Tag: dnasp

First complete mitogenome of Massarineae and its contribution to phylogenetic implications in Pleosporales

Crous, P. W. et al. Fungal Planet description sheets: 214–280. Persoonia 32, 184–306 (2014). Article  PubMed  PubMed Central  Google Scholar  Zhang, Y. et al. Multi-locus phylogeny of Pleosporales: A taxonomic, ecological and evolutionary re-evaluation. Stud. Mycol. 64, 85–105 (2009). Article  PubMed  PubMed Central  Google Scholar  Schoch, C. L. et al….

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Insight into chloroplast genome structural variation of the Mongolian endemic species Adonis mongolica (Ranunculaceae) in the Adonideae tribe

Wang, W. T. Revision of Adonis (Ranunculaceae). Bull. Bot. Res. 14, 1–31 (1994). Google Scholar  Gao, T. et al. Evaluating the feasibility of using candidate DNA Barcodes in discriminating species of the large Asteraceae family. BMC Evol. Biol. 10, 324 (2016). Article  Google Scholar  Conti, F. et al. Adonis fucensis…

Continue Reading Insight into chloroplast genome structural variation of the Mongolian endemic species Adonis mongolica (Ranunculaceae) in the Adonideae tribe

Anopheles gambiae on remote islands in the Indian Ocean: origins and prospects for malaria elimination by genetic modification of extant populations

Irish, S. R., Kyalo, D., Snow, R. W. & Coetzee, M. Updated list of Anopheles species (Diptera: Culicidae) by country in the Afrotropical Region and associated islands. Zootaxa 4747(3), 401–449. doi.org/10.1646/zootaxa.4747.3.1 (2020). Article  Google Scholar  Jacques, B. Les moustiques de l’archipel Comores. Série Entomologie Médicale et Parasitologie 15(2), 153–170 (1977)….

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Whole mitochondrial genome sequencing provides new insights into the phylogeography of loggerhead turtles (Caretta caretta) in the Mediterranean Sea

Andrews S (2010) FastQC: a quality control tool for high throughput sequence data. www.bioinformatics.babraham.ac.uk/projects/fastqc Avise JC (1986) Mitochondrial DNA and the evolutionary genetics of higher animals. Philos Trans R Soc Lond B 312:325–342. doi.org/10.1098/rstb.1986.0011 Article  CAS  Google Scholar  Baker CS, Steel D, Calambokidis J, Falcone E, González-Peral U, Barlow J,…

Continue Reading Whole mitochondrial genome sequencing provides new insights into the phylogeography of loggerhead turtles (Caretta caretta) in the Mediterranean Sea

Haplotype and phylogenetic diversity using mitochondrial 12S rRNA gene marker in Bali cattle | Suselowati

Haplotype and phylogenetic diversity using mitochondrial 12S rRNA gene marker in Bali cattle T. Suselowati  –  Graduate School of Animal Science Faculty, IPB University, Indonesia R. R. Noor  –  Department of Animal Production and Technology, Faculty of Animal Science, IPB University, Indonesia *J. Jakaria  –  Department of Animal Production and…

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Comparative chloroplast genome analysis of four Polygonatum species insights into DNA barcoding, evolution, and phylogeny

Chloroplast genome features of four Polygonatum species In this phase of our study, we pursued the sequencing of four Polygonatum species namely P. filipes, P. cyrtonema, P. zanlanscianense and P. odoratum, using the Illumina HiSeq 2500 sequencing platform. This endeavour yielded a corpus of Illumina reads ranging from 15,915,998 to…

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Calculating haplotype and nucleotide diversity with deep amplicon sequencing data

Calculating haplotype and nucleotide diversity with deep amplicon sequencing data 0 Hi, I want have deep amplicon sequencing data (illumina) where I have samples in row and haplotype (both sequences and names) in column and read counts.The dataframe is a CSV format and I have a separate file in fasta…

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The genetic variability of grapevine Pinot gris virus (GPGV) in Australia | Virology Journal

