Davison, A.J.; Eberle, R.; Ehlers, B.; Hayward, G.S.; McGeoch, D.J.; Minson, A.C.; Pellett, P.E.; Roizman, B.; Studdert, M.J.; Thiry, E. The Order Herpesvirales. Arch. Virol. 2009, 154, 171–177. [CrossRef] [PubMed]
Ackermann, M. Herpesviruses: A Brief Overview. Methods Mol. Biol. 2004, 256, 199–219. [CrossRef] [PubMed]
Pellett, P.E.; Roizman, B. The family Herpesviridae: A brief introduction. In Fields Virology; Lippincott Williams & Wilkins: Philadelphia, PA, USA, 2007; pp. 2479–2499. ISBN 978-0-7817-6060-7.
Pellett, P.E.; Davison, A.J.; Eberle, R.; Ehlers, B.; Hayward, G.S.; Lacoste, V.; Minson, A.C.; Nicholas, J.; Roizman, B.; Studdert, M.J.; et al. Order—Herpesvirales. In Virus Taxonomy; Ninth Report of the International Committee on Taxonomy of Viruses; Elsevier: Amsterdam, The Netherlands, 2012; pp. 99–107.
Boutier, M.; Morvan, L.; Delrez, N.; Origgi, F.; Doszpoly, A.; Vanderplasschen, A. Fish and Amphibian Alloherpesviruses; Elsevier: Amsterdam, The Netherlands, 2019; ISBN 978-0-12-809633-8.
Davison, A.J. Comparative analysis of the genomes. In Human Herpesviruses: Biology, Therapy, and Immunoprophylaxis; Arvin, A., Campadelli-Fiume, G., Mocarski, E., Moore, P.S., Roizman, B., Whitley, R., Yamanishi, K., Eds.; Cambridge University Press: Cambridge, UK, 2007; ISBN 978-0-521-82714-0.
McGeoch, D.J.; Davison, A.J.; Dolan, A.; Gatherer, D.; Sevilla-Reyes, E.E. Chapter 20—Molecular evolution of the Herpesvirales. In Origin and Evolution of Viruses, 2nd ed.; Domingo, E., Parrish, C.R., Holland, J.J., Eds.; Academic Press: London, UK, 2008; pp. 447–475. ISBN 978-0-12-374153-0.
Mocarski, E.S., Jr. Comparative analysis of herpesvirus-common proteins. In Human Herpesviruses: Biology, Therapy, and Immunoprophylaxis; Arvin, A., Campadelli-Fiume, G., Mocarski, E., Moore, P.S., Roizman, B., Whitley, R., Yamanishi, K., Eds.; Cambridge University Press: Cambridge, UK, 2007; ISBN 978-0-521-82714-0.
Van Beurden, S.J.; Bossers, A.; Voorbergen-Laarman, M.H.A.; Haenen, O.L.M.; Peters, S.; Abma-Henkens, M.H.C.; Peeters, B.P.H.; Rottier, P.J.M.; Engelsma, M.Y. Complete Genome Sequence and Taxonomic Position of Anguillid Herpesvirus 1. J. Gen. Virol. 2010, 91, 880–887. [CrossRef]
Van Beurden, S.J.; Engelsma, M.Y.; Roozenburg, I.; Voorbergen-Laarman, M.A.; van Tulden, P.W.; Kerkhoff, S.; van Nieuwstadt, A.P.; Davidse, A.; Haenen, O.L.M. Viral Diseases of Wild and Farmed European Eel Anguilla Anguilla with Particular Reference to The Netherlands. Dis. Aquat. Organ. 2012, 101, 69–86. [CrossRef]
Van Beurden, S.; Van Engelsma, M. Herpesviruses of fish, amphibians and invertebrates. In Herpesviridae—A Look into This Unique Family of Viruses; IntechOpen: London, UK, 2012.
Chang, P.H.; Pan, Y.H.; Wu, C.M.; Kuo, S.T.; Chung, H.Y. Isolation and Molecular Characterization of Herpesvirus from Cultured European Eels Anguilla Anguilla in Taiwan. Dis. Aquat. Organ. 2002, 50, 111–118. [CrossRef]
Haenen, O.L.M.; Dijkstra, S.G.; van Tulden, P.W.; Davidse, A.; van Nieuwstadt, A.P.; Wagenaar, F.; Wellenberg, G.J. Herpesvirus Anguillae (HVA) Isolations from Disease Outbreaks in Cultured European Eel, Anguilla Anguilla in the Netherlands since 1996. Bull. Eur. Assoc. Fish Pathol. 2002, 22, 247–257.
