Huang L. Phylogenetic Relationships in the Festuca-Lolium Complex (Loliinae; Poaceae): New Insights from Chloroplast Sequences. Front Ecol Evol 2016. [DOI: 10.3389/fevo.2016.00089] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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19
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Balanovsky OP, Zaporozhchenko VV. Chromosome as a chronicler: Genetic dating, historical events, and DNA-genealogic temptation. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416070048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Population genetic structure and post-LGM expansion of the plant bug Nesidiocoris tenuis (Hemiptera: Miridae) in China. Sci Rep 2016; 6:26755. [PMID: 27230109 PMCID: PMC4882614 DOI: 10.1038/srep26755] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/29/2016] [Indexed: 11/29/2022] Open
Abstract
The plant bug, Nesidiocoris tenuis (Hemiptera: Miridae), is one of the most thermophilous dicyphines in agroecosystems and is widely distributed in China. Little is known regarding the genetic structure of N. tenuis and the effect of historical climatic fluctuations on N. tenuis populations. We analyzed partial sequences of three mitochondrial protein-coding genes (COI, ND2 and CytB) and nuclear genes (5.8S, ITS2 and 28S) for 516 specimens collected from 37 localities across China. Analyses of the combined mitochondrial dataset indicated that the Southwestern China group (SWC) was significantly differentiated from the remaining populations, other Chinese group (OC). Asymmetric migration and high level of gene flow across a long distance within the OC group was detected. The long-distance dispersal of N. tenuis might be affected by air currents and human interference. Both the neutrality tests and mismatch distributions revealed the occurrence of historical population expansion. Bayesian skyline plot analyses with two different substitution rates indicated that N. tenuis might follow the post-LGM (the Last Glacial Maximum) expansion pattern for temperate species. Pleistocene climatic fluctuation, complicated topography and anthropogenic factors, along with other ecological factors (e.g. temperature and air current) might have accounted for the current population structure of N. tenuis.
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Malyarchuk BA, Derenko M, Denisova G, Woźniak M, Rogalla U, Dambueva I, Grzybowski T. Y chromosome haplotype diversity in Mongolic-speaking populations and gene conversion at the duplicated STR DYS385a,b in haplogroup C3-M407. J Hum Genet 2016; 61:491-6. [DOI: 10.1038/jhg.2016.14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 01/12/2016] [Accepted: 01/29/2016] [Indexed: 12/27/2022]
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22
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Raj P, Rai E, Song R, Khan S, Wakeland BE, Viswanathan K, Arana C, Liang C, Zhang B, Dozmorov I, Carr-Johnson F, Mitrovic M, Wiley GB, Kelly JA, Lauwerys BR, Olsen NJ, Cotsapas C, Garcia CK, Wise CA, Harley JB, Nath SK, James JA, Jacob CO, Tsao BP, Pasare C, Karp DR, Li QZ, Gaffney PM, Wakeland EK. Regulatory polymorphisms modulate the expression of HLA class II molecules and promote autoimmunity. eLife 2016; 5:e12089. [PMID: 26880555 PMCID: PMC4811771 DOI: 10.7554/elife.12089] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 02/13/2016] [Indexed: 12/15/2022] Open
Abstract
Targeted sequencing of sixteen SLE risk loci among 1349 Caucasian cases and controls produced a comprehensive dataset of the variations causing susceptibility to systemic lupus erythematosus (SLE). Two independent disease association signals in the HLA-D region identified two regulatory regions containing 3562 polymorphisms that modified thirty-seven transcription factor binding sites. These extensive functional variations are a new and potent facet of HLA polymorphism. Variations modifying the consensus binding motifs of IRF4 and CTCF in the XL9 regulatory complex modified the transcription of HLA-DRB1, HLA-DQA1 and HLA-DQB1 in a chromosome-specific manner, resulting in a 2.5-fold increase in the surface expression of HLA-DR and DQ molecules on dendritic cells with SLE risk genotypes, which increases to over 4-fold after stimulation. Similar analyses of fifteen other SLE risk loci identified 1206 functional variants tightly linked with disease-associated SNPs and demonstrated that common disease alleles contain multiple causal variants modulating multiple immune system genes.
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Affiliation(s)
- Prithvi Raj
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Ekta Rai
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Ran Song
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Shaheen Khan
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Benjamin E Wakeland
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Kasthuribai Viswanathan
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Carlos Arana
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Chaoying Liang
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Bo Zhang
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Igor Dozmorov
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Ferdicia Carr-Johnson
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Mitja Mitrovic
- Department of Neurology, Yale School of Medicine, New Haven, United States
| | - Graham B Wiley
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, United States
| | - Jennifer A Kelly
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, United States
| | - Bernard R Lauwerys
- Pole de pathologies rhumatismales, Institut de Recherche Expérimentale et Clinique, Université catholique de Louvain, Bruxelles, Belgium
| | - Nancy J Olsen
- Division of Rheumatology, Department of Medicine, Penn State Medical School, Hershey, United States
| | - Chris Cotsapas
- Department of Neurology, Yale School of Medicine, New Haven, United States
| | - Christine K Garcia
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, United States
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, United States
| | - Carol A Wise
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, United States
- Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center, Dallas, United States
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, United States
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, United States
| | - John B Harley
- Cincinnati VA Medical Center, Cincinnati, United States
- Cincinnati Children's Hospital Medical Center, Cincinnati, United States
| | - Swapan K Nath
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, United States
| | - Judith A James
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, United States
| | - Chaim O Jacob
- Department of Medicine, University of Southern California, Los Angeles, United States
| | - Betty P Tsao
- Department of Medicine, University of California, Los Angeles, Los Angeles, United States
| | - Chandrashekhar Pasare
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
| | - David R Karp
- Rheumatic Diseases Division, Department of Medicine, University of Texas Southwestern Medical Center, Dallas, United States
| | - Quan Zhen Li
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Patrick M Gaffney
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, United States
| | - Edward K Wakeland
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
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Mudrik EA, Polyakova TA, Shatokhina AV, Bondarenko GN, Politov DV. Spatial distribution of intron 2 of nad1 gene haplotypes in populations of Norway and Siberian spruce (Picea abies–P. obovata) species complex. RUSS J GENET+ 2015. [DOI: 10.1134/s1022795415100129] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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24
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Zhang L, Li H, Li S, Zhang A, Kou F, Xun H, Wang P, Wang Y, Song F, Cui J, Cui J, Gouge DH, Cai W. Phylogeographic structure of cotton pest Adelphocoris suturalis (Hemiptera: Miridae): strong subdivision in China inferred from mtDNA and rDNA ITS markers. Sci Rep 2015; 5:14009. [PMID: 26388034 PMCID: PMC4585665 DOI: 10.1038/srep14009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 08/13/2015] [Indexed: 11/09/2022] Open
Abstract
Phylogeographic patterns of some extant plant and vertebrate species have been well studied; however, they are poorly understood in the majority of insects. The study documents analysis of mitochondrial (COI, CYTB and ND5) and nuclear (5.8S rDNA, ITS2 and 28S rDNA) data from 419 individuals of Adelphocoris suturalis, which is one of the main cotton pests found in the 31 locations in China and Japan involved in the study. Results show that the species is highly differentiated between populations from central China and peripheral China regions. Analysis of molecular variance showed a high level of geographical differentiation at different hierarchical levels. Isolation-by-distance test showed no significant correlation between genetic distance and geographical distance among A. suturalis populations, which suggested gene flow is not restricted by distance. In seven peripheral populations, the high levels of genetic differentiation and the small Nem values implied that geographic barriers were more likely restrict gene flow. Neutrality tests and the Bayesian skyline plot suggested population expansion likely happened during the cooling transition between Last Interglacial and Last Glacial Maximum. All lines of evidence suggest that physical barriers, Pleistocene climatic oscillations and geographical heterogeneity have affected the population structure and distribution of this insect in China.