Giampetruzzi A, Roumi V, Roberto R, Malossini U, Yoshikawa N, La Notte P, et al. A new grapevine virus discovered by deep sequencing of virus-and viroid-derived small RNAs in Cv Pinot gris. Virus Res. 2012;163(1):262–8. doi.org/10.1016/j.virusres.2011.10.010. Article  CAS  PubMed  Google Scholar  Bertazzon N, Forte V, Filippin L, Causin R, Maixner…

Continue Reading The genetic variability of grapevine Pinot gris virus (GPGV) in Australia | Virology Journal

Diversity and geographic distribution of haplotypes of Dirofilaria immitis across European endemic countries | Parasites & Vectors

Genchi C, Mortarino M, Rinaldi L, Cringoli G, Traldi G, Genchi M. Changing climate and changing vector-borne disease distribution: the example of Dirofilaria in Europe. Vet Parasitol. 2011;176:295–9. Article  PubMed  Google Scholar  Simón F, González-Miguel J, Diosdado A, Gómez PJ, Morchón R, Kartashev V. The Complexity of zoonotic filariasis episystem…

Continue Reading Diversity and geographic distribution of haplotypes of Dirofilaria immitis across European endemic countries | Parasites & Vectors

Mitochondrial genomic investigation reveals a clear association between species and genotypes of Lucilia and geographic origin in Australia | Parasites & Vectors

Zumpt F. Myiasis in man and animals in the old world. A textbook for physicians, veterinarians and zoologists. London: Butterworth; 1965. Google Scholar  Stevens JR, Wall R. Genetic variation in populations of the blowflies Lucilia cuprina and Lucilia sericata (Diptera: Calliphoridae). Random amplified polymorphic DNA analysis and mitochondrial DNA sequences….

Continue Reading Mitochondrial genomic investigation reveals a clear association between species and genotypes of Lucilia and geographic origin in Australia | Parasites & Vectors

Infection of sheep by Echinococcus multilocularis in Gansu, China: evidence from mitochondrial and nuclear DNA analysis | Infectious Diseases of Poverty

Craig PS, Hegglin D, Lightowlers MW, Torgerson PR, Wang Q. Echinococcosis: control and prevention. Adv Parasitol. 2017;96:55–158. Article  CAS  PubMed  Google Scholar  Deplazes P, Dinkel A, Mathis A. Molecular tools for studies on the transmission biology of Echinococcus multilocularis. Parasitology. 2003;127(Suppl):S53–61. Article  CAS  PubMed  Google Scholar  Deplazes P, Rinaldi L,…

Continue Reading Infection of sheep by Echinococcus multilocularis in Gansu, China: evidence from mitochondrial and nuclear DNA analysis | Infectious Diseases of Poverty

Ancient DNA confirms diverse origins of early post-Columbian cattle in the Americas

Crosby, A. W. The Columbian Exchange: Biological and Cultural Consequences of 1492 (Praeger, 1972). Google Scholar  Ficek, R. E. Cattle, capital, colonization: Tracking creatures of the Anthropocene in and out of human projects. Curr. Anthropol. 60, S260–S271 (2019). Google Scholar  Delsol, N. Disassembling cattle and enskilling subjectivities: Butchering techniques and…

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Reduced polymorphism of Plasmodium vivax early transcribed membrane protein (PvETRAMP) 11.2 | Parasites & Vectors

WHO. World malaria report 2020. 20 years of global progress and challenges. 2020. www.who.int/publications/i/item/9789240015791. Datoo MS, Natama HM, Somé A, Bellamy D, Traoré O, Rouamba T, et al. Efficacy and immunogenicity of R21/Matrix-M vaccine against clinical malaria after 2 years’ follow-up in children in Burkina Faso: a phase 1/2b randomised…

Continue Reading Reduced polymorphism of Plasmodium vivax early transcribed membrane protein (PvETRAMP) 11.2 | Parasites & Vectors

Key triggers of adaptive genetic variability of sessile oak [Q. petraea (Matt.) Liebl.] from the Balkan refugia: outlier detection and association of SNP loci from ddRAD-seq data

