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Prakas P, Butkauskas D, Balčiauskienė L, Balčiauskas L. Low Genetic Variability of the Tundra Vole in Lithuania. Animals (Basel) 2024; 14:270. [PMID: 38254439 PMCID: PMC10812506 DOI: 10.3390/ani14020270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/10/2024] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
The distribution and spread of the tundra vole (Alexandromys oeconomus) in Lithuania have been documented over the last 70 years, but the genetic diversity of the species has not been studied. In this study, we examined A. oeconomus trapped in three sites in northern and western Lithuania using mtDNA sequence analysis of the cytb and control region. The western and northern sites are separated by anthropogenic landscape barriers. The western site is subject to regular spring flooding. Phylogenetic analyses of the studied individuals placed them in the Central European phylogroup, suggesting that Lithuanian A. oeconomus originated from northeastern Poland. In Lithuania, the genetic diversity of A. oeconomus at both mtDNA loci was relatively low (Hd < 0.6, π < 0.002) compared to that found in other European samples (Hd = 0.833-0.958; π = 0.00402-0.01552). Individuals analyzed in Lithuania were genetically different from samples collected in Poland and Northern Europe (ΦST > 0.15, p < 0.05). The genetic divergence between the western and northern samples of A. oeconomus in Lithuania, together with the low genetic variability among the voles studied, provides new insights into the phylogeography of the species and the influence of barriers on the colonization of the country.
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Affiliation(s)
- Petras Prakas
- Nature Research Centre, Akademijos Str. 2, LT-08412 Vilnius, Lithuania; (D.B.); (L.B.); (L.B.)
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Musa S. Mitochondrial genome amplification of avian haemosporidian parasites from single-infected wildlife samples using a novel nested PCR approach. Parasitol Res 2023; 122:2967-2975. [PMID: 37787788 PMCID: PMC10667411 DOI: 10.1007/s00436-023-07986-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 09/22/2023] [Indexed: 10/04/2023]
Abstract
Haemosporidian parasites that infect birds (Apicomplexa: Haemosporida) are blood parasites that require an invertebrate host (vector) and a vertebrate host for their lifecycle and cause malaria-like diseases. This group of parasites has provided valuable insights into host specificity, virulence, and parasite dispersal. Additionally, they have played a significant role in reshaping our understanding of the evolutionary history of apicomplexans. In order to accurately identify species and to address phylogenetic questions such as the timing of the haemosporidian radiation, the use of a sufficiently large genetic data set is crucial. However, acquiring this genetic data poses significant challenges. In this research, a sensitive nested PCR assay was developed. This assay allows for the easy amplification of complete mitochondrial genomes of haemosporidian parasites in birds, even during the chronic stage of infection. The effectiveness of this new nested PCR assay was evaluated using blood and tissue samples of birds with verified single parasite infections from previous studies. The approach involves amplifying four overlapping fragments of the mitochondrial genome and requires DNA extracts from single-infected samples. This method successfully amplified the complete mitochondrial genomes of 24 distinct haemosporidian parasite lineages found in various bird species. This data is invaluable for conducting phylogenetic analyses and accurately defining species. Furthermore, this study proposes the existence of at least 15 new haemosporidian parasite species based on the genetic information obtained. Data regarding pGRW04, previously categorized as Plasmodium relictum like pSGS1 and pGRW11, indicates that the pGRW04 lineage is actually a separate, hidden Plasmodium species.
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Affiliation(s)
- Sandrine Musa
- University of Hohenheim, Emil-Wolff-Str. 34, 70599, Stuttgart, Germany.
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Lima T, Fam B, Tavares GM, Falótico T, Cantele C, Fanti L, Landau L, Viscardi LH, Vargas-Pinilla P, Barrientos-Diaz O, Pissinatti A, Sortica VA, Ottoni EB, Segatto ALA, Turchetto-Zolet AC, Bortolini MC. Insights into the evolutionary history of the most skilled tool-handling platyrrhini monkey: Sapajus libidinosus from the Serra da Capivara National Park. Genet Mol Biol 2023; 46:e20230165. [PMID: 37948505 PMCID: PMC10637428 DOI: 10.1590/1678-4685-gmb-2023-0165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 10/08/2023] [Indexed: 11/12/2023] Open
Abstract
Sapajus libidinosus members of the Pedra Furada group, living in the Serra da Capivara National Park, use stone tools in a wider variety of behaviors than any other living animal, except humans. To rescue the evolutionary history of the Caatinga S. libidinosus and identify factors that may have contributed to the emergence and maintenance of their tool-use culture, we conducted fieldwork seasons to obtain biological samples of these capuchin monkeys. UsingCYTBsequences, we show a discrete but constant population growth from the beginning of the Holocene to the present, overlapping the emergence of the Caatinga biome. Our habitat suitability reconstruction reports the presence of plants whose hard fruits, seeds, or roots are processed by capuchins using tools. TheS. libidinosusindividuals in the Caatinga were capable of dynamically developing and maintaining their autochthonous culture thanks to: a) cognitive capacity to generate and execute innovation under selective pressure; b) tolerance favoring learning and cultural inheritance; c) an unknown genetic repertoire that underpins the adaptive traits; d) a high degree of terrestriality; e) presence and abundance of natural resources, which makes some places "hot spots" for innovation, and cultural diversification within a relatively short time.
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Affiliation(s)
- Thaynara Lima
- Universidade Federal do Rio Grande do Sul, Departamento de Genética,
Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Instituto de
Biociências, Porto Alegre, RS, Brazil
| | - Bibiana Fam
- Universidade Federal do Rio Grande do Sul, Departamento de Genética,
Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Instituto de
Biociências, Porto Alegre, RS, Brazil
| | - Gustavo Medina Tavares
- Universidade Federal do Rio Grande do Sul, Departamento de Genética,
Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Instituto de
Biociências, Porto Alegre, RS, Brazil
| | - Tiago Falótico
- Universidade de São Paulo, Escola de Artes, Ciências e Humanidades,
São Paulo, SP, Brazil
| | - Camila Cantele
- Universidade Federal do Rio Grande do Sul, Departamento de Genética,
Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Instituto de
Biociências, Porto Alegre, RS, Brazil
| | - Lucca Fanti
- Universidade Federal do Rio Grande do Sul, Departamento de Genética,
Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Instituto de
Biociências, Porto Alegre, RS, Brazil
| | - Luane Landau
- Universidade Federal do Rio Grande do Sul, Departamento de Genética,
Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Instituto de
Biociências, Porto Alegre, RS, Brazil
| | - Lucas Henriques Viscardi
- Universidade Federal do Rio Grande do Sul, Departamento de Genética,
Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Instituto de
Biociências, Porto Alegre, RS, Brazil
- Universidade Pontifícia Universidade Católica do Rio Grande do Sul,
Escola de Medicina, Programa de Pós-Graduação em Medicina e Ciências da Saúde, Porto
Alegre, RS, Brazil
| | - Pedro Vargas-Pinilla
- Universidade Federal do Rio Grande do Sul, Departamento de Genética,
Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Instituto de
Biociências, Porto Alegre, RS, Brazil
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto,
Ribeirão Preto, SP, Brazil
| | - Ossman Barrientos-Diaz
- Universidade Federal do Rio Grande do Sul, Departamento de Genética,
Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Instituto de
Biociências, Porto Alegre, RS, Brazil
| | | | - Vinicius A. Sortica
- Universidade Federal do Rio Grande do Sul, Departamento de Genética,
Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Instituto de
Biociências, Porto Alegre, RS, Brazil
- Universidade de São Paulo, Medicina Preventiva da Faculdade de
Medicina, São Paulo, SP, Brazil
| | - Eduardo B. Ottoni
- Universidade de São Paulo, Instituto de Psicologia, Departamento de
Psicologia Experimental, São Paulo, SP, Brazil
| | - Ana Lúcia A. Segatto
- Universidade Federal de Santa Maria, Centro de Ciências Naturais e
Exatas, Departamento de Bioquímica e Biologia Molecular, Santa Maria, RS,
Brazil
| | - Andreia Carina Turchetto-Zolet
- Universidade Federal do Rio Grande do Sul, Departamento de Genética,
Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Instituto de
Biociências, Porto Alegre, RS, Brazil
| | - Maria Cátira Bortolini
- Universidade Federal do Rio Grande do Sul, Departamento de Genética,
Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Instituto de
Biociências, Porto Alegre, RS, Brazil
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Kim SH, Yun SW, Park JY. A new species of torrent catfish, Liobagrusgeumgangensis (Teleostei, Siluriformes, Amblycipitidae), from Korea. Zookeys 2023; 1180:317-332. [PMID: 38318423 PMCID: PMC10843425 DOI: 10.3897/zookeys.1180.105233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 09/01/2023] [Indexed: 02/07/2024] Open
Abstract
In a recent survey of populations of the Korean torrent catfish Liobagrus, a distinctive species was discovered from the Geum River and its tributaries flowing into the western coast of Korea, and here described as a new species, L.geumgangensissp. nov. It is distinguishable from other congeners by a combination of the following characters: I, 8 pectoral fin-rays; 52-56 caudal-fin rays; a relatively short occiput to dorsal-fin origin distance (6.9-9.8% SL); a short pelvic-fin insertion to anal-fin origin distance (11.9-17.3% SL); a long dorsal-fin base (10.6-13.5% SL); 8-9 gill rakers; 5-8 serrations on the pectoral fin; the body and fins are dark yellow, the margins of the dorsal, anal, and caudal fins are dark brown, but the outermost rim is faintly yellow. Analysis of the cytb gene also confirmed that L.geumgangensis is a monophyletic lineage distinct from other congeners.