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Affiliation(s)
- Lijuan Zhang
- Department of Entomology, China Agricultural University, Beijing 100193, China.,Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, Henan 455000, China
| | - Hu Li
- Department of Entomology, China Agricultural University, Beijing 100193, China
| | - Shujuan Li
- Maricopa Agricultural Center, University of Arizona, Maricopa, AZ 85138, USA
| | - Aibing Zhang
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Fei Kou
- Department of Entomology, China Agricultural University, Beijing 100193, China
| | - Huaizhu Xun
- Department of Entomology, China Agricultural University, Beijing 100193, China
| | - Pei Wang
- Key Laboratory of Molluscan Quarantine and Identification of AQSIQ, Fujian Entry-Exit Inspection &Quarantine Bureau, Fuzhou, Fujian 350001, China
| | - Ying Wang
- Henan Institute of Science and Technology, Xinxiang, Henan 453003, China
| | - Fan Song
- Department of Entomology, China Agricultural University, Beijing 100193, China
| | - Jianxin Cui
- Henan Institute of Science and Technology, Xinxiang, Henan 453003, China
| | - Jinjie Cui
- Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, Henan 455000, China
| | - Dawn H Gouge
- Department of Entomology, University of Arizona, Maricopa, AZ 85721, USA
| | - Wanzhi Cai
- Department of Entomology, China Agricultural University, Beijing 100193, China
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25
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Yao YG, Kajigaya S, Young NS. Mitochondrial DNA mutations in single human blood cells. Mutat Res 2015; 779:68-77. [PMID: 26149767 DOI: 10.1016/j.mrfmmm.2015.06.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Revised: 06/16/2015] [Accepted: 06/18/2015] [Indexed: 01/07/2023]
Abstract
Determination mitochondrial DNA (mtDNA) sequences from extremely small amounts of DNA extracted from tissue of limited amounts and/or degraded samples is frequently employed in medical, forensic, and anthropologic studies. Polymerase chain reaction (PCR) amplification followed by DNA cloning is a routine method, especially to examine heteroplasmy of mtDNA mutations. In this review, we compare the mtDNA mutation patterns detected by three different sequencing strategies. Cloning and sequencing methods that are based on PCR amplification of DNA extracted from either single cells or pooled cells yield a high frequency of mutations, partly due to the artifacts introduced by PCR and/or the DNA cloning process. Direct sequencing of PCR product which has been amplified from DNA in individual cells is able to detect the low levels of mtDNA mutations present within a cell. We further summarize the findings in our recent studies that utilized this single cell method to assay mtDNA mutation patterns in different human blood cells. Our data show that many somatic mutations observed in the end-stage differentiated cells are found in hematopoietic stem cells (HSCs) and progenitors within the CD34(+) cell compartment. Accumulation of mtDNA variations in the individual CD34+ cells is affected by both aging and family genetic background. Granulocytes harbor higher numbers of mutations compared with the other cells, such as CD34(+) cells and lymphocytes. Serial assessment of mtDNA mutations in a population of single CD34(+) cells obtained from the same donor over time suggests stability of some somatic mutations. CD34(+) cell clones from a donor marked by specific mtDNA somatic mutations can be found in the recipient after transplantation. The significance of these findings is discussed in terms of the lineage tracing of HSCs, aging effect on accumulation of mtDNA mutations and the usage of mtDNA sequence in forensic identification.
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Affiliation(s)
- Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China.