Adamack AT, Gruber B (2014) PopGenReport: simplifying basic population genetic analyses in R. Methods Ecol Evol 5:384–387. doi.org/10.1111/2041-210x.12158 Article  Google Scholar  Aguirre-Liguori JA, Ramírez-Barahona S, Gaut BS (2021) The evolutionary genomics of species’ responses to climate change. Nat Ecol Evol 5:1350–60. doi.org/10.1038/s41559-021-01526-9 Article  PubMed  Google Scholar  Ahrens CW, Rymer PD,…

Continue Reading Key triggers of adaptive genetic variability of sessile oak [Q. petraea (Matt.) Liebl.] from the Balkan refugia: outlier detection and association of SNP loci from ddRAD-seq data

Phylogenomic analysis, cryptic species discovery, and DNA barcoding of the genus Cibotium in China based on plastome data

Introduction Traditional Chinese herbal medicine plays an indispensable role in the treatment of multiple diseases in China and other developing countries (Newman et al., 2008). Apart from the traditional usage, many medicinal plants, such as Artemisia annua L. (artemisinin, Tu, 2016), Huperzia javanica (Sw.) C. Y. Yang (Huperzine A, Zangara, 2003;…

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Characterization of nuclear DNA diversity in an individual Leymus chinensis

Introduction The definition of an individual organism, traditionally defined by the invariable presence of a physiological unit and genetic homogeneity, is challenged by situations such as intraorganismal genetic heterogeneity (IGH), which refers to the presence of more than one genotype in a single organism (Schweinsberg et al., 2015). Cells within a…

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Molecular evolution and phylogenomic analysis of complete chloroplast genomes of Cotinus (Anacardiaceae)

Abstract Cotinus is an oligo‐specific ornamentally valuable genus with a disjunct distribution in the Northern Hemisphere. Traditionally, the taxonomy of Cotinus was mainly based on leaf morphological characteristics. However, the limited availability of genomic information greatly hindered the study of molecular evolution and phylogeny of this genus. This study sequenced…

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Evolution and biogeography of apple stem grooving virus | Virology Journal

New Iranian isolates ASGV was detected in 18 (10.3%) of samples in both west and north west Iran (Table S1). All nine full-CP sequences contained open reading frames (ORFs) 714 nt in length with 237 deduced amino acid residues. ASGV has the codon UAG as stop codon in all sequences….

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A Comparative Phylogeographic Analysis of Mitochondrial DNA Variability in Four Fish Species (Salmonidae and Cyprinidae) in the Northwest Pacific

Bol’shakov, S.G., Some features of biology, growth, and age of Far Eastern redfins—Pacific redfin Tribolodon brandti and big-scaled redfin Tribolodon hakonensis—in southern Primorskii krai, Izv. Tikhookean. Nauchno-Issled. Inst. Rybn. Khoz. Okeanogr., 2013, pp. 141–158. Google Scholar  Brykov, V.A., Polyakova, N.E., and Semina, A.V., Comparative analysis of mitochondrial DNA variability in four…

Continue Reading A Comparative Phylogeographic Analysis of Mitochondrial DNA Variability in Four Fish Species (Salmonidae and Cyprinidae) in the Northwest Pacific

Comparative plastome genomics, taxonomic delimitation and evolutionary divergences of Tetraena hamiensis var. qatarensis and Tetraena simplex (Zygophyllaceae)

Liu, J. et al. Integrating a comprehensive DNA barcode reference library with a global map of yews (Taxus L.) for forensic identification. Mol. Ecol. Resour. 18, 1115–1131 (2018). Article  CAS  Google Scholar  Parveen, I., Singh, H. K., Raghuvanshi, S., Pradhan, U. C. & Babbar, S. B. DNA barcoding of endangered…

Continue Reading Comparative plastome genomics, taxonomic delimitation and evolutionary divergences of Tetraena hamiensis var. qatarensis and Tetraena simplex (Zygophyllaceae)

Possible origins and implications of atypical morphologies and domestication-like traits in wild golden jackals (Canis aureus)