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Affiliation(s)
- Su-hwan Kim
- National Institute of Ecology, Seocheon 33657, Republic of KoreaNational Institute of EcologySeocheonRepublic of Korea
| | - Seung-woon Yun
- Department of Biological Sciences, College of Natural Sciences, Jeonbuk National University, Jeonju 54986, Republic of KoreaJeonbuk National UniversityJeonjuRepublic of Korea
| | - Jong-young Park
- Department of Biological Sciences, College of Natural Sciences, Jeonbuk National University, Jeonju 54986, Republic of KoreaJeonbuk National UniversityJeonjuRepublic of Korea
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Alvi MA, Alshammari A, Ali RMA, Ul Haq S, Bashir R, Li L, Saqib M, Sajid MS, Ghafoor M, Imran M, Ijaz MU, Fu BQ, Saeed M, Ahmad I, Liu YY, Yan HB, Jia WZ. Revealing novel cytb and nad5 genes-based population diversity and benzimidazole resistance in Echinococcus granulosus of bovine origin. Front Vet Sci 2023; 10:1191271. [PMID: 37396990 PMCID: PMC10312306 DOI: 10.3389/fvets.2023.1191271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 05/17/2023] [Indexed: 07/04/2023] Open
Abstract
Cystic echinococcosis (CE) is a neglected zoonotic disease caused by Echinococcus granulosus (sensu stricto). The parasite affects a wide range of livestock and wild animals. In this study, the population diversity of the Echinococcus species was investigated based on mitochondrial cytochrome b (cytb) and NADH dehydrogenase subunit 5 (nad5) genes. In addition to this, β-tubulin gene isoforms of Echinococcus granulosus were amplified to determine the resistance against benzimidazoles. For this purpose, 40 cyst samples from cattle (n = 20) and buffaloes (n = 20) were collected from the main abattoir of Sialkot. DNA extraction was performed using Qiagen Blood and Tissue Kits. Amplification was performed through PCR. Each amplicon was confirmed by GelRed™ stained agarose gel (2%). Samples were sequenced in a DNA analyzer and viewed for any misread nucleotide by using MEGA (v.11). Corrections in nucleotide sequence and multiple sequence alignment were made through the same software. NCBI-BLAST was used for sample specific sequences to identify them as belonging to a particular species. Diversity indices were estimated using DnaSP (v.6) while phylogenetic analysis was inferred using the Bayesian method using MrBayes (v.1.1). β-tubulin gene isoforms sequence analysis was performed to find out the candidate gene causing benzimidazole resistance. All 40 isolates were found positive for E. granulosus. BLAST-based searches of sequences of each isolate for each gene (nad5 and cytb) confirmed their maximum similarity with the G1 genotype. Overall, high haplotype diversity (Hd nad5 = 1.00; Hd cytb = 0.833) and low nucleotide diversity (π nad5 = 0.00560; π = cytb = 0.00763) was identified based on diversity indices. For both the genes, non-significant values of Tajima's D (nad5 = -0.81734; cytb = -0.80861) and Fu's Fs (nad5 = -1.012; cytb = 0.731) indicate recent population expansion. Bayesian phylogeny-based results of nad5 and cytb sequences confirmed their genotypic status as distinct from other Echinococcus species. This study shed light on the status of benzimidazole resistance in Echinococcus granulosus for the very first time from Pakistan. The findings of this study will significantly add in the information available on genetic diversity of Echinoccous granulosus based on cytb and nad5 genes sequences.
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Affiliation(s)
- Mughees Aizaz Alvi
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, National Para-Reference Laboratory for Animal Echinococcosis, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Department of Clinical Medicine and Surgery, University of Agriculture, Faisalabad, Pakistan
| | - Ayed Alshammari
- Department of Biology, College of Science, University of Hafr Al Batin, Hafr Al Batin, Saudi Arabia
| | - Rana Muhammad Athar Ali
- Department of Clinical Medicine and Surgery, University of Agriculture, Faisalabad, Pakistan
| | - Shahbaz Ul Haq
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Rizwan Bashir
- Veterinary Disease Diagnostic Laboratory Sialkot, Livestock and Dairy Development Department, Government of Punjab, Lahore, Pakistan
| | - Li Li
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, National Para-Reference Laboratory for Animal Echinococcosis, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Muhammad Saqib
- Department of Clinical Medicine and Surgery, University of Agriculture, Faisalabad, Pakistan
| | | | - Muzafar Ghafoor
- Department of Clinical Medicine and Surgery, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Imran
- Department of Pathology, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Umar Ijaz
- Department of Zoology, Wildlife and Fisheries, University of Agriculture, Faisalabad, Pakistan
| | - Bao-Quan Fu
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, National Para-Reference Laboratory for Animal Echinococcosis, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Mohd Saeed
- Department of Biology, College of Science, University of Hail, Hail, Saudi Arabia
| | - Irfan Ahmad
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - You-Yu Liu
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, National Para-Reference Laboratory for Animal Echinococcosis, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Hong-Bin Yan
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, National Para-Reference Laboratory for Animal Echinococcosis, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Wan-Zhong Jia
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, National Para-Reference Laboratory for Animal Echinococcosis, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Disease, Yangzhou, China
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6
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Chatzoglou E, Tsaousi N, Apostolidis AP, Exadactylos A, Sandaltzopoulos R, Giantsis IA, Gkafas GA, Malandrakis EE, Sarantopoulou J, Tokamani M, Triantaphyllidis G, Miliou H. High-Resolution Melting (HRM) Analysis for Rapid Molecular Identification of Sparidae Species in the Greek Fish Market. Genes (Basel) 2023; 14:1255. [PMID: 37372435 DOI: 10.3390/genes14061255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/05/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
The red porgy (Pagrus pagrus) and the common dentex (Dentex dentex) are Sparidae species of high commercial value, traded in the Greek market. In some cases, fish species identification from Greek fisheries is difficult for the consumer due to the strong morphological similarities with their imported counterparts or closely related species such as Pagrus major, Pagrus caeroleustictus, Dentex gibbosus and Pagellus erythrinus, especially when specimens are frozen, filleted or cooked. Techniques based on DNA sequencing, such as COI barcoding, accurately identify species substitution incidents; however, they are time consuming and expensive. In this study, regions of mtDNA were analyzed with RFLPs, multiplex PCR and HRM in order to develop a rapid method for species identification within the Sparidae family. HRM analysis of a 113 bp region of cytb and/or a 156 bp region of 16s could discriminate raw or cooked samples of P. pagrus and D. dentex from the aforementioned closely related species and P. pagrus specimens sampled in the Mediterranean Sea when compared to those fished in the eastern Atlantic. HRM analysis exhibited high accuracy and repeatability, revealing incidents of mislabeling. Multiple samples can be analyzed within three hours, rendering this method a useful tool in fish fraud monitoring.
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Affiliation(s)
- Evanthia Chatzoglou
- Laboratory of Applied Hydrobiology, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, 11855 Athens, Greece
| | - Nefeli Tsaousi
- Laboratory of Applied Hydrobiology, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, 11855 Athens, Greece
| | - Apostolos P Apostolidis
- Laboratory of Fish & Fisheries, Department of Animal Production, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Athanasios Exadactylos
- Hydrobiology-Ichthyology Lab, Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece
| | - Raphael Sandaltzopoulos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Ioannis A Giantsis
- Department of Animal Science, Faculty of Agricultural Sciences, University of Western Macedonia, 53100 Florina, Greece
| | - Georgios A Gkafas
- Hydrobiology-Ichthyology Lab, Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece
| | - Emmanouil E Malandrakis
- Laboratory of Applied Hydrobiology, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, 11855 Athens, Greece
| | - Joanne Sarantopoulou
- Hydrobiology-Ichthyology Lab, Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece
| | - Maria Tokamani
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - George Triantaphyllidis
- Laboratory of Applied Hydrobiology, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, 11855 Athens, Greece
| | - Helen Miliou
- Laboratory of Applied Hydrobiology, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, 11855 Athens, Greece
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Mathias BDS, Minozzo GA, Biondo AW, Costa JDOJ, Soares HS, Marcili A, Guimarães LDO, Anjos CCD, Santos APD, Riediger IN, Fecchio A, Bueno MG, Pinho JB, Kirchgatter K. Molecular Investigation Confirms Myotis Genus Bats as Common Hosts of Polychromophilus in Brazil. Microorganisms 2023; 11:1531. [PMID: 37375033 DOI: 10.3390/microorganisms11061531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 05/30/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023] Open
Abstract
Plasmodium spp. and some other blood parasites belonging to the order Haemosporida are the focus of many epidemiological studies worldwide. However, haemosporidian parasites from wild animals are largely neglected in scientific research. For example, Polychromophilus parasites, which are exclusive to bats, are described in Europe, Asia, Africa, and Oceania, but little is known about their presence and genetic diversity in the New World. In this study, 224 samples of bats from remaining fragments of the Atlantic Forest and Pantanal biomes, as well as urbanized areas in southern and southeastern Brazil, were analyzed for the presence of haemosporidian parasites by PCR of the mitochondrial gene that encodes cytochrome b (cytb). The PCR fragments of the positive samples were sequenced and analyzed by the Bayesian inference method to reconstruct the phylogenetic relationships between Polychromophilus parasites from bats in Brazil and other countries. Sequences from Brazilian lineages of Polychromophilus were recovered in a clade with sequences from Polychromophilus murinus and close to the one Polychromophilus sequence obtained in Panama, the only available sequence for the American continent. This clade was restricted to bats of the family Vespertilionidae and distinct from Polychromophilus melanipherus, a parasite species mainly found in bats of the family Miniopteridae. The detection of Polychromophilus and the genetic proximity to P. murinus were further confirmed with the amplification of two other genes (clpc and asl). We also found a Haemosporida parasite sequence in a sample of Noctilio albiventris collected in the Pantanal biome, which presents phylogenetic proximity with avian Haemoproteus sequences. Morphological and molecular studies are still needed to conclude and describe the Polychromophilus species in Brazilian Myotis bats in more detail and to confirm Haemoproteus parasites in bats. Nevertheless, these molecular results in Brazilian bats confirm the importance of studying these neglected genera.
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Affiliation(s)
- Bruno da Silva Mathias
- Programa de Pós-Graduação em Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil
| | | | - Alexander Welker Biondo
- Departamento de Medicina Veterinária, Universidade Federal do Paraná, Curitiba 80035-050, PR, Brazil
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907, USA
| | | | - Herbert Sousa Soares
- Programa de Medicina e Bem-Estar Animal e Saúde Única, Universidade Santo Amaro, São Paulo 04829-300, SP, Brazil
| | - Arlei Marcili
- Departamento de Medicina Veterinária Preventiva e Saúde Animal, Universidade de São Paulo, São Paulo 05508-270, SP, Brazil
- Programa de Medicina e Bem-Estar Animal e Saúde Única, Universidade Santo Amaro, São Paulo 04829-300, SP, Brazil
| | | | - Carolina Clares Dos Anjos
- Programa de Pós-Graduação em Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil
| | | | | | - Alan Fecchio
- Centro de Investigación Esquel de Montaña y Estepa Patagónica (CIEMEP), CONICET, Universidad Nacional de la Patagonia San Juan Bosco, Esquel 9200, Chubut, Argentina
| | - Marina Galvão Bueno
- Laboratório de Virologia Comparada e Ambiental (LVCA), Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Fiocruz Rio de Janeiro, Rio de Janeiro 21041-250, RJ, Brazil
| | - João Batista Pinho
- Programa de Pós-Graduação em Ecologia e Conservação da Biodiversidade, Universidade Federal de Mato Grosso, Cuiabá 78060-900, MT, Brazil
| | - Karin Kirchgatter
- Programa de Pós-Graduação em Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil
- Laboratório de Bioquímica e Biologia Molecular, Instituto Pasteur, São Paulo 01027-000, SP, Brazil
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8
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Nieto-Lopez EH, Cerritos-Garcia DG, Koch Bach RA, Petkar A, Smart CD, Hoepting C, Langston D, Rideout S, Dutta B, Everhart SE. Species Identification and Fungicide Sensitivity of Fungi Causing Alternaria Leaf Blight and Head Rot in Cole Crops in the Eastern United States. Plant Dis 2023:PDIS06221318SC. [PMID: 36324201 DOI: 10.1094/pdis-06-22-1318-sc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Alternaria leaf blight and head rot is an important disease of broccoli and other cole crops. With no resistant host varieties, fungicides are utilized to manage this disease. However, anecdotal evidence suggests that, in southeastern U.S. broccoli-producing states, there is a loss of disease control through the use of quinone outside inhibitor (QoI) fungicides. To understand why there is a reduced sensitivity to QoI fungicides in these states, we isolated Alternaria spp. from symptomatic lesions on cole crops from Georgia and Virginia (two states with observations of loss of fungicide sensitivity) as well as New York (a state with no observations of loss of fungicide sensitivity). Using multilocus sequencing and phylogenetic analysis, we identified two species, Alternaria brassicicola and A. japonica. Whereas A. brassicicola was isolated in all states, A. japonica was only isolated in Georgia. Next, we wanted to determine the sensitivity of these isolates to azoxystrobin-an active ingredient in some QoI fungicides-by estimating the effective concentration at which only 50% of spores germinate (EC50). The EC50 of A. brassicicola ranged from 0.01 to 0.17 ppm, whereas that of A. japonica was 8.1 to 28.1 ppm. None of the known target-site mutations that confer resistance to QoI fungicides were identified during screening of either species. A. japonica was first reported on the east coast of the United States in 2020 in South Carolina. The substantially higher EC50 value suggests that its emergence in the southeastern United States may play at least a part in the observed loss of disease control. However, further in planta and field studies are needed to thoroughly test this hypothesis.