| | - Sachiko Kajigaya
- Hematology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Neal S Young
- Hematology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
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26
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Bianco E, Soto HW, Vargas L, Pérez-Enciso M. The chimerical genome of Isla del Coco feral pigs (Costa Rica), an isolated population since 1793 but with remarkable levels of diversity. Mol Ecol 2015; 24:2364-78. [DOI: 10.1111/mec.13182] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 03/18/2015] [Accepted: 03/24/2015] [Indexed: 01/27/2023]
Affiliation(s)
- E. Bianco
- Centre for Research in Agricultural Genomics (CRAG); CSIC-IRTA-UAB-UB Consortium; 08193 Bellaterra Spain
- Department of Animal Science; Universitat Autònoma de Barcelona; 08193 Bellaterra Spain
| | - H. W. Soto
- Escuela de Zootecnia; Universidad de Costa Rica; 10501 San José Costa Rica
| | - L. Vargas
- Sistema Nacional de Áreas de Conservación (SINAC); Ministerio de Ambiente y Energía (MINAE); Avenida 15, Calle 1, San José Costa Rica
| | - M. Pérez-Enciso
- Centre for Research in Agricultural Genomics (CRAG); CSIC-IRTA-UAB-UB Consortium; 08193 Bellaterra Spain
- Department of Animal Science; Universitat Autònoma de Barcelona; 08193 Bellaterra Spain
- Institut Català de Recerca I Estudis Avançats (ICREA); Carrer de Lluís Companys 23 Barcelona 08010 Spain
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27
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Peng MS, Fan L, Shi NN, Ning T, Yao YG, Murphy RW, Wang WZ, Zhang YP. DomeTree: a canonical toolkit for mitochondrial DNA analyses in domesticated animals. Mol Ecol Resour 2015; 15:1238-42. [PMID: 25655564 DOI: 10.1111/1755-0998.12386] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 02/01/2015] [Accepted: 02/02/2015] [Indexed: 01/01/2023]
Abstract
Mitochondrial DNA (mtDNA) is widely used in various genetic studies of domesticated animals. Many applications require comprehensive knowledge about the phylogeny of mtDNA variants. Herein, we provide the most up-to-date mtDNA phylogeny (i.e. haplogroup tree or matrilineal genealogy) and a standardized hierarchical haplogroup nomenclature system for domesticated cattle, dogs, goats, horses, pigs, sheep, yaks and chickens. These high-resolution mtDNA haplogroup trees based on 1240 complete or near-complete mtDNA genome sequences are available in open resource DomeTree (http://www.dometree.org). In addition, we offer the software MitoToolPy (http://www.mitotool.org/mp.html) to facilitate the mtDNA data analyses. We will continuously and regularly update DomeTree and MitoToolPy.
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Affiliation(s)
- Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, and Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650204, China
| | - Long Fan
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, 999077, China
| | - Ni-Ni Shi
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, and Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650204, China
| | - Tiao Ning
- Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, Yunnan, 650091, China
| | - Yong-Gang Yao
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650204, China.,Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, and Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China.,Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, Ontario, M5S 2C6, Canada
| | - Wen-Zhi Wang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, and Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, and Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650204, China.,Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, Yunnan, 650091, China
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28
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A genetic contribution from the Far East into Ashkenazi Jews via the ancient Silk Road. Sci Rep 2015; 5:8377. [PMID: 25669617 PMCID: PMC4323646 DOI: 10.1038/srep08377] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 01/14/2015] [Indexed: 11/08/2022] Open
Abstract
Contemporary Jews retain a genetic imprint from their Near Eastern ancestry, but obtained substantial genetic components from their neighboring populations during their history. Whether they received any genetic contribution from the Far East remains unknown, but frequent communication with the Chinese has been observed since the Silk Road period. To address this issue, mitochondrial DNA (mtDNA) variation from 55,595 Eurasians are analyzed. The existence of some eastern Eurasian haplotypes in eastern Ashkenazi Jews supports an East Asian genetic contribution, likely from Chinese. Further evidence indicates that this connection can be attributed to a gene flow event that occurred less than 1.4 kilo-years ago (kya), which falls within the time frame of the Silk Road scenario and fits well with historical records and archaeological discoveries. This observed genetic contribution from Chinese to Ashkenazi Jews demonstrates that the historical exchange between Ashkenazim and the Far East was not confined to the cultural sphere but also extended to an exchange of genes.
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29
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Ramírez O, Burgos-Paz W, Casas E, Ballester M, Bianco E, Olalde I, Santpere G, Novella V, Gut M, Lalueza-Fox C, Saña M, Pérez-Enciso M. Genome data from a sixteenth century pig illuminate modern breed relationships. Heredity (Edinb) 2015; 114:175-84. [PMID: 25204303 PMCID: PMC4815627 DOI: 10.1038/hdy.2014.81] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 07/09/2014] [Accepted: 08/06/2014] [Indexed: 01/16/2023] Open
Abstract
Ancient DNA (aDNA) provides direct evidence of historical events that have modeled the genome of modern individuals. In livestock, resolving the differences between the effects of initial domestication and of subsequent modern breeding is not straight forward without aDNA data. Here, we have obtained shotgun genome sequence data from a sixteenth century pig from Northeastern Spain (Montsoriu castle), the ancient pig was obtained from an extremely well-preserved and diverse assemblage. In addition, we provide the sequence of three new modern genomes from an Iberian pig, Spanish wild boar and a Guatemalan Creole pig. Comparison with both mitochondrial and autosomal genome data shows that the ancient pig is closely related to extant Iberian pigs and to European wild boar. Although the ancient sample was clearly domestic, admixture with wild boar also occurred, according to the D-statistics. The close relationship between Iberian, European wild boar and the ancient pig confirms that Asian introgression in modern Iberian pigs has not existed or has been negligible. In contrast, the Guatemalan Creole pig clusters apart from the Iberian pig genome, likely due to introgression from international breeds.
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Affiliation(s)
- O Ramírez
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, Barcelona, Spain
| | - W Burgos-Paz
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - E Casas
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Spain
| | - M Ballester
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - E Bianco
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - I Olalde
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, Barcelona, Spain
| | - G Santpere
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, Barcelona, Spain
| | - V Novella
- Departament de Prehistòria, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - M Gut
- Centro Nacional de Análisis Genómico (CNAG), PCB, Barcelona, Spain
| | - C Lalueza-Fox
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, Barcelona, Spain
| | - M Saña
- Departament de Prehistòria, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - M Pérez-Enciso
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Institut Català de Recerca i Estudis Avançats (ICREA), Carrer de Lluís Companys 23, Barcelona, Spain
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30
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Huber KT, Van Iersel L, Moulton V, Wu T. How much information is needed to infer reticulate evolutionary histories? Syst Biol 2014; 64:102-11. [PMID: 25236959 PMCID: PMC4265143 DOI: 10.1093/sysbio/syu076] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Phylogenetic networks are a generalization of evolutionary trees and are an important tool for analyzing reticulate evolutionary histories. Recently, there has been great interest in developing new methods to construct rooted phylogenetic networks, that is, networks whose internal vertices correspond to hypothetical ancestors, whose leaves correspond to sampled taxa, and in which vertices with more than one parent correspond to taxa formed by reticulate evolutionary events such as recombination or hybridization. Several methods for constructing evolutionary trees use the strategy of building up a tree from simpler building blocks (such as triplets or clusters), and so it is natural to look for ways to construct networks from smaller networks. In this article, we shall demonstrate a fundamental issue with this approach. Namely, we show that even if we are given all of the subnetworks induced on all proper subsets of the leaves of some rooted phylogenetic network, we still do not have all of the information required to completely determine that network. This implies that even if all of the building blocks for some reticulate evolutionary history were to be taken as the input for any given network building method, the method might still output an incorrect history. We also discuss some potential consequences of this result for constructing phylogenetic networks.