Camera surveillance and spatial analyses Camera surveillance took place between August and December 2020, at twelve ~ 30 km2 sites located in the central and northern Golan Heights (Supplementary Table 1). The sampling sites designated for this study belonged to four different land-use categories: “high culling risk”, “low culling risk”, nature reserves…

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Protocols to Study Host-Pathosystems | SpringerLink

Alkooranee JT, Liu S, Aledan TR, Yin Y, Li M (2015) First report of powdery mildew caused by erysiphe cruciferarum on brassica napus in China. Plant Dis 99(11):1651 CrossRef  Google Scholar  Al-Lami HFD, You MP, Barbetti MJ (2019a) Incidence, pathogenicity and diversity of Alternaria spp. associated with alternaria leaf spot…

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Molecular characterization of oriental eyeworm (Thelazia callipaeda) detected from raccoon (Procyon lotor) and Japanese raccoon dog (Nyctereutes viverrinus) in Kanto region, Japan | Parasites & Vectors

Shen J, Gasser RB, Chu D, Wang Z, Cantacessi C, Otranto D. Human thelaziasis—a neglected parasitic disease of the eye. J Parasitol. 2006;92:872–5. Article  PubMed  Google Scholar  Otranto D, Mendoza-Roldan JA, Dantas-Torres F. Thelazia callipaeda. Trends Parasitol. 2021;37:263–4. Article  PubMed  Google Scholar  Otranto D, Lia RP, Buono V, Traversa D,…

Continue Reading Molecular characterization of oriental eyeworm (Thelazia callipaeda) detected from raccoon (Procyon lotor) and Japanese raccoon dog (Nyctereutes viverrinus) in Kanto region, Japan | Parasites & Vectors

Extensive prevalence and significant genetic differentiation of Blastocystis in high- and low-altitude populations of wild rhesus macaques in China | Parasites & Vectors

Andersen LO, Stensvold CR. Blastocystis in health and disease: are we moving from a clinical to a public health perspective? J Clin Microbiol. 2016;54:524–8. Article  CAS  PubMed  PubMed Central  Google Scholar  Hublin JSY, Maloney JG, Santin M. Blastocystis in domesticated and wild mammals and birds. Res Vet Sci. 2021;135:260–82. Article …

Continue Reading Extensive prevalence and significant genetic differentiation of Blastocystis in high- and low-altitude populations of wild rhesus macaques in China | Parasites & Vectors

Phylogeny and Genetic Diversity of Philippine Native Pigs (Sus scrofa) as Revealed by Mitochondrial DNA Analysis

Ai H, Fang X, Yang B, Huang Z, Chen H, Mao L, Zhang F, Zhang L, Cui L, He W, Yang J, Yao X, Zhou L, Han L, Li J, Sun S, Xie X, Lai B, Su Y, Lu Y, Yang H, Huang T, Deng W, Nielsen R, Ren J,…

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Novel equi merozoite antigen (ema-1) gene heterogeneity in a geographically isolated Theileria equi population in Croatia | Parasites & Vectors

Richter S. Vrste haemosporidia u konja i goveda NR Hrvatskoj. Thesis: Veterinary faculty university of zagreb; 1954. Google Scholar  Rothschild CM. Equine piroplasmosis. J Equine Vet Sci. 2013;33:497–508. Article  Google Scholar  Ueti MW, Palmer GH, Scoles GA, Kappmeyer LS, Knowles DP. Persistently infected horses are reservoirs for intrastadial tick-borne transmission…

Continue Reading Novel equi merozoite antigen (ema-1) gene heterogeneity in a geographically isolated Theileria equi population in Croatia | Parasites & Vectors

Remarkably low host specificity in the bat fly Penicillidia fulvida (Diptera: Nycteribiidae) as assessed by mitochondrial COI and nuclear 28S sequence data | Parasites & Vectors

Zachos FE. Species concepts in biology: historical development, theoretical foundations and practical relevance. Berlin: Springer; 2016. Google Scholar  Perkins SL. Species concepts and malaria parasites: detecting a cryptic species of Plasmodium. Proc Biol Sci. 2000;267:2345–50. CAS  PubMed  PubMed Central  Google Scholar  Mayr E. Systematics and the origin of species. New…