Sano, M.; Fukuda, H.; Sano, T. Isolation and characterization of a new herpesvirus from eel. In Pathology in Marine Science; Perkins, F.O., Cheng, T.C., Eds.; Academic Press: San Diego, CA, USA, 1990; pp. 15–31. ISBN 978-0-12-550755-4.
Bandín, I.; Souto, S.; Cutrín, J.M.; López-Vázquez, C.; Olveira, J.G.; Esteve, C.; Alcaide, E.; Dopazo, C.P. Presence of Viruses in Wild Eels Anguilla Anguilla L., from the Albufera Lake (Spain). J. Fish Dis. 2014, 37, 597–607. [CrossRef]
Dekker, W. The Fractal Geometry of the European Eel Stock. ICES J. Mar. Sci. 2000, 57, 109–121. [CrossRef]
Moriarty, C.; Dekker, W. (Eds.) Management of the European Eel; Irish Fisheries Bulletin, Marine Institute: Galway, Ireland, 1997.
Van Ginneken, V.J.T.; Maes, G.E. The European Eel (Anguilla Anguilla, Linnaeus), Its Lifecycle, Evolution and Reproduction: A Literature Review. Rev. Fish Biol. Fish. 2005, 15, 367–398. [CrossRef]
Békési, L.; Horváth, I.; Kovács-Gayer, E.; Csaba, G. Demonstration of Herpesvirus like Particles in Skin Lesions of European Eel (Anguilla Anguilla). J. Appl. Ichthyol. 1986, 2, 190–192. [CrossRef]
Chen, S.-N.; Kou, G.-H.; Ueno, Y. A Cell Line Derived from Japanese Eel (Anguilla Japonica) kidney. Proc. Natl. Sci. Counc. Repub. China Part B 1982, 6, 93–100.
Van Beurden, S.J.; Leroy, B.; Wattiez, R.; Haenen, O.L.; Boeren, S.; Vervoort, J.J.; Peeters, B.P.; Rottier, P.J.; Engelsma, M.Y.; Vanderplasschen, A.F. Identification and Localization of the Structural Proteins of Anguillid Herpesvirus 1. Vet. Res. 2011, 42, 105. [CrossRef] [PubMed]
Davidse, A.; Haenen, O.L.M.; Dijkstra, S.G.; van Nieuwstadt, A.P.; van der Vorst, T.J.K.; Wagenaar, F.; Wellenberg, G.J. First Isolation of Herpesvirus of Eel (Herpesvirus Anguillae) in Diseased European Eel (Anguilla Anguilla L.) in Europe. Bull. Eur. Assoc. Fish Pathol. 1999, 19, 137–141.
Boutier, M.; Ronsmans, M.; Ouyang, P.; Fournier, G.; Reschner, A.; Rakus, K.; Wilkie, G.S.; Farnir, F.; Bayrou, C.; Lieffrig, F.; et al. Rational Development of an Attenuated Recombinant Cyprinid Herpesvirus 3 Vaccine Using Prokaryotic Mutagenesis and In Vivo Bioluminescent Imaging. PLoS Pathog. 2015, 11, e1004690. [CrossRef]
Rakus, K.; Ronsmans, M.; Forlenza, M.; Boutier, M.; Piazzon, M.C.; Jazowiecka-Rakus, J.; Gatherer, D.; Athanasiadis, A.; Farnir, F.; Davison, A.J.; et al. Conserved Fever Pathways across Vertebrates: A Herpesvirus Expressed Decoy TNF-α Receptor Delays Behavioral Fever in Fish. Cell Host Microbe 2017, 21, 244–253. [CrossRef] [PubMed]
Kumar, S.; Stecher, G.; Li, M.; Knyaz, C.; Tamura, K. MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Mol. Biol. Evol. 2018, 35, 1547–1549. [CrossRef] [PubMed]
Martin, D.P.; Murrell, B.; Golden, M.; Khoosal, A.; Muhire, B. RDP4: Detection and Analysis of Recombination Patterns in Virus Genomes. Virus Evol. 2015, 1. [CrossRef]
Martin, D.; Rybicki, E. RDP: Detection of Recombination amongst Aligned Sequences. Bioinformatics 2000, 16, 562–563. [CrossRef]
Mansai, S.P.; Innan, H. The Power of the Methods for Detecting Interlocus Gene Conversion. Genetics 2010, 184, 517–527. [CrossRef]