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Affiliation(s)
- Katharina T Huber
- School of Computing Sciences, University of East Anglia, Norwich, UK, and Centrum Wiskunde & Informatica (CWI), Amsterdam, Netherlands
| | - Leo Van Iersel
- School of Computing Sciences, University of East Anglia, Norwich, UK, and Centrum Wiskunde & Informatica (CWI), Amsterdam, Netherlands
| | - Vincent Moulton
- School of Computing Sciences, University of East Anglia, Norwich, UK, and Centrum Wiskunde & Informatica (CWI), Amsterdam, Netherlands
| | - Taoyang Wu
- School of Computing Sciences, University of East Anglia, Norwich, UK, and Centrum Wiskunde & Informatica (CWI), Amsterdam, Netherlands
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31
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A simple repeat polymorphism in the MITF-M promoter is a key regulator of white spotting in dogs. PLoS One 2014; 9:e104363. [PMID: 25116146 PMCID: PMC4130573 DOI: 10.1371/journal.pone.0104363] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Accepted: 07/12/2014] [Indexed: 01/19/2023] Open
Abstract
The white spotting locus (S) in dogs is colocalized with the MITF (microphtalmia-associated transcription factor) gene. The phenotypic effects of the four S alleles range from solid colour (S) to extreme white spotting (sw). We have investigated four candidate mutations associated with the sw allele, a SINE insertion, a SNP at a conserved site and a simple repeat polymorphism all associated with the MITF-M promoter as well as a 12 base pair deletion in exon 1B. The variants associated with white spotting at all four loci were also found among wolves and we conclude that none of these could be a sole causal mutation, at least not for extreme white spotting. We propose that the three canine white spotting alleles are not caused by three independent mutations but represent haplotype effects due to different combinations of causal polymorphisms. The simple repeat polymorphism showed extensive diversity both in dogs and wolves, and allele-sharing was common between wolves and white spotted dogs but was non-existent between solid and spotted dogs as well as between wolves and solid dogs. This finding was unexpected as Solid is assumed to be the wild-type allele. The data indicate that the simple repeat polymorphism has been a target for selection during dog domestication and breed formation. We also evaluated the significance of the three MITF-M associated polymorphisms with a Luciferase assay, and found conclusive evidence that the simple repeat polymorphism affects promoter activity. Three alleles associated with white spotting gave consistently lower promoter activity compared with the allele associated with solid colour. We propose that the simple repeat polymorphism affects cooperativity between transcription factors binding on either flanking sides of the repeat. Thus, both genetic and functional evidence show that the simple repeat polymorphism is a key regulator of white spotting in dogs.
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32
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Incorporation of aurochs into a cattle herd in Neolithic Europe: single event or breeding? Sci Rep 2014; 4:5798. [PMID: 25052335 PMCID: PMC4107343 DOI: 10.1038/srep05798] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 07/04/2014] [Indexed: 12/02/2022] Open
Abstract
Domestication is an ongoing process continuously changing the lives of animals and humans and the environment. For the majority of European cattle (Bos taurus) genetic and archaeozoological evidence support initial domestication ca. 11'000 BP in the Near East from few founder aurochs (Bos primigenius) belonging to the mitochondrial DNA T macro-haplogroup. Gene flow between wild European aurochs of P haplogroup and domestic cattle of T haplogroup, coexisting over thousands of years, appears to have been sporadic. We report archaeozoological and ancient DNA evidence for the incorporation of wild stock into a domestic cattle herd from a Neolithic lake-dwelling in Switzerland. A complete metacarpus of a small and compact adult bovid is morphologically and genetically a female. With withers height of ca. 112 cm, it is comparable in size with small domestic cattle from contemporaneous sites in the area. The bone is directly dated to 3360–3090 cal BC and associated to the Horgen culture, a period of the secondary products revolution. The cow possessed a novel mtDNA P haplotype variant of the European aurochs. We argue this is either a single event or, based on osteological characteristics of the Horgen cattle, a rare instance of intentional breeding with female aurochs.