Continue Reading Remarkably low host specificity in the bat fly Penicillidia fulvida (Diptera: Nycteribiidae) as assessed by mitochondrial COI and nuclear 28S sequence data | Parasites & Vectors

Comparative chloroplast genome and phylogenetic analyses of Chinese Polyspora

Choo, L. M., Niissalo, M. A., Leong, P. K. F. & Khew, G. S. The complete plastome sequence of Gordonia penangensis Ridl. supports the transfer of Asian Gordonia into Polyspora (Theaceae). Phytotaxa 458, 159–166 (2020). Nguyet, H. N. L. et al. An updated checklist of Theaceae and a new species…

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Plastomes of limestone karst gesneriad genera Petrocodon and Primulina, and the comparative plastid phylogenomics of Gesneriaceae

Features of the newly sequenced Petrocodon and Primulina plastomes Sizes of the nine newly sequenced plastomes of Petrocodon and Primulina range from 152,323 bp in Pr. medica (D.Fang ex W.T.Wang) Yin Z.Wang to 153,786 bp in Pr. cordata Mich.Möller & A.Weber (Tables 1, S1). These nine plastomes display the typical quadripartite structure…

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Unveiling new perspective of phylogeography, genetic diversity, and population dynamics of Southeast Asian and Pacific chickens

Food and Agriculture Organization. The state of the world’s animal genetic resources for food and agriculture (Rome, 2007). Lawler, A. Dawn of the chicken revealed in Southeast Asia. Science 368, 1411 (2020). ADS  CAS  PubMed  Article  Google Scholar  Sykes, N. A social perspective on the introduction of exotic animals: the…

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Antiplatelet response to clopidogrel is associated with a haplotype in CYP2C19 gene in Pakistani patients

Amsterdam, E. A. et al. 2014 AHA/ACC guideline for the management of patients with non-ST-elevation acute coronary syndromes: Executive summary: A report of the American College of Cardiology/American Heart Association Task Force on Practice Guidelines. Circulation 130, 2354–2394 (2014). Google Scholar  Kernan, W. N. et al. Guidelines for the prevention…

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The Clam Cyclina sinensis (Gmelin) Phylogeography Study with 28S rRNA Gene and Potential of Nuclear rRNA Genes in Genetic Assessments of Molluscs

Avise, J. C., 2009. Phylogeography: Retrospect and prospect. Journal of Biogeography, 36: 3–15. Article  Google Scholar  Beheregaray, L. B., 2008. Twenty years of phylogeography: The state of the field and the challenges for the Southern Hemisphere. Molecular Ecology, 17: 3754–3774. Google Scholar  Clement, M., Posada, D., and Crandall, K. A.,…

Continue Reading The Clam Cyclina sinensis (Gmelin) Phylogeography Study with 28S rRNA Gene and Potential of Nuclear rRNA Genes in Genetic Assessments of Molluscs

New insight into the taxonomic resolution of the genus Bythotrephes Leydig (Crustacea: Cladocera) based on molecular data from Central Europe

1. Therriault, T. W. et al. Taxonomic resolution of the genus Bythotrephes Leydig using molecular markers and re-evaluation of its global distribution. Divers. Distrib. 8, 67–84 (2002). Google Scholar  2. Karpowicz, M., Ejsmont-Karabin, J., Kozłowska, J., Feniova, I. & Dzialowski, A. R. Zooplankton community responses to oxygen stress. Water 12,…

Continue Reading New insight into the taxonomic resolution of the genus Bythotrephes Leydig (Crustacea: Cladocera) based on molecular data from Central Europe

Two divergent haplogroups of a sacsin-like gene in Acropora corals

Verification of coding sequence (CDS) of a sacsin-like gene The genomic assembly version 2.01 of A. millepora13 was downloaded from the web site (przeworskilab.com/acropora-millepora-genome/). RNA-seq reads of one A. millepora (accession: SRR2086157) were mapped (similarity fraction > 0.8, length fraction > 0.9) to the genome assembly using CLC Genomics Workbench (www.qiagenbioinformatics.com/). Mapping results were…