Martin, D.P.; Posada, D.; Crandall, K.A.; Williamson, C. A Modified Bootscan Algorithm for Automated Identification of Recombinant Sequences and Recombination Breakpoints. AIDS Res. Hum. Retrovir. 2005, 21, 98–102. [CrossRef]
Posada, D.; Crandall, K.A. Evaluation of Methods for Detecting Recombination from DNA Sequences: Computer Simulations. Proc. Natl. Acad. Sci. USA 2001, 98, 13757–13762. [CrossRef]
Gibbs, M.J.; Armstrong, J.S.; Gibbs, A.J. Sister-Scanning: A Monte Carlo Procedure for Assessing Signals in Recombinant Sequences. Bioinformatics 2000, 16, 573–582. [CrossRef]
Lam, H.M.; Ratmann, O.; Boni, M.F. Improved Algorithmic Complexity for the 3SEQ Recombination Detection Algorithm. Mol. Biol. Evol. 2018, 35, 247–251. [CrossRef] [PubMed]
Tajima, F. Simple Methods for Testing the Molecular Evolutionary Clock Hypothesis. Genetics 1993, 135, 599–607. [CrossRef]
Xu, B.; Yang, Z. PamlX: A Graphical User Interface for PAML. Mol. Biol. Evol. 2013, 30, 2723–2724. [CrossRef]
Brandt, A.; Schaefer, I.; Glanz, J.; Schwander, T.; Maraun, M.; Scheu, S.; Bast, J. Effective Purifying Selection in Ancient Asexual Oribatid Mites. Nat. Commun. 2017, 8, 873. [CrossRef]
Gao, F.; Chen, C.; Arab, D.A.; Du, Z.; He, Y.; Ho, S.Y.W. EasyCodeML: A Visual Tool for Analysis of Selection Using CodeML. Ecol. Evol. 2019, 9, 3891–3898. [CrossRef]
Yang, Z. PAML 4: Phylogenetic Analysis by Maximum Likelihood. Mol. Biol. Evol. 2007, 24, 1586–1591. [CrossRef]
R Core Team. R: A Language and Environment for Statistical Computing; R Foundation for Statistical Computing: Vienna, Austria, 2020.
Tamura, K.; Tao, Q.; Kumar, S. Theoretical Foundation of the RelTime Method for Estimating Divergence Times from Variable Evolutionary Rates. Mol. Biol. Evol. 2018, 35, 1770–1782. [CrossRef]
Tamura, K.; Battistuzzi, F.U.; Billing-Ross, P.; Murillo, O.; Filipski, A.; Kumar, S. Estimating Divergence Times in Large Molecular Phylogenies. Proc. Natl. Acad. Sci. USA 2012, 109, 19333–19338. [CrossRef] [PubMed]
Kumar, S.; Stecher, G.; Suleski, M.; Hedges, S.B. TimeTree: A Resource for Timelines, Timetrees, and Divergence Times. Mol. Biol. Evol. 2017, 34, 1812–1819. [CrossRef] [PubMed]
Mello, B. Estimating TimeTrees with MEGA and the TimeTree Resource. Mol. Biol. Evol. 2018, 35, 2334–2342. [CrossRef] [PubMed]
Kassambara, A. Ggpubr: “ggplot2” Based Publication Ready Plots. 2021. Available online: https://cran.r-project.org/web/packages/ggpubr/(accessed on 3 May 2021).
Kolb, A.W.; Ané, C.; Brandt, C.R. Using HSV-1 Genome Phylogenetics to Track Past Human Migrations. PLoS ONE 2013, 8, e76267. [CrossRef]
Norberg, P.; Tyler, S.; Severini, A.; Whitley, R.; Liljeqvist, J.-Å.; Bergström, T. A Genome-Wide Comparative Evolutionary Analysis of Herpes Simplex Virus Type 1 and Varicella Zoster Virus. PLoS ONE 2011, 6. [CrossRef] [PubMed]
Sakaoka, H.; Kurita, K.; Iida, Y.; Takada, S.; Umene, K.; Kim, Y.T.; Ren, C.S.; Nahmias, A.J. Quantitative Analysis of Genomic Polymorphism of Herpes Simplex Virus Type 1 Strains from Six Countries: Studies of Molecular Evolution and Molecular Epidemiology of the Virus. J. Gen. Virol. 1994, 75, 513–527. [CrossRef] [PubMed]
Nei, M.; Kumar, S. Genetic polymorphism and evolution. In Molecular Evolution and Phylogenetics; Oxford University Press: Oxford, UK, 2000; pp. 231–264. ISBN 978-0-19-513585-5.