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33
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Li R, Wang SQ, Xu SY, Huang JP, Wang FQ, Ma ZJ, Dang RH, Lan XY, Chen H, Lei CZ. Novel Y-chromosome polymorphisms in Chinese domestic yak. Anim Genet 2014; 45:449-52. [DOI: 10.1111/age.12139] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2014] [Indexed: 11/29/2022]
Affiliation(s)
- R. Li
- Shaanxi Key Laboratory of Molecular Biology for Agriculture; College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi 712100 China
| | - S.-Q. Wang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture; College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi 712100 China
| | - S.-Y. Xu
- Shaanxi Key Laboratory of Molecular Biology for Agriculture; College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi 712100 China
| | - J.-P. Huang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture; College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi 712100 China
| | - F.-Q. Wang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture; College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi 712100 China
| | - Z.-J. Ma
- Qinghai Academy of Animal Science and Veterinary Medicine; Xining Qinghai 810016 China
| | - R.-H. Dang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture; College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi 712100 China
| | - X.-Y. Lan
- Shaanxi Key Laboratory of Molecular Biology for Agriculture; College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi 712100 China
| | - H. Chen
- Shaanxi Key Laboratory of Molecular Biology for Agriculture; College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi 712100 China
| | - C.-Z. Lei
- Shaanxi Key Laboratory of Molecular Biology for Agriculture; College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi 712100 China
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34
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Y-chromosome diversity in the Kalmyks at the ethnical and tribal levels. J Hum Genet 2013; 58:804-11. [DOI: 10.1038/jhg.2013.108] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 09/16/2013] [Accepted: 09/27/2013] [Indexed: 01/15/2023]
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35
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Sans M, Figueiro G, Hidalgo PC. A new mitochondrial C1 lineage from the prehistory of Uruguay: population genocide, ethnocide, and continuity. Hum Biol 2013; 84:287-305. [PMID: 23020097 DOI: 10.3378/027.084.0303] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Uruguayan population has been considered as of European descent, as its Native populations victims of genocide apparently disappeared in the 19th century. Contradicting this national belief, genetic studies have shown a substantial Native contribution. However, the continuity between prehistoric, historic, and present populations remains unproved. With the aim of adding elements to prove a possible population continuity, we studied a mitochondrial lineage, part of haplogroup C1, analyzing the complete genome of a modern Uruguayan individual and the hypervariable region I (HVRI) in prehistoric, historic, and contemporary individuals. Several individuals carried the mutations that characterize this lineage: two from an archaeological mound located in the east of the country, the Charrúa Indian chief Vaimaca Perú and five individuals from the present population. The lineage was initially characterized by its HVRI sequence, having the four typical C1 mutations and adding 16051G and 16288C; other mutations were also found: 16140C was found in all but the oldest individual, dated 1,610 years BP, while 16209C, 16422C, and 16519C were found only in some individuals. Hypervariable region II showed the typical C1 mutations and 194T. The coding region, analyzed in modern individuals, was characterized by 12378T, while other mutations found were not common to all of them. In summary, we have found and described a new lineage that shows continuity from prehistoric mound builders to the present population, through a representative of the extinct Charrúa Indians. The lineage appeared at least 1,600 years ago and is carried by approximately 0.7% of the modern Uruguayan population. The continuity of the lineage supports alternative perspectives about Uruguayan national identity and the meaning of the genocide, best labeled as ethnocide because of its consequences. It also contributes to the discussion about who the prehistoric mound builders were, and to the origin, at least in the maternal line, of a Charrúa Indian. From a more general perspective, we can conclude that the characteristics, evolution, and expansion of founder haplogroup C in America have not yet been elucidated.
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Affiliation(s)
- Monica Sans
- Department of Biological Anthropology, College of Humanities and Educational Sciences, University of the Republic, Magallanes 1577, 11,200 Montevideo, Uruguay.
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36
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Almerão MP, Fagundes NJR, de Araújo PB, Verne S, Grandjean F, Bouchon D, Araújo AM. First record of Wolbachia in South American terrestrial isopods: Prevalence and diversity in two species of Balloniscus (Crustacea, Oniscidea). Genet Mol Biol 2012; 35:980-9. [PMID: 23413179 PMCID: PMC3571423 DOI: 10.1590/s1415-47572012000600013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Wolbachia are endosymbiotic bacteria that commonly infect arthropods, inducing certain phenotypes in their hosts. So far, no endemic South American species of terrestrial isopods have been investigated for Wolbachia infection. In this work, populations from two species of Balloniscus (B. sellowii and B. glaber) were studied through a diagnostic PCR assay. Fifteen new Wolbachia 16S rDNA sequences were detected. Wolbachia found in both species were generally specific to one population, and five populations hosted two different Wolbachia 16S rDNA sequences. Prevalence was higher in B. glaber than in B. sellowii, but uninfected populations could be found in both species. Wolbachia strains from B. sellowii had a higher genetic variation than those isolated from B. glaber. AMOVA analyses showed that most of the genetic variance was distributed among populations of each species rather than between species, and the phylogenetic analysis suggested that Wolbachia strains from Balloniscus cluster within Supergroup B, but do not form a single monophyletic clade, suggesting multiple infections for this group. Our results highlight the importance of studying Wolbachia prevalence and genetic diversity in Neotropical species and suggest that South American arthropods may harbor a great number of diverse strains, providing an interesting model to investigate the evolution of Wolbachia and its hosts.
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Affiliation(s)
- Mauricio Pereira Almerão
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil. ; Departamento de Zoologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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Soares I, Goios A, Amorim A. Sequence comparison alignment-free approach based on suffix tree and L-words frequency. ScientificWorldJournal 2012; 2012:450124. [PMID: 22997494 PMCID: PMC3444837 DOI: 10.1100/2012/450124] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 08/05/2012] [Indexed: 11/17/2022] Open
Abstract
The vast majority of methods available for sequence comparison rely on a first sequence alignment step, which requires a number of assumptions on evolutionary history and is sometimes very difficult or impossible to perform due to the abundance of gaps (insertions/deletions). In such cases, an alternative alignment-free method would prove valuable. Our method starts by a computation of a generalized suffix tree of all sequences, which is completed in linear time. Using this tree, the frequency of all possible words with a preset length L-L-words--in each sequence is rapidly calculated. Based on the L-words frequency profile of each sequence, a pairwise standard Euclidean distance is then computed producing a symmetric genetic distance matrix, which can be used to generate a neighbor joining dendrogram or a multidimensional scaling graph. We present an improvement to word counting alignment-free approaches for sequence comparison, by determining a single optimal word length and combining suffix tree structures to the word counting tasks. Our approach is, thus, a fast and simple application that proved to be efficient and powerful when applied to mitochondrial genomes. The algorithm was implemented in Python language and is freely available on the web.
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Affiliation(s)
- Inês Soares
- Faculdade de Ciências da Universidade do Porto, 4169 Porto, Portugal.
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Roesch Goodman K, Welter SC, Roderick GK. Genetic divergence is decoupled from ecological diversification in the Hawaiian Nesosydne planthoppers. Evolution 2012; 66:2798-814. [PMID: 22946804 DOI: 10.1111/j.1558-5646.2012.01643.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Adaptive radiation involves ecological shifts coupled with isolation of gene pools. However, we know little about what drives the initial stages of divergence. We study a system in which ecological diversification is found within a chronologically well-defined geological matrix to provide insight into this enigmatic phase of radiation. We tested the hypothesis that a period of geographic isolation precedes ecological specialization in an adaptive radiation of host-specialized Hawaiian planthoppers. We examined population structure and history using mitochondrial and multiple independent microsatellite loci in a species whose geographic distribution on the island of Hawaii enabled us to observe the chronology of divergence in its very earliest stages. We found that genetic divergence is associated with geographic features but not different plant hosts and that divergence times are very recent and on the same timescales as the dynamic geology of the island. Our results suggest an important role for geography in the dynamics of the early stages of divergence.