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Affiliation(s)
- Edgar H Nieto-Lopez
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583
| | - Daniel G Cerritos-Garcia
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT 06269
| | - Rachel A Koch Bach
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT 06269
| | - Aparna Petkar
- Department of Plant Pathology, Coastal Plain Experiment Station, University of Georgia, Tifton, GA 31793
| | - Christine D Smart
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456
| | - Christy Hoepting
- Cornell Vegetable Program, Cornell Cooperative Extension, Cornell University, Albion, NY 14411
| | - David Langston
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061
| | - Steven Rideout
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061
| | - Bhabesh Dutta
- Department of Plant Pathology, Coastal Plain Experiment Station, University of Georgia, Tifton, GA 31793
| | - Sydney E Everhart
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT 06269
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9
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Alvi MA, Ali RMA, Li L, Saqib M, Qamar W, Hassan A, Ghafoor M, Rahman SU, Khan MUZ, Fu BQ, Liu Y, Yin H, Yan HB, Jia WZ. Phylogeny and population structure of Echinococcus granulosus (sensu stricto) based on full-length cytb-nad2-atp6 mitochondrial genes - First report from Sialkot District of Pakistan. Mol Biochem Parasitol 2023; 253:111542. [PMID: 36584819 DOI: 10.1016/j.molbiopara.2022.111542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/16/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022]
Abstract
Cystic echinococcosis is a zoonotic disease of livestock having serious economic setbacks. The etiological agents of the disease belong to Echinococcus granulosus sensu lato. Despite of worldwide distribution of the disease, the molecular studies mainly employ amplification of cox1, nad1 and nad5 genes. To further strengthen the knowledge about significance of other molecular markers and to investigate the genetic diversity and population structure of Echinococcus species in Pakistan, the current study was designed in which full length mitochondrial cytb, atp6 and nad2 genes were amplified. Based on BLAST searches of the generated cytb, atp6 and nad2 gene sequences from a total of 18 hydatid cysts collected from cattle, 12 isolates were identified as E. granulousus G3 and 6 as E. granulosus (G1). The phylogeny inferred by the Bayesian method using nucleotide sequences of cytb-atp6-nad2 further confirmed their identity. The diversity indices indicated a high haplotype and a low nucleotide diversity. The negative values of Tajima's D and Fu's Fs test demonstrated deviation from neutrality suggesting a recent population expansion. To the best of our knowledge, the present study described the genetic variation of E. granulosus population for the first time in Pakistan using full-length cytb, atp6 and nad2 mitochondrial genes. The findings on the genetic variation of E. granulosus in Pakistan will constitute useful baseline information for future studies on the prevalence and population structure of E. granulosus based on full-length cytb, atp6 and nad2.
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Affiliation(s)
- Mughees Aizaz Alvi
- State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, National Para-reference Laboratory for Animal Echinococcosis, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China; Department of Clinical Medicine and Surgery, University of Agriculture, Faisalabad, Pakistan
| | - Rana Muhammad Athar Ali
- Department of Clinical Medicine and Surgery, University of Agriculture, Faisalabad, Pakistan
| | - Li Li
- State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, National Para-reference Laboratory for Animal Echinococcosis, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Muhammad Saqib
- Department of Clinical Medicine and Surgery, University of Agriculture, Faisalabad, Pakistan
| | - Warda Qamar
- Department of Parasitology, University of Agriculture, Faisalabad, Pakistan
| | - Ali Hassan
- Department of Clinical Medicine and Surgery, University of Agriculture, Faisalabad, Pakistan
| | - Muzafar Ghafoor
- Department of Clinical Medicine and Surgery, University of Agriculture, Faisalabad, Pakistan
| | - Siddiq Ur Rahman
- Department of Computer Science and Bioinformatics, Khushal Khan Khattak University, Karak, Khyber Pakhtunkhwa, Pakistan
| | | | - Bao-Quan Fu
- State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, National Para-reference Laboratory for Animal Echinococcosis, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Youyu Liu
- State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, National Para-reference Laboratory for Animal Echinococcosis, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Hong Yin
- State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, National Para-reference Laboratory for Animal Echinococcosis, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Hong-Bin Yan
- State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, National Para-reference Laboratory for Animal Echinococcosis, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China.
| | - Wan-Zhong Jia
- State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, National Para-reference Laboratory for Animal Echinococcosis, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.
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10
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Li Z, Ren XX, Zhao YJ, Yang LT, Duan BF, Hu NY, Zou FC, Zhu XQ, He JJ, Liu QS. First report of haemosporidia and associated risk factors in red junglefowl (Gallus gallus) in China. Parasit Vectors 2022; 15:275. [PMID: 35915463 PMCID: PMC9344640 DOI: 10.1186/s13071-022-05389-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/28/2022] [Indexed: 12/01/2022] Open
Abstract
Background Avian haemosporidia infect both domestic and wild birds, causing anemia, acute tissue degeneration, and depopulation in wild birds. Poultry and wild birds have been reported as common reservoirs of haemosporidia, but limited information is available for red junglefowl (Gallus gallus) in China. The present study investigated the prevalence and molecular characterization of haemosporidia in red junglefowl. Methods Blood samples were collected from 234 red junglefowl from Jinghong City of Yunnan Province, and genomic DNA was extracted from these samples. The prevalence of haemosporidia was determined by nested PCR targeting the mitochondrial cytochrome b (cytb) gene. Molecular characterization was investigated based on phylogenetic analysis of cytb sequences, and associated risk factors were analyzed using the Chi-square (χ2) test. Results The overall prevalence of haemosporidia was 74.8% (175/234), and three species were identified, namely Haemoproteus enucleator, Leucocytozoon californicus, and Plasmodium juxtanucleare. The prevalence of haemosporidia in adult fowl (81.1%, 107/132) was significantly higher (χ2 = 6.32, df = 1, P = 0.012) than that in juveniles (66.7%, 68/102). Three novel haemosporidian lineages were revealed. Conclusions This study examined the prevalence and identified species of avian haemosporidians in red junglefowl, providing new information on the molecular epidemiology and geographical distribution of haemosporidian parasites. Our results indicated high prevalence and diverse species distribution of these haemosporidians in red junglefowl. To the best of our knowledge, this is the first record of haemosporidian infection in red junglefowl in China. Graphical Abstract ![]()
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Affiliation(s)
- Zhao Li
- Animal Research and Resource Center, Yunnan University, Kunming, Yunnan Province, 650500, People's Republic of China. .,State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science, School of Life Sciences, Yunnan University, Kunming, Yunnan Province, 650500, People's Republic of China. .,Key Laboratory of Veterinary Public Health of Yunnan Province, College of Veterinary Medicine, Yunnan Agricultural University, Kunming, Yunnan Province, 650201, People's Republic of China. .,College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi Province, 030801, People's Republic of China.
| | - Xiao-Xia Ren
- Animal Research and Resource Center, Yunnan University, Kunming, Yunnan Province, 650500, People's Republic of China.,State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science, School of Life Sciences, Yunnan University, Kunming, Yunnan Province, 650500, People's Republic of China
| | - Yin-Jiao Zhao
- Animal Research and Resource Center, Yunnan University, Kunming, Yunnan Province, 650500, People's Republic of China.,State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science, School of Life Sciences, Yunnan University, Kunming, Yunnan Province, 650500, People's Republic of China
| | - Lian-Tao Yang
- Animal Research and Resource Center, Yunnan University, Kunming, Yunnan Province, 650500, People's Republic of China.,State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science, School of Life Sciences, Yunnan University, Kunming, Yunnan Province, 650500, People's Republic of China
| | - Bo-Fang Duan
- Yunnan Province Center for Animal Disease Control and Prevention, Kunming, Yunnan Province, 650201, People's Republic of China
| | - Na-Ying Hu
- Xishuangbanna Dai Autonomous Prefecture Technical Extension Station for Animal Husbandry and Veterinary Medicine, Jinghong, Yunnan Province, 666100, People's Republic of China
| | - Feng-Cai Zou
- Key Laboratory of Veterinary Public Health of Yunnan Province, College of Veterinary Medicine, Yunnan Agricultural University, Kunming, Yunnan Province, 650201, People's Republic of China
| | - Xing-Quan Zhu
- Key Laboratory of Veterinary Public Health of Yunnan Province, College of Veterinary Medicine, Yunnan Agricultural University, Kunming, Yunnan Province, 650201, People's Republic of China.,College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi Province, 030801, People's Republic of China
| | - Jun-Jun He
- Key Laboratory of Veterinary Public Health of Yunnan Province, College of Veterinary Medicine, Yunnan Agricultural University, Kunming, Yunnan Province, 650201, People's Republic of China.
| | - Qi-Shuai Liu
- Animal Research and Resource Center, Yunnan University, Kunming, Yunnan Province, 650500, People's Republic of China. .,State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science, School of Life Sciences, Yunnan University, Kunming, Yunnan Province, 650500, People's Republic of China.
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11
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Inumaru M, Nishiumi I, Kawakami K, Sato Y. A widespread survey of avian haemosporidia in deceased wild birds of Japan: the hidden value of personally collected samples. J Vet Med Sci 2022; 84:1253-1260. [PMID: 35858821 PMCID: PMC9523285 DOI: 10.1292/jvms.22-0179] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Widespread surveys of avian haemosporidia (Plasmodium, Haemoproteus, and Leucocytozoon) in wild birds have substantially advanced
information on the haemosporidian fauna of Japan. However, many areas and bird species remain insufficiently investigated. Bird carcasses collected for personal specimen collection seldom
reach academic audience particularly in the veterinary field. The presence of avian haemosporidia was investigated in these personally collected bird carcasses, in order to better understand
the avian haemosporidian fauna in Japan. Bird carcasses were donated through personal contact upon approval of the study. Tissue samples were collected from the birds and examined for
haemosporidian parasites using nested-PCR targeting the cytochrome b gene. One hundred and forty-three birds of 85 species were donated, including 34 species and two
subspecies that were molecularly or collectively investigated for the first time in Japan. Avian haemosporidian DNA was detected from 37 of the 134 tested birds (27.61%). In 8 bird species,
avian haemosporidia was detected for the first time. Twenty-nine lineages were detected, including 8 novel and 9 known lineages detected in Japan for the first time. Furthermore, 16 lineages
were detected from novel host species. While information that could be drawn was limited and risk management of zoonotic diseases needs re-consideration, these findings expanded information
on the host range and distribution of several lineages. Collectively, this method of investigation using personally collected bird samples can provide important additions to more fully
understand the avian haemosporidian fauna of Japan, as well as other areas with limited investigations.