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The mtDNA Control Region Variability of Microtus rossiaemeridionalis (Rodentia, Arvicolini) from Two Invasive Populations of the Russian Far East

1 Hobbs, R.J., Arico, S., Aronson, J., et al., Novel ecosystems: theoretical and management aspects of the new ecological world order, Global Ecol. Biogeography, 2006, vol. 15, pp. 1–7. doi.org/10.1111/j.1466-822x.2006.00212.x Article  Google Scholar  2 Bellard, C., Cassey, P., and Blackburn, T.M., Alien species as a driver of recent extinctions, Biol….

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Drug resistance mutations & genetic diversity of HIV1 in ART

Introduction At the end of 2018, 19.5 million people living with HIV were accessing ART globally.1 However, virological failure and development of drug resistance are becoming a bottleneck for the success of ART program. A global study involving 36 countries and 1926 patients with treatment failure from 1998–2015 reported that…

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Organelle DNA sequence data provide new insights into the maternal and paternal lineages of Musa species germplasms

Argent GCG (1976) The wild bananas of Papua new Guinea. Notes Roy Bot Gard Edinb 35:77–114 Google Scholar  Baker JG (1893) A synopsis of the genera and species of Musaceae. Ann Bot 7:189–229. doi.org/10.1093/aob/os-7.2.189 Article  Google Scholar  Barrett CF, Specht CD, Leebens-Mack J, Stevenson DW, Zomlefer WB, Davis JI (2014)…

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Following the Trace of HVS II Mitochondrial Region Within the Nine Iranian Ethnic Groups Based on Genetic Population Analysis

Akbari MT, Izadi P, Izadyar M, Kyriacou K, Kleanthous M (2008) Molecular basis of thalassemia intermedia in Iran. Hemoglobin 32:462–470 CAS  Article  Google Scholar  Al-Allawi NA, Jubrael JM, Hughson M (2006) Molecular characterization of β-thalassemia in the Dohuk region of Iraq. Hemoglobin 30:479–486 CAS  Article  Google Scholar  Alibakhshi R, Kianishirazi…

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Haplotype Diversity of Mongolian and Tuvan Goat Breeds (Capra hircus) Based on mtDNA and Y-Chromosome Polymorphism

1 Zonaed Siddiki, A., Miah, G., Islam, M.S., et al., Goat genomic resources: the search for genes associated with its economic traits, Int. J. Genomics, 2020, 5940205. doi.org/10.1155/2020/5940205 2 Amills, M., Capote, J., and Tosser-Klopp, G., Goat domestication and breeding: a jigsaw of historical, biological and molecular data with missing…

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Cenozoic climatic changes drive evolution and dispersal of coastal benthic foraminifera in the Southern Ocean

1. Thomson, M. R. A. Geological and palaeoenvironmental history of the Scotia Sea region as a basis for biological interpretation. Deep Sea Res. II 51, 1467–1487 (2004). Article  ADS  Google Scholar  2. Maldonado, A. et al. A model of oceanic development by ridge jumping: Opening of the Scotia Sea. Glob….

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Connectivity, diversity, and hybridization between two endemic fish species (Percilia spp.) in a complex temperate landscape

Anderson EC, Thompson EA (2002) A model-based method for identifying species hybrids using multilocus genetic data. Genetics 160:1217–1229. doi.org/10.1175/1520-0442(1992)0052.0.CO;2 CAS  Article  PubMed  PubMed Central  Google Scholar  Arratia G (1982) A Review of freshwater percoids from South America (Pisces, Osteichthyes, Perciformes, Percichthyidae, and Peciliidae). Abh Senckenb Naturforsch Ges 15:1–52 Google Scholar …

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Dnasp Tutorial For Beginner

Dnasp Tutorial For Beginner 1 Hi Can someone help me? I need to know which data is required to perform different test with DNAsp: intra or interspecies sequences thank you • 6.1k views The “sp” in DNAsp stands for “sequence polymorphism” which reflects that this software is principally designed for…

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