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Affiliation(s)
- Kari Roesch Goodman
- Department of Environmental Science, Policy and Management, 130 Mulford Hall, University of California, Berkeley, California 94720-3114, USA.
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39
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Martínez A, Ferrando A, Manunza A, Gómez M, Landi V, Jordana J, Capote J, Badaoui B, Vidal O, Delgado J, Amills M. Inferring the demographic history of a highly endangered goat breed through the analysis of nuclear and mitochondrial genetic signatures. Small Rumin Res 2012. [DOI: 10.1016/j.smallrumres.2011.11.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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40
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Madrigal L, Posthumously LC, Melendez-Obando M, Villegas-Palma R, Barrantes R, Raventos H, Pereira R, Luiselli D, Pettener D, Barbujani G. High mitochondrial mutation rates estimated from deep-rooting Costa Rican pedigrees. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2012; 148:327-33. [PMID: 22460349 DOI: 10.1002/ajpa.22052] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 02/10/2012] [Indexed: 11/07/2022]
Abstract
Estimates of mutation rates for the noncoding hypervariable Region I (HVR-I) of mitochondrial DNA vary widely, depending on whether they are inferred from phylogenies (assuming that molecular evolution is clock-like) or directly from pedigrees. All pedigree-based studies so far were conducted on populations of European origin. In this article, we analyzed 19 deep-rooting pedigrees in a population of mixed origin in Costa Rica. We calculated two estimates of the HVR-I mutation rate, one considering all apparent mutations, and one disregarding changes at sites known to be mutational hot spots and eliminating genealogy branches which might be suspected to include errors, or unrecognized adoptions along the female lines. At the end of this procedure, we still observed a mutation rate equal to 1.24 × 10(-6) , per site per year, i.e., at least threefold as high as estimates derived from phylogenies. Our results confirm that mutation rates observed in pedigrees are much higher than estimated assuming a neutral model of long-term HVRI evolution. We argue that until the cause of these discrepancies will be fully understood, both lower estimates (i.e., those derived from phylogenetic comparisons) and higher, direct estimates such as those obtained in this study, should be considered when modeling evolutionary and demographic processes.
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Affiliation(s)
- Lorena Madrigal
- Department of Anthropology, University of South Florida, Tampa, FL 3360, USA
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41
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Wang HW, Li YC, Sun F, Zhao M, Mitra B, Chaudhuri TK, Regmi P, Wu SF, Kong QP, Zhang YP. Revisiting the role of the Himalayas in peopling Nepal: insights from mitochondrial genomes. J Hum Genet 2012; 57:228-34. [PMID: 22437208 DOI: 10.1038/jhg.2012.8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Himalayas was believed to be a formidably geographical barrier between South and East Asia. The observed high frequency of the East Eurasian paternal lineages in Nepal led some researchers to suggest that these lineages were introduced into Nepal from Tibet directly; however, it is also possible that the East Eurasian genetic components might trace their origins to northeast India where abundant East Eurasian maternal lineages have been detected. To trace the origin of the Nepalese maternal genetic components, especially those of East Eurasian ancestry, and then to better understand the role of the Himalayas in peopling Nepal, we have studied the matenal genetic composition extensively, especially the East Eurasian lineages, in Nepalese and its surrounding populations. Our results revealed the closer affinity between the Nepalese and the Tibetans, specifically, the Nepalese lineages of the East Eurasian ancestry generally are phylogenetically closer with the ones from Tibet, albeit a few mitochondrial DNA haplotypes, likely resulted from recent gene flow, were shared between the Nepalese and northeast Indians. It seems that Tibet was most likely to be the homeland for most of the East Eurasian in the Nepalese. Taking into account the previous observation on Y chromosome, now it is convincing that bearer of the East Eurasian genetic components had entered Nepal across the Himalayas around 6 kilo years ago (kya), a scenario in good agreement with the previous results from linguistics and archeology.
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Affiliation(s)
- Hua-Wei Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan Province, China
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42
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Abilev S, Malyarchuk B, Derenko M, Wozniak M, Grzybowski T, Zakharov I. The Y-chromosome C3* Star-Cluster Attributed to Genghis Khan's Descendants is Present at High Frequency in the Kerey Clan from Kazakhstan. Hum Biol 2012; 84:79-89. [DOI: 10.3378/027.084.0106] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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43
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Schlumbaum A, van Glabeke S, Roldan-Ruiz I. Towards the onset of fruit tree growing north of the Alps: Ancient DNA from waterlogged apple (Malus sp.) seed fragments. Ann Anat 2012; 194:157-62. [DOI: 10.1016/j.aanat.2011.03.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Revised: 02/25/2011] [Accepted: 03/07/2011] [Indexed: 12/01/2022]
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44
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Li QQ, Li DY, Ye H, Liu XF, Shi W, Cao N, Duan YQ. Using COI gene sequence to barcode two morphologically alike species: the cotton bollworm and the oriental tobacco budworm (Lepidoptera: Noctuidae). Mol Biol Rep 2011; 38:5107-13. [PMID: 21181271 DOI: 10.1007/s11033-010-0658-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Accepted: 12/04/2010] [Indexed: 11/30/2022]
Abstract
Due to limited morphological difference, the two closely related sister species, the cotton bollworm, Helicoverpa armigera (Hübner) and the oriental tobacco budworm, H. assulta (Guenée) (Lepidoptera: Noctuidae), are very difficult to distinguish, especially at the larvae stage. Recently, DNA sequence has been widely used as a bio-barcode for species identification. In this study, we attempted to distinguish H. armigera and H. assulta using the mitochondrial cytochrome C oxidase subunit I gene (COI) gene sequence as the barcode. We determined a 658 bp segment of the COI gene for 28 individuals of H. armigera, 8 individuals of H. assulta, and 10 individuals of Mamestra brassicae (as the outgroup) in Yunnan Province, southwest of P. R. China, together with one H. assulta and two H. armigera reported sequences from GenBank. Twenty-three haplotypes were identified in all 49 samples. As expected, network analysis of the haplotypes of the three species presented a clustering pattern consistent with the respective species status. Haplotypes of the same species differed from each other by no more than three nucleotide substitutions. However, each haplotype of H. armigera differed from that of H. assulta by at least 22 nucleotide substitutions. Both species differed from M. brassicae by more than 50 nucleotide substitutions. 17 unique diagnostic nucleotides were also used to discriminate the two species. The finding of large COI sequence differences between H. armigera and H. assulta suggested that it could be used to distinguish the two morphologically alike species and be employed for quick species identification during pest control.