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Affiliation(s)
- Mizue Inumaru
- Laboratory of Biomedical Science, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University.,Current address: Department of Medical Entomology, National Institute of Infectious Diseases
| | - Isao Nishiumi
- Department of Zoology, National Museum of Nature and Science Tokyo
| | | | - Yukita Sato
- Laboratory of Biomedical Science, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University
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12
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Shumenko PG, Tatonova YV. Assessing the population structure of trematode Metagonimus suifunensis using three mitochondrial markers. Parasitol Res 2022; 121:915-923. [PMID: 35133488 DOI: 10.1007/s00436-022-07456-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 01/26/2022] [Indexed: 11/27/2022]
Abstract
In this work, for the first time, the genetic variability of the Metagonimus suifunensis population in the Russian southern Far East was estimated based on the full-length sequences of the nad1 gene of mitochondrial DNA. In addition, for a sample of the same size, the sequences of cox1 and cytb genes, previously used for population studies for M. suifunensis, were reanalysed. Three markers were combined to a common sequence, and the obtained data were studied. Despite the higher level of variability, nad1 and cox1 mtDNA genes did not reveal subdivisions within the population. The combined dataset made it possible to determine that the sample from the Odyr River was the centre of the species' range formation and clarified the continental migration route of the parasite from south to north. According to the data obtained, it was presumed that piscivorous birds participate in the life cycle of the parasite. The subdivision within population revealed that using all three mitochondrial markers is consistent with the features of differentiation within populations of related species, but the reasons for its formation remain unclear due to the insufficient amount of data and the use of different markers in studies of different species.
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Affiliation(s)
- Polina G Shumenko
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch, Russian Academy of Sciences, 100-letiya Street, 159, Vladivostok, 690022, Russia
| | - Yulia V Tatonova
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch, Russian Academy of Sciences, 100-letiya Street, 159, Vladivostok, 690022, Russia. .,School of Biomedicine, Far Eastern Federal University, Sukhanova Street, 8, Vladivostok, 690091, Russia.
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13
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Costa GDS, Júnior AMP, Castro TS, de Paulo PFM, Ferreira GEM, Medeiros JF. Sand fly fauna and molecular detection of Leishmania species and blood meal sources in different rural environments in western Amazon. Acta Trop 2021; 224:106150. [PMID: 34562421 DOI: 10.1016/j.actatropica.2021.106150] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 11/20/2022]
Abstract
Cutaneous Leishmaniasis (CL) is a disease caused by Leishmania species and transmitted by the bites of infected female sand fly species. The diversity of these insects in Rondônia State (where CL is the predominant form) is large but unexplored, and consequently the vector species are unknown. The purpose of this study was to evaluate the sand fly fauna in two environments (forest fragment and peridomicile) in rural areas of four municipalities of the state, DNA amplification of Leishmania species and the presence of blood meal sources for these insects. After identifying the species, sample coverage was applied to estimate the fauna coverage in each environment. Females were used to amplify and detect Leishmania DNA and blood meal sources, then posteriorly identified by sequencing. A total of 1706 individuals were included in 61 species, which was a sample coverage of 97% for the forest fragments (56 species), whereas 98% was observed (32 species) in peridomiciles. Next, 41 pools were prepared from 1227 females, and none were positive for Leishmania DNA. We observed 160 engorged females (forest fragments: 21, peridomiciles: 139) belonging to females of the Antunesi complex and another eight species. Two of these females were positive for Leishmania braziliensis-DNA: one in the Antunesi complex and one in Psychodopygus hirsutus. Seven blood meal sources were identified by sequencing analysis: Bos taurus and Sus scrofa from the peridomiciles, and Dasypus novemcinctus, Pecari tajacu, Philander canus, Plecturocebus bernhardi, and Tamandua tetradactyla from the forest fragments. Our data confirmed the feeding behavior of field-caught sand flies and could contribute to our understanding about local vectors and possible reservoirs in the transmission of Leishmania spp.
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14
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Khan A, Ahmed H, Simsek S, Shahzad K, Celik F, Afzal MS, Khan MR, Liu H, Shen Y, Cao J. Haplotype comparisons of Echinococcus granulosus sensu lato via mitochondrial gene sequences ( co1, cytb, nadh1) among Pakistan and its neighbouring countries. Parasitology 2021; 148:1019-1029. [PMID: 33896429 PMCID: PMC11010185 DOI: 10.1017/s0031182021000688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 04/08/2021] [Accepted: 04/15/2021] [Indexed: 11/07/2022]
Abstract
Echinococcus granulosus sensu lato (s.l.) is a zoonotic parasite that causes cystic echinococcosis (CE) in humans. However, E. granulosus sensu stricto (s.s.) is considered the predominant species in CE infections worldwide. According to the population genetic diversity and structure of E. granulosus s.l., gene flow can explain the parasite drift among the neighbouring countries of Pakistan. The mitochondrial (mt) co1 (n = 47), nadh1 (n = 37) and cytb (n = 35) nucleotide sequences of E. granulosus s.l. isolates from Pakistan, Iran, China and India were retrieved from the National Centre for Biotechnology Information database to determine the genealogical relationships. The sequences were grouped as the mt-co1 (genotypes G1 and G3, G6-G7), mt-cytb (genotypes G1 and G3), and mt-nadh1(genotypes G1 and G3). The data were analysed using bioinformatic tools. A total of 19 polymorphic sites for the mt-co1 sequence (374 bp) were observed of which 31.6% (6/19) were parsimony-informative sites. Unique singleton haplotypes within the E. granulosus s.s. haplotype network based on the mt-co1 gene were highly prevalent (68.4%; 13/19) in Pakistani isolates followed by Chinese, Indian and Iranian isolates; four polymorphic sites were detected in the E. canadensis (G6/G7). In E. canadensis mt-co1 haplotype network, 75% (3/4) unique singleton haplotypes were from the Iranian isolates. Twelve polymorphic sites were found using the mt-cytb sequence (547 bp); 25% (3/12) were parsimony-informative and there were 66.7% (8/12) unique singleton haplotypes within the mt-cytb haplotype network in E. granulosus s.s. with the most reported from Pakistan followed by Iran and China. 20 polymorphic sites were detected in E. granulosus s.s. mt-nadh1 sequences (743 bp); 20% (4/20) were parsimony-informative. There were 66.7% (8/12) main single haplotypes within the mt-nadh1 haplotype network, with the most reported from Pakistan followed by that from India, Iran and China. The sequence analyses show low nucleotide diversity and high haplotype diversity in general.
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Affiliation(s)
- Aisha Khan
- National Institute of Parasitic Diseases, Chinese Centre for Disease Control and Prevention (Chinese Center for Tropical Diseases Research); Key Laboratory of Parasite and Vector Biology; National Health Commission of the People's Republic of China; WHO Collaborating Centre for Tropical Diseases; National Center for International Research on Tropical Diseases; Shanghai; China
- The School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Haroon Ahmed
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Sami Simsek
- Department of Parasitology, Faculty of Veterinary Medicine, University of Firat, Elazig, Turkey
| | - Khuram Shahzad
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Figen Celik
- Department of Parasitology, Faculty of Veterinary Medicine, University of Firat, Elazig, Turkey
| | - Muhammad Sohail Afzal
- Department of Lifesciences, School of Science, University of Management & Technology (UMT), Lahore, Pakistan
| | - Mobushir Riaz Khan
- School of Environmental Science, Charles Sturt University, Albury, NSW, Australia
| | - Hua Liu
- National Institute of Parasitic Diseases, Chinese Centre for Disease Control and Prevention (Chinese Center for Tropical Diseases Research); Key Laboratory of Parasite and Vector Biology; National Health Commission of the People's Republic of China; WHO Collaborating Centre for Tropical Diseases; National Center for International Research on Tropical Diseases; Shanghai; China
- The School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yujuan Shen
- National Institute of Parasitic Diseases, Chinese Centre for Disease Control and Prevention (Chinese Center for Tropical Diseases Research); Key Laboratory of Parasite and Vector Biology; National Health Commission of the People's Republic of China; WHO Collaborating Centre for Tropical Diseases; National Center for International Research on Tropical Diseases; Shanghai; China
- The School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianping Cao
- National Institute of Parasitic Diseases, Chinese Centre for Disease Control and Prevention (Chinese Center for Tropical Diseases Research); Key Laboratory of Parasite and Vector Biology; National Health Commission of the People's Republic of China; WHO Collaborating Centre for Tropical Diseases; National Center for International Research on Tropical Diseases; Shanghai; China
- The School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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15
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Mohammadi Z, Ghorbani F, Kami HG, Khajeh A, Olsson U. Molecular Phylogeny of the Subgenus Karstomys Reveals Genetic Signature of Post-Glacial Colonization of Apodemus mystacinus (Rodentia: Muridae) in the Zagros Mountains from Different Refugia. Zoolog Sci 2021; 38:72-81. [PMID: 33639721 DOI: 10.2108/zs200065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 09/10/2020] [Indexed: 11/17/2022]
Abstract
Eastern broad-toothed field mouse, Apodemus mystacinus, is a rocky habitat dwelling rodent distributed in Asia Minor, the Levant, the Caucasus, and the Zagros Mountains. In this study, we investigated the phylogenetic relationship between different populations of A. mystacinus throughout its range, based on the mitochondrial cytb marker. Phylogenetic analyses revealed the existence of five separately evolving lineages within A. mystacinus, of which two previously unrecognized lineages were identified in the Zagros Mountains and the Levant. Divergence between two major clades of the subgenus Karstomys, corresponding to A. mystacinus and Apodemus epimelas, is inferred to coincide with the Messinian Salinity Crisis (Late Miocene), whereas the splits between major lineages of A. mystacinus are inferred to have occurred during the Pleistocene. Colonization of the Zagros may have occurred from different refugia via eastward migration of the Turkish population and then again by a more recent colonization from the Caucasus, after reopening of the land corridor between the Caucasus and the Zagros Mountains during the Holocene drought.