Friedman, M. The Use of Ranks to Avoid the Assumption of Normality Implicit in the Analysis of Variance. J. Am. Stat. Assoc. 1937, 32, 675–701. [CrossRef]
Durbin, J. Incomplete Blocks in Ranking Experiments. Br. J. Stat. Psychol. 1951, 4, 85–90. [CrossRef]
Pohlert, T. PMCMR: Calculate Pairwise Multiple Comparisons of Mean Rank Sums; R Foundation for Statistical Computing: Vienna, Austria, 2018.
Delrez, N.; Zhang, H.; Lieffrig, F.; Mélard, C.; Farnir, F.; Boutier, M.; Donohoe, O.; Vanderplasschen, A. European Eel Restocking Programs Based on Wild-Caught Glass Eels: Feasibility of Quarantine Stage Compatible with Implementation of Prophylactic Measures Prior to Scheduled Reintroduction to the Wild. J. Nat. Conserv. 2021, 59, 125933. [CrossRef]
Waltzek, T.B.; Kelley, G.O.; Alfaro, M.E.; Kurobe, T.; Davison, A.J.; Hedrick, R.P. Phylogenetic Relationships in the Family Alloherpesviridae. Dis. Aquat. Organ. 2009, 84, 179–194. [CrossRef] [PubMed]
Freudenberg-Hua, Y.; Freudenberg, J.; Kluck, N.; Cichon, S.; Propping, P.; Nöthen, M.M. Single Nucleotide Variation Analysis in 65 Candidate Genes for CNS Disorders in a Representative Sample of the European Population. Genome Res. 2003, 13, 2271–2276. [CrossRef] [PubMed]
Zhang, J. Rates of Conservative and Radical Nonsynonymous Nucleotide Substitutions in Mammalian Nuclear Genes. J. Mol. Evol. 2000, 50, 56–68. [CrossRef] [PubMed]
Bielawski, J.P.; Yang, Z. Maximum likelihood methods for detecting adaptive protein evolution. In Statistical Methods in Molecular Evolution; Statistics for Biology and Health; Springer: New York, NY, USA, 2005; pp. 103–124. ISBN 978-0-387-27733-2.
Delport, W.; Scheffler, K.; Seoighe, C. Models of Coding Sequence Evolution. Brief. Bioinform. 2009, 10, 97–109. [CrossRef]
Kosakovsky Pond, S.L.; Poon, A.F.; Frost, S.D.W. Estimating selection pressures on alignments of coding sequences. In The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing; Cambridge University Press: Cambridge, UK, 2009; ISBN 978-1-139-47861-8.
Yang, Z. Neutral and adaptive protein evolution. In Computational Molecular Evolution; Oxford University Press: Oxford, UK, 2006; ISBN 978-0-19-172828-0.
Yang, Z.; Nielsen, R. Codon-Substitution Models for Detecting Molecular Adaptation at Individual Sites along Specific Lineages. Mol. Biol. Evol. 2002, 19, 908–917. [CrossRef]
Zhang, J.; Nielsen, R.; Yang, Z. Evaluation of an Improved Branch-Site Likelihood Method for Detecting Positive Selection at the Molecular Level. Mol. Biol. Evol. 2005, 22, 2472–2479. [CrossRef]
Yang, Z.; dos Reis, M. Statistical Properties of the Branch-Site Test of Positive Selection. Mol. Biol. Evol. 2011, 28, 1217–1228. [CrossRef]
Pitcher, T. Sensory Information and the Organization of Behaviour in a Shoaling Cyprinid Fish. Anim. Behav. 1979, 27, 126–149. [CrossRef]
Smith, J. Social behaviour, homing and migration. In Cyprinid Fishes: Systematics, Biology and Exploitation; Fish & Fisheries Series; Springer: Dordrecht, The Netherlands, 1991; ISBN 978-94-010-5369-3.
Huntingford, F.A.; Andrew, G.; Mackenzie, S.; Morera, D.; Coyle, S.M.; Pilarczyk, M.; Kadri, S. Coping Strategies in a Strongly Schooling Fish, the Common Carp Cyprinus Carpio. J. Fish Biol. 2010, 76, 1576–1591. [CrossRef] [PubMed]
Malyukina, G.A.; Aleksandryuk, S.P.; Shtefanesku, M. On the Role of Vision in the Schooling Behavior of Minnows (Phoxinus Phoxinus) and the Crucian Carp (Carassius Carassius). Voprosy Ichtiologii 1962, 2, 511–516.
Mann, R.H.K. Growth and production. In Cyprinid Fishes: Systematics, Biology and Exploitation; Fish & Fisheries Series; Springer: Dordrecht, The Netherlands, 1991; ISBN 978-94-010-5369-3.