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Affiliation(s)
- Qing-Qing Li
- Life Science College, Yunnan Normal University, 650092 Kunming, Yunnan, China
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45
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Luo M, Liu Z, Pan H, Zhao L, Li M. Historical geographic dispersal of the golden snub-nosed monkey (Rhinopithecus roxellana) and the influence of climatic oscillations. Am J Primatol 2011; 74:91-101. [PMID: 22025257 DOI: 10.1002/ajp.21006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Revised: 08/01/2011] [Accepted: 08/25/2011] [Indexed: 11/12/2022]
Abstract
Current understanding of historic climate oscillations that have occurred over the past few million years has modified scientific views on evolution. Major climatic events have caused local and global extinction of plants and animals and have impacted the spatial distribution of many species. The endangered golden snub-nosed monkey (Rhinopithecus roxellana) currently inhabits three isolated regions of China: the Sichuan and Gansu provinces (SG), the Qinling Mountains in Shaanxi province (QL), and the Shennongjia Forestry District in Hubei province (SNJ). However, considerable uncertainty still exists about their historical dispersal routes under the influence of environment change. To date, two dispersal routes have been proposed: (1) the QL and SNJ populations originated from the SG population; and (2) the SG population recolonized from the QL and SNJ populations. We used the mitochondrial DNA complete control region to perform statistical assessments of the relative probability of alternative migration scenarios and the role of environmental change on the geographic dispersal of Rhinopithecus roxellana. Thirty haplotypes were identified from the three geographic regions and a high degree of genetic structure was observed. The most recent common ancestor among the mitochondrial DNA haplotypes was estimated to live around 0.47-1.88 million years ago and five notable haplotype clusters were found. Phylogenetic analysis and historical gene flow estimates suggested that the QL and SNJ populations originated from the SG population, with at least two dispersal events from the SG population occurring during the Pleistocene (1.17±0.70 and 0.53±0.30 Ma). Composite dispersal history of the golden snub-nosed monkey can be explained by both environmental change inducing global climate change and the influence of the Tibetan Plateau uplift. Such range shifts involved considerable demographic changes, as revealed in the dramatic decreases in population size during the last 25,000 years.
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Affiliation(s)
- Maofang Luo
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Chaoyang, Beijing, People's Republic of China
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46
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Zhang AM, Bandelt HJ, Jia X, Zhang W, Li S, Yu D, Wang D, Zhuang XY, Zhang Q, Yao YG. Is mitochondrial tRNA(phe) variant m.593T>C a synergistically pathogenic mutation in Chinese LHON families with m.11778G>A? PLoS One 2011; 6:e26511. [PMID: 22039503 PMCID: PMC3198432 DOI: 10.1371/journal.pone.0026511] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2011] [Accepted: 09/28/2011] [Indexed: 01/28/2023] Open
Abstract
Mitochondrial transfer RNA (mt-tRNA) mutations have been reported to be associated with a variety of diseases. In a previous paper that studied the mtDNA background effect on clinical expression of Leber's hereditary optic neuropathy (LHON) in 182 Chinese families with m.11778G>A, we found a strikingly high frequency (7/182) of m.593T>C in the mitochondrially encoded tRNA phenylalanine (MT-TF) gene in unrelated LHON patients. To determine the potential role of m.593T>C in LHON, we compared the frequency of this variant in 479 LHON patients with m.11778G>A, 843 patients with clinical features of LHON but without the three known primary mutations, and 2374 Han Chinese from the general populations. The frequency of m.593T>C was higher in LHON patients (14/479) than in suspected LHON subjects (12/843) or in general controls (49/2374), but the difference was not statistically significant. The overall penetrance of LHON in families with both m.11778G>A and m.593T>C (44.6%) was also substantially higher than that of families with only m.11778G>A (32.9%) (P = 0.083). Secondary structure prediction of the MT-TF gene with the wild type or m.593T>C showed that this nucleotide change decreases the free energy. Electrophoretic mobility of the MT-TF genes with the wild type or m.593T>C transcribed in vitro further confirmed the change of secondary structure in the presence of this variant. Although our results could suggest a modest synergistic effect of variant m.593T>C on the LHON causing mutation m.11778G>A, the lack of statistical significance probably due to the relatively small sample size analyzed, makes necessary more studies to confirm this effect.
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Affiliation(s)
- A-Mei Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China
- Graduate School of the Chinese Academy of Sciences, Beijing, China
| | | | - Xiaoyun Jia
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wen Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China
- Graduate School of the Chinese Academy of Sciences, Beijing, China
| | - Shiqiang Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Dandan Yu
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China
| | - Dong Wang
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China
- Graduate School of the Chinese Academy of Sciences, Beijing, China
| | - Xin-Ying Zhuang
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China
| | - Qingjiong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, Guangdong, China
- * E-mail: (QZ); (YGY)
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China
- * E-mail: (QZ); (YGY)
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Lymbery AJ, Thompson RCA. The molecular epidemiology of parasite infections: tools and applications. Mol Biochem Parasitol 2011; 181:102-16. [PMID: 22027028 DOI: 10.1016/j.molbiopara.2011.10.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 10/10/2011] [Accepted: 10/12/2011] [Indexed: 10/16/2022]
Abstract
Molecular epidemiology, broadly defined, is the application of molecular genetic techniques to the dynamics of disease in a population. In this review, we briefly describe molecular and analytical tools available for molecular epidemiological studies and then provide an overview of how they can be applied to better understand parasitic disease. A range of new molecular tools have been developed in recent years, allowing for the direct examination of parasites from clinical or environmental samples, and providing access to relatively cheap, rapid, high throughput molecular assays. At the same time, new analytical approaches, in particular those derived from coalescent theory, have been developed to provide more robust estimates of evolutionary processes and demographic parameters from multilocus, genotypic data. To date, the primary application of molecular epidemiology has been to provide specific and sensitive identification of parasites and to resolve taxonomic issues, particularly at the species level and below. Population genetic studies have also been used to determine the extent of genetic diversity among populations of parasites and the degree to which this diversity is associated with different host cycles or epidemiologically important phenotypes. Many of these studies have also shed new light on transmission cycles of parasites, particularly the extent to which zoonotic transmission occurs, and on the prevalence and importance of mixed infections with different parasite species or intraspecific variants (polyparasitism). A major challenge, and one which is now being addressed by an increasing number of studies, is to find and utilize genetic markers for complex traits of epidemiological significance, such as drug resistance, zoonotic potential and virulence.