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Affiliation(s)
- Zeinolabedin Mohammadi
- Department of Biology, Faculty of Sciences, Golestan University, Gorgan, 39361-79142, Golestan, Iran, .,Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad 9177948974, Iran
| | - Fatemeh Ghorbani
- Department of Biology, Faculty of Sciences, Golestan University, Gorgan, 39361-79142, Golestan, Iran
| | - Haji Gholi Kami
- Department of Biology, Faculty of Sciences, Golestan University, Gorgan, 39361-79142, Golestan, Iran
| | - Asghar Khajeh
- Department of Crop Productions Technology, Faculty of Agriculture, Higher Educational Complex of Saravan, Saravan 99516-34145, Iran
| | - Urban Olsson
- University of Gothenburg, Department of Biology and Environmental Sciences, Systematics and Biodiversity, SE-405 30 Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, SE-405 30 Göteborg, Sweden
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16
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Gubanova A, Drapun I, Garbazey O, Krivenko O, Vodiasova E. Pseudodiaptomus marinus Sato, 1913 in the Black Sea: morphology, genetic analysis, and variability in seasonal and interannual abundance. PeerJ 2020; 8:e10153. [PMID: 33150076 PMCID: PMC7585723 DOI: 10.7717/peerj.10153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 09/21/2020] [Indexed: 12/02/2022] Open
Abstract
Calanoid copepod Peudodiaptomus marinus Sato, 1913 was first recorded in Sevastopol Bay in the northern Black Sea in September 2016. We performed regular observations of this new invasive species between October 2016 and December 2018. We conducted bi-weekly plankton sampling at three stations located within or adjacent to Sevastopol Bay. This is the first paper to combine (i) a detailed morphological study, (ii) molecular genetic analysis, and (iii) an investigation of P. marinus seasonal dynamics and interannual abundance variability in the coastal Black Sea. Our morphological research showed similarities between Pseudodiaptomus specimens and existing P. marinus illustrations and descriptions. Our morphological analysis results were confirmed using molecular genetic studies. Based on the genetic variability of ITS2 and cytb, we found that all investigated specimens from Sevastopol Bay belonged to P. marinus. Investigations of P. marinus seasonal and interannual abundance variability showed the same seasonal patterns throughout the studied period, with a higher seasonal abundance from October to November and one pronounced density peak in autumn. The highest abundances (2,000 ind m–3 at the mouth of the bay and more than 5,000 ind m–3at its centre) were recorded in November 2018. In the samples, we found adults of both sexes, including ovigerous females, copepodites I–V, and nauplii, suggesting that the species reproduce in Sevastopol Bay. Our research indicated that P. marinus is a new non-indigenous species (NIS) in the Black Sea, and we will discuss a possible vector of its introduction into this basin.
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Affiliation(s)
- Alexandra Gubanova
- Plankton department, A.O. Kovalevsky Institute of Biology of the Southern Seas of RAS, Sevastopol, Russia
| | - Inna Drapun
- Plankton department, A.O. Kovalevsky Institute of Biology of the Southern Seas of RAS, Sevastopol, Russia
| | - Oksana Garbazey
- Plankton department, A.O. Kovalevsky Institute of Biology of the Southern Seas of RAS, Sevastopol, Russia
| | - Olga Krivenko
- Marine biodiversity and functional genomics laboratory, A.O. Kovalevsky Institute of Biology of the Southern Seas of RAS, Sevastopol, Russia
| | - Ekaterina Vodiasova
- Marine biodiversity and functional genomics laboratory, A.O. Kovalevsky Institute of Biology of the Southern Seas of RAS, Sevastopol, Russia
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17
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Sun T, Wang S, Hanif Q, Chen N, Chen H, Lei C. Genetic diversity of mitochondrial cytochrome b gene in swamp buffalo. Anim Genet 2020; 51:977-981. [PMID: 32910515 DOI: 10.1111/age.12997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 07/12/2020] [Accepted: 08/18/2020] [Indexed: 11/26/2022]
Abstract
The swamp buffalo (Bubalus carabanensis) is mainly bred for meat, transport and rice cultivation in China and Southeast Asian countries. In the current study, we investigated the genetic diversity, maternal origin and phylogenetic relationship of swamp buffalo by analyzing 1,786 mitochondrial cytochrome b (cytb) sequences from China, Vietnam, Laos, Thailand, India and Bangladesh. Our results indicated that the swamp buffalo can be divided into two major lineages (SA and SB with the sublineages) and three rare lineages (SC, SD and SE), which showed strong geographic differentiation. The SA1 lineage represented a major domestication event, which involved population expansion. Regions III and V showed higher haplotype diversity than the other regions, indicating that the regions of Southwest China and IndoChina are potential domestication centers for the swamp buffalo. In addition, the swamp buffalo showed a closer phylogenetic relationship to tamaraw. In conclusion, our findings revealed a high level of genetic diversity and the phylogenetic pattern of the swamp buffalo.
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Affiliation(s)
- T Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - S Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Q Hanif
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, 577, Pakistan.,Department of Biotechnology, Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, 45650, Pakistan
| | - N Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - H Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - C Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
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Guo WP, Xie GC, Li D, Su M, Jian R, Du LY. Molecular detection and genetic characteristics of Babesia gibsoni in dogs in Shaanxi Province, China. Parasit Vectors 2020; 13:366. [PMID: 32698848 DOI: 10.1186/s13071-020-04232-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 07/15/2020] [Indexed: 11/10/2022] Open
Abstract
Background Several members of genus Babesia are important pathogens causing babesiosis in dogs. In China, at least five Babesia species have been described in dogs or ticks. This study sought to determine the prevalence and molecular characteristics of various Babesia spp. in dogs in cities in Shaanxi Province in China, including Xi’an and Hanzhong. Methods A total of 371 blood samples were collected from pet dogs presenting to veterinary clinics in the cities of Xi’an and Hanzhong in Shaanxi, China. Babesia spp. DNA was detected via amplification of partial 18S rRNA genes by semi-nested PCR. Almost full-length 18S rRNA, ITS, partial TRAP and complete cytb genes were recovered for analysis of the genetic characteristics and relationships with known isolates. Results A single species, Babesia gibsoni, was identified in dogs in Xi’an and Hanzhong. Consistently, B. gibsoni was also detected in 14 ticks collected from positive dogs. Sequence similarities and phylogenetic analysis suggested that the isolates identified herein showed a closer genetic relationship with isolates from East Asian countries rather than India, Bangladesh, or the USA. Sequence analysis based on tandem repeat analysis of the TRAP gene further revealed that specific haplotypes were circulating in both Xi’an and Hanzhong, with no specific regionality. In addition, 10.9% of all isolates with atovaquone (ATV)-resistance were identified because of M121I mutation in the deduced cytb protein. Conclusions This study revealed a high prevalence rate of Babesia infection. Babesia gibsoni was the only Babesia species identified in cases of canine babesiosis in the cities of Xi’an and Hanzhong cities in Shaanxi, China. In addition, the TRAP gene presented high genetic diversity across isolates. Such information is useful for elucidating the epidemiological characteristics of canine babesiosis, as well as the overall genetic diversity of Babesia spp. circulating in dog populations in Shaanxi Province.![]()
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Wang S, Guo J, Hou F. Identification of the original species of cubilose based on DNA barcode. Mitochondrial DNA B Resour 2019; 4:3079-3082. [PMID: 33365864 PMCID: PMC7706791 DOI: 10.1080/23802359.2019.1666681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 08/16/2019] [Indexed: 10/26/2022] Open
Abstract
Cubilose, a valuable traditional Chinese medicine, is mainly composed of the saliva by several species of Aerodramus or Collocalia in the Apodidae. Due to rarity, high economic value and huge market demand, its fake or adulteration is frequently found in the market. Therefore, it is urgent to establish a simple and accurate method for authenticating cubilose. DNA barcoding, which is an easy, quick and reliable method, is widely used to trace the origin of traditional Chinese medicine. For identifying the original species of cubilose, cytb gene of 18 cubilose samples including 15 officer cubilose and 3 feather cubilose were amplified and entered into the GenBank database using the BLAST search tool. The genetic distances among 18 cubilose samples were calculated based on the Kimura two parameter (K2P) model. To construct the reference database, 18 cytb sequences of Aerodramus or Collocalia were downloaded from GenBank. The neighbor-joining (NJ) and unweighted pair group method with arithmetic average (UPGMA) trees were constructed based on sequences from GenBank and our dataset. Blast analysis showed that all cubilose samples had the highest similarity with A. fuciphagus, and the sequence similarity reached over 99%. Genetic distance of 18 cubilose samples ranged from 0.000-0.010. Trees constructed by NJ and UPGMA gave similar topology: all cubilose samples clustered together with A. fuciphagus. These result demonstrated that the original species of all 18 cubilose samples were A. fuciphagus, and cytb gene is a good candidate for identifying cubilose.
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Affiliation(s)
- Shasha Wang
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Jinlin Guo
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Feixia Hou
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
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Chaisi ME, Osinubi ST, Dalton DL, Suleman E. Occurrence and diversity of avian haemosporidia in Afrotropical landbirds. Int J Parasitol Parasites Wildl 2019; 8:36-44. [PMID: 30619708 PMCID: PMC6312862 DOI: 10.1016/j.ijppaw.2018.12.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 12/05/2018] [Accepted: 12/06/2018] [Indexed: 12/17/2022]
Abstract
Avian haemosporidian infections are widespread and can result in the decline of wild bird populations or in some cases contribute to extinction of species. We determined the prevalence and genetic diversity of avian haemosporidia in 93 samples from 22 landbird species from South Africa (N = 76) and West Africa (N = 17), of which six are intra-African migrants and one is a Palearctic migrant. The samples were analysed for the presence of avian haemosporidian DNA using real-time quantitative PCR (qPCR) and nested PCR assays targeting specific mitochondrial genes of these parasites. The cytochrome b (cytb) gene was sequenced for all samples that tested positive and phylogenetic analysis was conducted in order to determine the relationship of the new sequences with previously published sequences from the MalAvi database. The overall prevalence of avian haemosporidiosis was 68.82% (95% CI: 56.4%-78.87%) and 82.80% (95% CI: 65.68%-86.11%) as determined by qPCR and nested PCR respectively. Eighteen (19.36%; 95% CI; 10.78%-29.97%) samples had mixed infections. Infection prevalence of all haemosporidian spp. were significantly higher (p < 0.05) in samples from West Africa. Forty-six mitochondrial sequences obtained from 14 avian species grouped into three distinct clusters of Haemoproteus (36), Leucocytozoon (8) and Plasmodium (2). These represent eight published and nine new cytb lineages. The most common lineage was Haemoproteus sp. (VIMWE1) which was identified in two bird species from West Africa and seven bird species from South Africa. This study adds to our knowledge of host-parasite relationships of avian haemosporidia of Afrotropical birds.