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Affiliation(s)
- A J Lymbery
- Fish Health Unit, School of Veterinary and Biomedical Sciences, Murdoch University, Murdoch WA 6150, Australia.
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De Barro P, Ahmed MZ. Genetic networking of the Bemisia tabaci cryptic species complex reveals pattern of biological invasions. PLoS One 2011; 6:e25579. [PMID: 21998669 PMCID: PMC3184991 DOI: 10.1371/journal.pone.0025579] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Accepted: 09/07/2011] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND A challenge within the context of cryptic species is the delimitation of individual species within the complex. Statistical parsimony network analytics offers the opportunity to explore limits in situations where there are insufficient species-specific morphological characters to separate taxa. The results also enable us to explore the spread in taxa that have invaded globally. METHODOLOGY/PRINCIPAL FINDINGS Using a 657 bp portion of mitochondrial cytochrome oxidase 1 from 352 unique haplotypes belonging to the Bemisia tabaci cryptic species complex, the analysis revealed 28 networks plus 7 unconnected individual haplotypes. Of the networks, 24 corresponded to the putative species identified using the rule set devised by Dinsdale et al. (2010). Only two species proposed in Dinsdale et al. (2010) departed substantially from the structure suggested by the analysis. The analysis of the two invasive members of the complex, Mediterranean (MED) and Middle East - Asia Minor 1 (MEAM1), showed that in both cases only a small number of haplotypes represent the majority that have spread beyond the home range; one MEAM1 and three MED haplotypes account for >80% of the GenBank records. Israel is a possible source of the globally invasive MEAM1 whereas MED has two possible sources. The first is the eastern Mediterranean which has invaded only the USA, primarily Florida and to a lesser extent California. The second are western Mediterranean haplotypes that have spread to the USA, Asia and South America. The structure for MED supports two home range distributions, a Sub-Saharan range and a Mediterranean range. The MEAM1 network supports the Middle East - Asia Minor region. CONCLUSION/SIGNIFICANCE The network analyses show a high level of congruence with the species identified in a previous phylogenetic analysis. The analysis of the two globally invasive members of the complex support the view that global invasion often involve very small portions of the available genetic diversity.
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Affiliation(s)
- Paul De Barro
- CSIRO Ecosystem Sciences, Brisbane, Queensland, Australia.
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Association of mtDNA haplogroup F with healthy longevity in the female Chuang population, China. Exp Gerontol 2011; 46:987-93. [PMID: 21945877 DOI: 10.1016/j.exger.2011.09.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2010] [Revised: 07/26/2011] [Accepted: 09/07/2011] [Indexed: 11/20/2022]
Abstract
Human longevity is a complex heritable genetic trait. Based on substantial evidence from model organisms, it is clear that mitochondria play a pivotal role in aging and lifespan. However, the effects that mitochondrial genome variations have upon longevity and longevity-related phenotypes in Chuang people in China have yet to be established. By genotyping 15 variants for 10 haplogroups in 738 Chuang subjects, including 367 long-lived individuals and 371 controls, we found that haplogroup F was significantly associated with longevity in females of Zhuang population of China (p=0.003, OR: 2.01, 95%CI: 1.263-3.197). Additionally, haplogroup F was related to higher HDL levels (p<0.05) in long-lived individuals. Further analysis suggests that the non-synonymous variant m.13928G>C in haplogroup F was also associated with longevity in female Zhuang Chinese which might account for the beneficial effect of F.
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50
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Malyarchuk B, Derenko M, Denisova G, Maksimov A, Wozniak M, Grzybowski T, Dambueva I, Zakharov I. Ancient links between Siberians and Native Americans revealed by subtyping the Y chromosome haplogroup Q1a. J Hum Genet 2011; 56:583-8. [PMID: 21677663 DOI: 10.1038/jhg.2011.64] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
To investigate the structure of Y chromosome haplogroups R-M207 and Q-M242 in human populations of North Asia, we have performed high-resolution genotyping using both single nucleotide polymorphisms and short tandem repeat (STR)-based approaches of 121 M207- and M242-derived samples from 885 males of 16 ethnic groups of Siberia and East Asia. As a result, the following Y chromosome haplogroups were revealed: R1b1b1-M73 (2.0%), R1b1b2-M269 (0.7%), R2-M124 (1.1%), Q1a*-MEH2 (0.5%), Q1a2-M25 (0.1%), Q1a3*-M346 (9.2%) and Q1a3a-M3 (0.2%). Despite the low coalescence age of haplogroup Q1a3*-M346, which is estimated in South Siberia as about 4.5±1.5 thousand years ago (Ka), divergence time between these Q1a3*-M346 haplotypes and Amerindian-specific haplogroup Q1a3a-M3 is equal to 13.8±3.9 Ka, pointing to a relatively recent entry date to America. In addition, unique cluster of haplotypes belonging to Q1a*-MEH2 was found in Koryaks inhabiting the Sea of Okhotsk coast (at a frequency of 10.3%). Although the level of STR diversity associated with Q1a*-MEH2 is very low, this lineage appears to be closest to the extinct Palaeo-Eskimo individuals belonging to the Saqqaq culture arisen in the New World Arctic about 5.5 Ka. This finding suggests that Q1a*-MEH2 likely traces a population migration originating in Northeast Siberia across the Bering Strait.
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Affiliation(s)
- Boris Malyarchuk
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya street 18, Magadan, Russia.
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