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Affiliation(s)
- Mamohale E. Chaisi
- Department of Research and Scientific Services, National Zoological Garden, South African National Biodiversity Institute (SANBI), 232 Boom Street, Pretoria, 0001, South Africa
| | - Samuel T. Osinubi
- FitzPatrick Institute of African Ornithology, University of Cape Town, Private Bag X3, Rondebosch, 7701, Cape Town, South Africa
| | - Desire L. Dalton
- Department of Research and Scientific Services, National Zoological Garden, South African National Biodiversity Institute (SANBI), 232 Boom Street, Pretoria, 0001, South Africa
| | - Essa Suleman
- Department of Research and Scientific Services, National Zoological Garden, South African National Biodiversity Institute (SANBI), 232 Boom Street, Pretoria, 0001, South Africa
- Council for Scientific and Industrial Research (CSIR), P.O. Box 395, Pretoria, 0001, South Africa
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Corona-Santiago DK, Domínguez-Domínguez O, Tovar-Mora L, Pardons-Blas JR, Herrerías-Diego Y, Pérez-Rodríguez R, Doadrio I. Historical biogeography reveals new independent evolutionary lineages in the Pantosteus plebeius-nebuliferus species-group (Actinopterygii: Catostomidae). BMC Evol Biol 2018; 18:173. [PMID: 30453887 PMCID: PMC6245702 DOI: 10.1186/s12862-018-1286-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 10/31/2018] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND The Pantosteus plebeius-nebuliferus species-group is a group of freshwater fishes distributed in endo- and exorheic drainage basins in the Mexican Sierra Madre Occidental mountain range system and central North Mexico. The geological history of this region is considered an important factor in explaining the evolutionary history of low vagility animals like freshwaters fishes. The aim of this study was to examine the phylogenetic relationships and describe the evolutionary history of the species-group. We hypothesized that the genetic structure and distribution of the main clades of Pantosteus plebeius-nebuliferus are associated with the geological history of Northern Mexico. To this end, we obtained DNA sequences of mitochondrial and nuclear genes and performed phylogenetic and phylogeographic analyses. Divergence time estimation and ancestral area reconstruction were also carried out to propose a biogeographical hypothesis, and species boundaries within the species-group were also tested. RESULTS We identified four clades within the Pantosteus plebeius-nebuliferus species-group in both markers. Divergence ranged from 5.9% to 9.2% for cytb and 0.1% to 0.9% for GHI. We observed significant genetic structure and no shared haplotypes between clades. We estimated that the clades diverged during the last 5.1 Myr, with a biogeographic scenario suggesting eight vicariant and four dispersal events through the historic range of the species-group. We found that the best species-delimitation model is when four species are assumed, which correspond to the main clades. We identified nine evolutionary significance units (ESUs), pertinent to the conservation of the group, each representing populations present in distinct drainage basins. CONCLUSIONS The evolutionary history of the Pantosteus plebeius-nebuliferus species-group is characterized by vicariant post-dispersal processes, linked to geological changes in the Sierra Madre Occidental and central Northern Mexico since the Pliocene. This is congruent with biogeographic patterns described for other co-distributed fish species. We propose a new phylogenetic hypothesis for the species-group, clarifying the taxonomy of this evolutionarily complex group. Our results suggest that the species-group consists of at least four clades with independent evolutionary histories, two of which may represent new undescribed species. Our identification of ESUs provides a basis upon which conservation measures can be developed for the species-group.
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Affiliation(s)
- Diushi Keri Corona-Santiago
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC. c/José Gutiérrez Abascal, 2, 28006 Madrid, Spain
| | - Omar Domínguez-Domínguez
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán Mexico
- Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán Mexico
| | - Llanet Tovar-Mora
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán Mexico
| | - José Ramón Pardons-Blas
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC. c/José Gutiérrez Abascal, 2, 28006 Madrid, Spain
| | - Yvonne Herrerías-Diego
- Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán Mexico
| | - Rodolfo Pérez-Rodríguez
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán Mexico
| | - Ignacio Doadrio
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC. c/José Gutiérrez Abascal, 2, 28006 Madrid, Spain
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Jagielski T, Gawor J, Bakuła Z, Decewicz P, Maciszewski K, Karnkowska A. cytb as a New Genetic Marker for Differentiation of Prototheca Species. J Clin Microbiol 2018; 56:e00584-18. [PMID: 30068534 DOI: 10.1128/JCM.00584-18] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 07/21/2018] [Indexed: 11/20/2022] Open
Abstract
Achlorophyllous unicellular microalgae of the genus Prototheca (Trebouxiophyceae, Chlorophyta) are the only known plants that cause infections in both humans and animals, collectively referred to as protothecosis. Human protothecosis, most commonly manifested as cutaneous, articular, and disseminated disease, is primarily caused by Protothecawickerhamii, followed by Protothecazopfii and, sporadically, by Protothecacutis and Protothecamiyajii In veterinary medicine, however, P. zopfii is a major pathogen responsible for bovine mastitis, which is a predominant form of protothecal disease in animals. Historically, identification of Prototheca spp. has relied upon phenotypic criteria; these were later replaced by molecular typing schemes, including DNA sequencing. However, the molecular markers interrogated so far, mostly located in the ribosomal DNA (rDNA) cluster, do not provide sufficient discriminatory power to distinguish among all Prototheca spp. currently recognized. Our study is the first attempt to develop a fast, reliable, and specific molecular method allowing identification of all Prototheca spp. We propose the mitochondrial cytb gene as a new and robust marker for diagnostics and phylogenetic studies of the Prototheca algae. The cytb gene displayed important advantages over the rDNA markers. Not only did the cytb gene have the highest discriminatory capacity for resolving all Prototheca species, but it also performed best in terms of technical feasibility, understood as ease of amplification, sequencing, and multiple alignment analysis. Based on the species-specific polymorphisms in the partial cytb gene, we developed a fast and straightforward PCR-restriction fragment length polymorphism (RFLP) assay for identification and differentiation of all Prototheca species described so far. The newly proposed method is advocated to be a new gold standard in diagnostics of protothecal infections in human and animal populations.
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Torres L, Welch AJ, Zanchetta C, Chesser RT, Manno M, Donnadieu C, Bretagnolle V, Pante E. Evidence for a duplicated mitochondrial region in Audubon's shearwater based on MinION sequencing. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 30:256-263. [PMID: 30043666 DOI: 10.1080/24701394.2018.1484116] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Mitochondrial genetic markers have been extensively used to study the phylogenetics and phylogeography of many birds, including seabirds of the order Procellariiformes. Evidence suggests that part of the mitochondrial genome of Procellariiformes, especially albatrosses, is duplicated, but no DNA fragment covering the entire duplication has been sequenced. We sequenced the complete mitochondrial genome of a non-albatross species of Procellariiformes, Puffinus lherminieri (Audubon's shearwater) using the long-read MinION (ONT) technology. Two mitogenomes were assembled from the same individual, differing by 52 SNPs and in length. The shorter was 19 kb long while the longer was 21 kb, due to the presence of two identical copies of nad6, three tRNA, and two dissimilar copies of the control region (CR). Contrary to albatrosses, cob was not duplicated. We further detected a complex repeated region of undetermined length between the CR and 12S. Long-read sequencing suggests heteroplasmy and a novel arrangement within the duplicated region, indicating a complex evolution of the mitogenome in Procellariiformes.
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Affiliation(s)
- Lucas Torres
- a Centre d'Etudes Biologiques de Chizé, UMR 7372, CNRS , Université de La Rochelle , Villiers en Bois , France.,b Littoral, Environnement et Sociétés, UMR 7266 CNRS , Université de La Rochelle , La Rochelle , France
| | | | - Catherine Zanchetta
- d Centre INRA de Toulouse Midi-Pyrénées , US1426 Get-PlaGe , Castanet-Tolosan , France
| | - R Terry Chesser
- e USGS Patuxent Wildlife Research Center , National Museum of Natural History, Smithsonian Institution , Washington , DC , USA
| | - Maxime Manno
- d Centre INRA de Toulouse Midi-Pyrénées , US1426 Get-PlaGe , Castanet-Tolosan , France
| | - Cécile Donnadieu
- d Centre INRA de Toulouse Midi-Pyrénées , US1426 Get-PlaGe , Castanet-Tolosan , France
| | - Vincent Bretagnolle
- a Centre d'Etudes Biologiques de Chizé, UMR 7372, CNRS , Université de La Rochelle , Villiers en Bois , France
| | - Eric Pante
- b Littoral, Environnement et Sociétés, UMR 7266 CNRS , Université de La Rochelle , La Rochelle , France
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Surendran SN, Sivabalakrishnan K, Gajapathy K, Arthiyan S, Jayadas TTP, Karvannan K, Raveendran S, Parakrama Karunaratne SHP, Ramasamy R. Genotype and biotype of invasive Anopheles stephensi in Mannar Island of Sri Lanka. Parasit Vectors 2018; 11:3. [PMID: 29298698 PMCID: PMC5753456 DOI: 10.1186/s13071-017-2601-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 12/20/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Anopheles stephensi, the major vector of urban malaria in India, was recently detected for the first time in Sri Lanka in Mannar Island on the northwestern coast. Since there are different biotypes of An. stephensi with different vector capacities in India, a study was undertaken to further characterise the genotype and biotype of An. stephensi in Mannar Island. METHODS Mosquito larvae were collected in Pesalai village in Mannar and maintained in the insectary until adulthood. Adult An. stephensi were identified morphologically using published keys. Identified adult An. stephensi were molecularly characterized using two mitochondrial (cox1 and cytb) and one nuclear (ITS2) markers. Their PCR-amplified target fragments were sequenced and checked against available sequences in GenBank for phylogenetic analysis. The average spiracular and thoracic lengths and the spiracular index were determined to identify biotypes based on corresponding indices for Indian An. stephensi. RESULTS All DNA sequences for the Mannar samples matched reported sequences for An. stephensi from the Middle East and India. However, a single nucleotide variation in the cox1 sequence suggested an amino acid change from valine to methionine in the cox1 protein in Sri Lankan An. stephensi. Morphological data was consistent with the presence of the Indian urban vector An. stephensi type-form in Sri Lanka. CONCLUSIONS The present study provides a more detailed molecular characterization of An. stephensi and suggests the presence of the type-form of the vector for the first time in Sri Lanka. The single mutation in the cox1 gene may be indicative of a founder effect causing the initial diversification of An. stephensi in Sri Lanka from the Indian form. The distribution of the potent urban vector An. stephensi type-form needs to be established by studies throughout the island as its spread adds to the challenge of maintaining the country's malaria-free status.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Ranjan Ramasamy
- ID-FISH Technology Inc., 797 San Antonio Road, Palo Alto, CA, 94303, USA
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Koç H, Bülbül U, Kurnaz M, İhsan Eroğlu A, Kutrup B. Phylogenetic relationships of Podarcis siculus (Rafinesque-Schmaltz, 1810) and Podarcis tauricus (Pallas, 1814) in Turkey, based on mitochondrial DNA. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:664-673. [PMID: 28673190 DOI: 10.1080/24701394.2017.1342245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The Italian wall lizard and the Balkan wall lizard have a series of taxonomic revisions. However, their phylogenetic relationships still remain uncertain in Turkey. In the present study, we have assessed taxonomic relationships, both of Podarcis siculus and Podarcis tauricus through estimation of phylogenetic relationships among 43 and 42 specimens, respectively, using mtDNA (16 S rRNA and cytb) from great main populations in Turkey. The genetic distances among the populations of P. siculus in Turkey were very low and they were ranged from 0.2 to 1.6% in 16 S rRNA while they were ranged from 0.0% to 3.3% in cytb. On the other hand, the p-distances among the populations of P. tauricus were ranged from 0.0 to 0.6% in 16 S rRNA while they were 0.2% cytb in Turkey. Finally, most of the topologically identical trees of phylogenetic analyses and p-distances showed that monophyly was found in extant populations of P. siculus and P. tauricus. The nominate subspecies, P. s. siculus and P. t. tauricus are representatives of these lizards in Turkey.
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Affiliation(s)
- Halime Koç
- a Department of Biology , Karadeniz Technical University , Trabzon , Turkey
| | - Ufuk Bülbül
- a Department of Biology , Karadeniz Technical University , Trabzon , Turkey
| | - Muammer Kurnaz
- a Department of Biology , Karadeniz Technical University , Trabzon , Turkey
| | - Ali İhsan Eroğlu
- a Department of Biology , Karadeniz Technical University , Trabzon , Turkey
| | - Bilal Kutrup
- a Department of Biology , Karadeniz Technical University , Trabzon , Turkey
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Zhu C, Li J, Xie S, Ding H, Pan Z, Wang H, Chang G. Genetic diversity analysis of Asian clam Corbicula fluminea in the Hongze Lake based on mitochondrial cytochrome b gene. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:419-426. [PMID: 28340307 DOI: 10.1080/24701394.2017.1298101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The Asian clam Corbicula fluminea is a small bivalve with high nutritional and medical values. However, natural resources of C. fluminea have declined in many areas of China including the Hongze Lake. In this study, 119 individuals from 10 sites of this lake and 2 outgroups were analyzed using a 456 bp mitochondrial cytochrome b (cytb) gene segment. Totally, 19 polymorphic sites were detected, which defined 16 haplotypes. Polymorphism varied among the 10 populations with those at the water inlet being more polymorphic. Most FST values among these populations were below 0.15 with the overall value of 0.060 (p < .05), meanwhile, the overall gene flow was 7.67, both of which indicated the low level of population differentiation in this lake. Neutrality test and mismatch analyses indicated that population explosion may have occurred in this lake. The results obtained in this study will provide useful information for artificial breeding and resource protection of this species in the Hongze Lake.
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Affiliation(s)
- Chuankun Zhu
- a Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University , Huai'an , China.,b Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University , Huai'an , China
| | - Jin Li
- c The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences , Wuhan , China
| | - Songguang Xie
- b Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University , Huai'an , China.,c The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences , Wuhan , China
| | - Huaiyu Ding
- a Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University , Huai'an , China.,b Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University , Huai'an , China
| | - Zhengjun Pan
- a Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University , Huai'an , China.,b Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University , Huai'an , China
| | - Hui Wang
- a Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University , Huai'an , China.,b Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University , Huai'an , China
| | - Guoliang Chang
- a Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University , Huai'an , China.,b Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University , Huai'an , China
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Koç H, Kutrup B, Eroğlu O, Bülbül U, Kurnaz M, Afan F, Eroğlu Aİ. Phylogenetic relationships of D. rudis (Bedriaga, 1886) and D. bithynica(Mehely, 1909) based on microsatellite and mitochondrial DNA in Turkey. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:814-825. [PMID: 27681412 DOI: 10.1080/24701394.2016.1197215] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The spiny-tailed lizard of the genus Darevskia have a series of taxonomic revisions, but still their phylogenetic relationships remain uncertain. In the present study, we have assessed taxonomic relationships among Darevskia bithynica and Darevskia rudis populations through estimation of phylogenetic relationships among 96 specimens using microsatellite DNA (Du215, Du281, Du323 and Du418 loci) and 53 specimens using mtDNA (16S rRNA and cytb) from main populations in Turkey. Although D. b. bithynica and D. r. mirabilis were separated based on the PCoA analysis at low level from other D. rudis and D. bithynica populations, the distance values of Nei's genetic distance, Nei's unbiased genetic distance, Fst and Linear Fst were not high among taxa in microsatellite DNA. On the other hand, our phylogenetic analyses (NJ, ML, MP and BI) did not separate D. rudis and D. bithynica populations. Finally, most of the topologically identical trees of phylogenetic analyses and microsatellite results showed that the extant populations of D. rudis and D. bithynica were found to be polytomy. Based on our molecular phylogenetic study, D. rudis complex is still ongoing revisions.
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Affiliation(s)
- Halime Koç
- a Department of Biology , Karadeniz Technical University , Trabzon , Turkey
| | - Bilal Kutrup
- a Department of Biology , Karadeniz Technical University , Trabzon , Turkey
| | - Oğuzhan Eroğlu
- b Department of Breeding and Genetics , Central Fisheries Research Institute , Yomra/Trabzon , Turkey
| | - Ufuk Bülbül
- a Department of Biology , Karadeniz Technical University , Trabzon , Turkey
| | - Muammer Kurnaz
- a Department of Biology , Karadeniz Technical University , Trabzon , Turkey
| | - Feridun Afan
- b Department of Breeding and Genetics , Central Fisheries Research Institute , Yomra/Trabzon , Turkey
| | - Ali İhsan Eroğlu
- a Department of Biology , Karadeniz Technical University , Trabzon , Turkey
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Mabuchi K. Complete mitochondrial genome of the parrotfish Calotomus japonicus (Osteichthyes: Scaridae) with implications based on the phylogenetic position. Mitochondrial DNA B Resour 2016; 1:643-645. [PMID: 33473581 PMCID: PMC7800201 DOI: 10.1080/23802359.2016.1214553] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The complete mitochondrial genome sequence was determined for a specimen of Calotomus japonicus, a temperate parrotfish endemic to coastal East Asia. It was compared phylogenetically with previously published partial sequences from this species and other parrotfishes. The obtained tree indicated that the three cytb sequences of C. japonicus from a recent molecular study (LC068806-8) probably resulted from introgression through intergeneric hybridization, or possibly from sample confusion. Taking the presently obtained mitogenome as representative of C. japonicus, the species most closely related to this one among congeners is C. zonarchus, which is endemic to the Hawaiian islands.
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Affiliation(s)
- Kohji Mabuchi
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
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Fernandez-Silva I, Randall JE, Golani D, Bogorodsky SV. Mulloidichthys flavolineatus flavicaudus Fernandez-Silva & Randall (Perciformes, Mullidae), a new subspecies of goatfish from the Red Sea and Arabian Sea. Zookeys 2016:131-57. [PMID: 27551217 PMCID: PMC4978075 DOI: 10.3897/zookeys.605.8060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Accepted: 04/15/2016] [Indexed: 11/12/2022] Open
Abstract
The number of goatfish species has increased recently, thanks in part to the application of molecular approaches to the taxonomy of a family with conservative morphology and widespread intraspecific color variation. A new subspecies Mulloidichthysflavolineatusflavicaudus Fernandez-Silva & Randall is described from the Red Sea and Arabian Sea, including Socotra and Gulf of Oman. It is characterized by a yellow caudal fin, 25–28 gill rakers, and 37–38 lateral-line scales and it is differentiated from nominal subspecies Mulloidichthysflavolineatusflavolineatus by 1.7% sequence divergence at the mitochondrial cytochrome b gene. The morphometric examination of specimens of Mulloidichthysflavolineatusflavolineatus revealed variation in head length, eye diameter, and barbel length, in western direction from the Hawaiian Islands, South Pacific, Micronesia, and the East Indies to the Indian Ocean. The population of Mulloidichthysflavolineatusflavicaudussubsp. n. in the Gulf of Aqaba differs from that of the remaining Red Sea by shorter barbels, smaller eyes, shorter head, and shorter pelvic fins. We present a list of 26 endemic fishes from the Gulf of Aqaba and discuss the probable basis for the endemism in the light of the geological history of this region.
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Affiliation(s)
- Iria Fernandez-Silva
- Section of Ichthyology, California Academy of Sciences, 55 Music Concourse Dr, San Francisco, CA 94118, U.S.A.; Departament of Biochemistry, Genetics and Immunology, Campus Universitario, University of Vigo, 36310 Vigo, Spain
| | - John E Randall
- Bishop Museum, Honolulu, 1525 Bernice Street, Honolulu, HI 96817, U.S.A
| | - Daniel Golani
- Department of Evolution, Systematics and Ecology, the Hebrew University of Jerusalem, Israel
| | - Sergey V Bogorodsky
- Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, 60325 Frankfurt a.M., Germany; Station of Naturalists, Tulenina Str 13-29, Omsk, Russia
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Kvie KS, Heggenes J, Røed KH. Merging and comparing three mitochondrial markers for phylogenetic studies of Eurasian reindeer (Rangifer tarandus). Ecol Evol 2016; 6:4347-58. [PMID: 27386080 PMCID: PMC4893353 DOI: 10.1002/ece3.2199] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 04/25/2016] [Accepted: 05/02/2016] [Indexed: 01/12/2023] Open
Abstract
Phylogenetic analyses provide information that can be useful in the conservation of genetic variation by identifying intraspecific genetic structure. Reconstruction of phylogenetic relationships requires the use of markers with the appropriate amount of variation relative to the timeframe and purpose of the study. Here, genetic structure and clustering are inferred from comparative analyses of three widely used mitochondrial markers, the CR, cytb and the COI region, merged and separately, using Eurasian reindeer as a model. A Bayesian phylogeny and a MJ network, both based on the merged dataset, indicate several distinct maternal haplotype clusters within Eurasian reindeer. In addition to confirm previously described clusters, two new subclusters were found. When comparing the results from the merged dataset with the results from analyses of the three markers separately, similar clustering was found in the CR and COI phylogenies, whereas the cytb region showed poor resolution. Phylogenetic analyses of the merged dataset and the CR revealed congruent results, implying that single sequencing analysis of the CR is an applicable method for studying the haplotype structure in Eurasian reindeer.
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Affiliation(s)
- Kjersti S Kvie
- Department of Environmental Studies University College of Southeast Norway Bø in Telemark Norway; Department of Basic Sciences and Aquatic Medicine Norwegian University of Life Sciences Oslo Norway
| | - Jan Heggenes
- Department of Environmental Studies University College of Southeast Norway Bø in Telemark Norway
| | - Knut H Røed
- Department of Basic Sciences and Aquatic Medicine Norwegian University of Life Sciences Oslo Norway
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Llanes-Acevedo IP, Arcones C, Gálvez R, Martin O, Checa R, Montoya A, Chicharro C, Cruz S, Miró G, Cruz I. DNA sequence analysis suggests that cytb-nd1 PCR-RFLP may not be applicable to sandfly species identification throughout the Mediterranean region. Parasitol Res 2016; 115:1287-95. [PMID: 26755361 PMCID: PMC4759228 DOI: 10.1007/s00436-015-4865-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 11/30/2015] [Indexed: 12/04/2022]
Abstract
Molecular methods are increasingly used for both species identification of sandflies and assessment of their population structure. In general, they are based on DNA sequence analysis of targets previously amplified by PCR. However, this approach requires access to DNA sequence facilities, and in some circumstances, it is time-consuming. Though DNA sequencing provides the most reliable information, other downstream PCR applications are explored to assist in species identification. Thus, it has been recently proposed that the amplification of a DNA region encompassing partially both the cytochrome-B (cytb) and the NADH dehydrogenase 1 (nd1) genes followed by RFLP analysis with the restriction enzyme Ase I allows the rapid identification of the most prevalent species of phlebotomine sandflies in the Mediterranean region. In order to confirm the suitability of this method, we collected, processed, and molecularly analyzed a total of 155 sandflies belonging to four species including Phlebotomus ariasi, P. papatasi, P. perniciosus, and Sergentomyia minuta from different regions in Spain. This data set was completed with DNA sequences available at the GenBank for species prevalent in the Mediterranean basin and the Middle East. Additionally, DNA sequences from 13 different phlebotomine species (P. ariasi, P. balcanicus, P. caucasicus, P. chabaudi, P. chadlii, P. longicuspis, P. neglectus, P. papatasi, P. perfiliewi, P. perniciosus, P. riouxi, P. sergenti, and S. minuta), from 19 countries, were added to the data set. Overall, our molecular data revealed that this PCR-RFLP method does not provide a unique and specific profile for each phlebotomine species tested. Intraspecific variability and similar RFLP patterns were frequently observed among the species tested. Our data suggest that this method may not be applicable throughout the Mediterranean region as previously proposed. Other molecular approaches like DNA barcoding or phylogenetic analyses would allow a more precise molecular species identification.
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Affiliation(s)
- Ivonne Pamela Llanes-Acevedo
- Servicio de Parasitología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, World Health Organization Collaborating Center for Leishmaniasis, Ctra. Majadahonda-Pozuelo Km2, Majadahonda, 28220, Madrid, Spain.
| | - Carolina Arcones
- Servicio de Parasitología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, World Health Organization Collaborating Center for Leishmaniasis, Ctra. Majadahonda-Pozuelo Km2, Majadahonda, 28220, Madrid, Spain.
| | - Rosa Gálvez
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Avda. Puerta de Hierro s/n, 28040, Madrid, Spain.
| | - Oihane Martin
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Avda. Puerta de Hierro s/n, 28040, Madrid, Spain.
| | - Rocío Checa
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Avda. Puerta de Hierro s/n, 28040, Madrid, Spain.
| | - Ana Montoya
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Avda. Puerta de Hierro s/n, 28040, Madrid, Spain.
| | - Carmen Chicharro
- Servicio de Parasitología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, World Health Organization Collaborating Center for Leishmaniasis, Ctra. Majadahonda-Pozuelo Km2, Majadahonda, 28220, Madrid, Spain.
| | - Susana Cruz
- Servicio de Parasitología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, World Health Organization Collaborating Center for Leishmaniasis, Ctra. Majadahonda-Pozuelo Km2, Majadahonda, 28220, Madrid, Spain.
| | - Guadalupe Miró
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Avda. Puerta de Hierro s/n, 28040, Madrid, Spain.
| | - Israel Cruz
- Neglected Tropical Diseases Programme, Foundation for Innovative New Diagnostics-FIND, Chemin des Mines 9, Campus Biotech, 1202, Geneva, Switzerland.
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Kapustina SY, Brandler OV, Adiya Y. [Phylogeny of genus Spermophilus and position of Alashan ground squirrel (Spermophilus alashanicus, Buchner, 1888) on phylogenetic tree of Paleartic short-tailed ground squirrels]. Mol Biol (Mosk) 2015; 49:442-8. [PMID: 26107897 DOI: 10.7868/s0026898415030088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 12/17/2014] [Indexed: 11/23/2022]
Abstract
Phylogenetic relationships within a group of Paleartic short tailed ground squirrels (Spermophilus), recently defined as genus, are not sufficiently clear and need a critical revision. Interspecies hybridization, found in Eurasian Spermophilus, can affect the results of reconstruction of molecular phylogeny. Alashan ground squirrel position on the phylogenetic tree needs clarification. We analyzed eight nucleotide sequences of cytb gene of S. alashanicus and 127 sequences of other Spermophilus species form GenBank. S.alashanicus and S. dauricus close phylogenetic relationship, and their affinity to ancestral forms of the group are revealed. Monophyly of Colobotis subgenus was confirmed. Paraphyly of eastern and western forms of S. relictus was shown.
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Affiliation(s)
- S Yu Kapustina
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, 119334 Russia.,
| | - O V Brandler
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| | - Ya Adiya
- Institute of Biology, Mongolian Academy of Sciences, Ulaanbaatar210351, Mongolia
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Guerra D, Ghiselli F, Passamonti M. The largest unassigned regions of the male- and female-transmitted mitochondrial DNAs in Musculista senhousia (Bivalvia Mytilidae). Gene 2013; 536:316-25. [PMID: 24342661 DOI: 10.1016/j.gene.2013.12.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 09/24/2013] [Accepted: 12/01/2013] [Indexed: 11/17/2022]
Abstract
Musculista senhousia is a marine mussel with doubly uniparental inheritance (DUI) of mitochondria. In this study we analyzed the largest unassigned region (LUR) of its female- and male-transmitted mitochondrial genomes, described their fine characteristics and searched for shared features. Our results suggest that both LURs contain the control region of their respective mitochondrial genomes. The female-transmitted control region is duplicated in tandem, with the two copies evolving in concert. This makes the F-mtDNA of M. senhousia the first Bivalve mitochondrial genome with this feature. We also compared M. senhousia control regions to that of other Mytilidae, and demonstrated that signals for basic mtDNA functions are retained over evolutionary times even among the fast-evolving mitochondrial genomes of DUI species. Finally, we discussed how similarities between female and male LURs may be explained in the context of DUI evolution and if the duplicated female control region might have influenced the DUI system in this species.
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Affiliation(s)
- Davide Guerra
- Department of Biological Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126 Bologna, Italy.
| | - Fabrizio Ghiselli
- Department of Biological Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126 Bologna, Italy
| | - Marco Passamonti
- Department of Biological Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126 Bologna, Italy
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D’Amato ME, Alechine E, Cloete KW, Davison S, Corach D. Where is the game? Wild meat products authentication in South Africa: a case study. Investig Genet 2013; 4:6. [PMID: 23452350 PMCID: PMC3621286 DOI: 10.1186/2041-2223-4-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 02/14/2013] [Indexed: 11/10/2022]
Abstract
BACKGROUND Wild animals' meat is extensively consumed in South Africa, being obtained either from ranching, farming or hunting. To test the authenticity of the commercial labels of meat products in the local market, we obtained DNA sequence information from 146 samples (14 beef and 132 game labels) for barcoding cytochrome c oxidase subunit I and partial cytochrome b and mitochondrial fragments. The reliability of species assignments were evaluated using BLAST searches in GenBank, maximum likelihood phylogenetic analysis and the character-based method implemented in BLOG. The Kimura-2-parameter intra- and interspecific variation was evaluated for all matched species. RESULTS The combined application of similarity, phylogenetic and character-based methods proved successful in species identification. Game meat samples showed 76.5% substitution, no beef samples were substituted. The substitutions showed a variety of domestic species (cattle, horse, pig, lamb), common game species in the market (kudu, gemsbok, ostrich, impala, springbok), uncommon species in the market (giraffe, waterbuck, bushbuck, duiker, mountain zebra) and extra-continental species (kangaroo). The mountain zebra Equus zebra is an International Union for Conservation of Nature (IUCN) red listed species. We also detected Damaliscus pygargus, which is composed of two subspecies with one listed by IUCN as 'near threatened'; however, these mitochondrial fragments were insufficient to distinguish between the subspecies. The genetic distance between African ungulate species often overlaps with within-species distance in cases of recent speciation events, and strong phylogeographic structure determines within-species distances that are similar to the commonly accepted distances between species. CONCLUSIONS The reliability of commercial labeling of game meat in South Africa is very poor. The extensive substitution of wild game has important implications for conservation and commerce, and for the consumers making decisions on the basis of health, religious beliefs or personal choices.Distance would be a poor indicator for identification of African ungulates species. The efficiency of the character-based method is reliant upon availability of large reference data. The current higher availability of cytochrome b data would make this the marker of choice for African ungulates. The encountered problems of incomplete or erroneous information in databases are discussed.
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Affiliation(s)
- Maria Eugenia D’Amato
- Biotechnology Department, Forensic DNA Lab, University of the Western Cape, Modderdam Road, Bellville, 7535, South Africa
| | - Evguenia Alechine
- Servicio de Huellas Digitales Genéticas, School of Pharmacy and Biochemistry, University of Buenos Aires, Junín 956, Buenos Aires, 1113, Argentina
| | - Kevin Wesley Cloete
- Biotechnology Department, Forensic DNA Lab, University of the Western Cape, Modderdam Road, Bellville, 7535, South Africa
| | - Sean Davison
- Biotechnology Department, Forensic DNA Lab, University of the Western Cape, Modderdam Road, Bellville, 7535, South Africa
| | - Daniel Corach
- Servicio de Huellas Digitales Genéticas, School of Pharmacy and Biochemistry, University of Buenos Aires, Junín 956, Buenos Aires, 1113, Argentina
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de Mendonça Dantas GP, Meyer D, Godinho R, Ferrand N, Morgante JS. Genetic variability in mitochondrial and nuclear genes of Larus dominicanus (Charadriiformes, Laridae) from the Brazilian coast. Genet Mol Biol 2012; 35:874-85. [PMID: 23271950 PMCID: PMC3526097 DOI: 10.1590/s1415-47572012005000065] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Accepted: 06/28/2012] [Indexed: 12/04/2022] Open
Abstract
Several phylogeographic studies of seabirds have documented low genetic diversity that has been attributed to bottleneck events or individual capacity for dispersal. Few studies have been done in seabirds on the Brazilian coast and all have shown low genetic differentiation on a wide geographic scale. The Kelp Gull is a common species with a wide distribution in the Southern Hemisphere. In this study, we used mitochondrial and nuclear markers to examine the genetic variability of Kelp Gull populations on the Brazilian coast and compared this variability with that of sub-Antarctic island populations of this species. Kelp Gulls showed extremely low genetic variability for mitochondrial markers (cytb and ATPase) and high diversity for a nuclear locus (intron 7 of the β-fibrinogen). The intraspecific evolutionary history of Kelp Gulls showed that the variability found in intron 7 of the β-fibrinogen gene was compatible with the variability expected under neutral evolution but suggested an increase in population size during the last 10,000 years. However, none of the markers revealed evidence of a bottleneck population. These findings indicate that the recent origin of Kelp Gulls is the main explanation for their nuclear diversity, although selective pressure on the mtDNA of this species cannot be discarded.
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Affiliation(s)
- Gisele Pires de Mendonça Dantas
- Laboratório de Biologia Evolutiva e Conservação de Vertebrados, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Diogo Meyer
- Laboratório de Biologia Evolutiva e Conservação de Vertebrados, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Raquel Godinho
- Centro de Investigação em Biodiversidade e Recursos Naturais, Porto, Portugal
| | - Nuno Ferrand
- Centro de Investigação em Biodiversidade e Recursos Naturais, Porto, Portugal
| | - João Stenghel Morgante
- Laboratório de Biologia Evolutiva e Conservação de Vertebrados, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
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