Pitcher, T.J.; Magurran, A.E.; Winfield, I.J. Fish in Larger Shoals Find Food Faster. Behav. Ecol. Sociobiol. 1982, 10, 149–151. [CrossRef]
Knights, B. Agonistic Behaviour and Growth in the European Eel, Anguilla Anguilla L., in Relation to Warm-Water Aquaculture. J. Fish Biol. 1987, 31, 265–276. [CrossRef]
Burgerhout, E.; Tudorache, C.; Brittijn, S.A.; Palstra, A.P.; Dirks, R.P.; van den Thillart, G.E.E.J.M. Schooling Reduces Energy Consumption in Swimming Male European Eels, Anguilla Anguilla L. J. Exp. Mar. Biol. Ecol. 2013, 448, 66–71. [CrossRef]
Tsukamoto, K.; Otake, T.; Mochioka, N.; Lee, T.-W.; Fricke, H.; Inagaki, T.; Aoyama, J.; Ishikawa, S.; Kimura, S.; Miller, M.J.; et al. Seamounts, New Moon and Eel Spawning: The Search for the Spawning Site of the Japanese Eel. Environ. Biol. Fishes 2003, 66, 221–229. [CrossRef]
Beatty, S.J.; Allen, M.G.; Whitty, J.M.; Lymbery, A.J.; Keleher, J.J.; Tweedley, J.R.; Ebner, B.C.; Morgan, D.L. First Evidence of Spawning Migration by Goldfish (Carassius Auratus): Implications for Control of a Globally Invasive Species. Ecol. Freshw. Fish 2017, 26, 444–455. [CrossRef]
Conallin, A.J.; Smith, B.B.; Thwaites, L.A.; Walker, K.F.; Gillanders, B.M. Exploiting the Innate Behaviour of Common Carp, Cyprinus Carpio, to Limit Invasion and Spawning in Wetlands of the River Murray, Australia. Fish. Manag. Ecol. 2016, 23, 431–449. [CrossRef]
Lucas, J.S.; Southgate, P.C.; Tucker, C.S. Aquaculture: Farming Aquatic Animals and Plants; John Wiley & Sons: Hoboken, NJ, USA, 2019; ISBN 978-1-119-23086-1.
Sarkar, A.; Upadhyay, B. Histochemical Detection of Steroid Synthesizing Cells in the Testes of Goldfish, Carassius Auratus, during the Annual Reproductive Cycle. Biotech. Histochem. 2014, 89, 114–120. [CrossRef]
Şaşı, H. The Length and Weight Relations of Some Reproduction Characteristics of Prussian Carp, Carassius Gibelio (Bloch, 1782) in the South Aegean Region (Aydın-Turkey). Turk. J. Fish. Aquat. Sci. 2008, 8, 87–92.
Sivakumaran, K.P.; Brown, P.; Stoessel, D.; Giles, A. Maturation and Reproductive Biology of Female Wild Carp, Cyprinus Carpio, in Victoria, Australia. Environ. Biol. Fishes 2003, 68, 321–332. [CrossRef]
Teletchea, F.; Fostier, A.; Kamler, E.; Gardeur, J.-N.; Le Bail, P.-Y.; Jalabert, B.; Fontaine, P. Comparative Analysis of Reproductive Traits in 65 Freshwater Fish Species: Application to the Domestication of New Fish Species. Rev. Fish Biol. Fish. 2009, 19, 403–430. [CrossRef]
Berry, L.; Brookes, D.; Walker, B. The Problem of the Migration of the European Eel (Anguilla Anguilla). Sci. Prog. 1972, 60, 465–485.
Cresci, A. A Comprehensive Hypothesis on the Migration of European Glass Eels (Anguilla Anguilla). Biol. Rev. 2020, 95, 1273–1286. [CrossRef] [PubMed]
Hanson, L.; Dishon, A.; Kotler, M. Herpesviruses That Infect Fish. Viruses 2011, 3, 2160–2191. [CrossRef]
Rakus, K.; Ronsmans, M.; Vanderplasschen, A. Behavioral Fever in Ectothermic Vertebrates. Dev. Comp. Immunol. 2017, 66, 84–91. [CrossRef]
Gilad, O.; Yun, S.; Zagmutt-Vergara, F.J.; Leutenegger, C.M.; Bercovier, H.; Hedrick, R.P. Concentrations of a Koi Herpesvirus (KHV) in Tissues of Experimentally Infected Cyprinus Carpio Koi as Assessed by Real-Time TaqMan PCR. Dis. Aquat. Organ. 2004, 60, 179–187. [CrossRef]
Gilad, O.; Yun, S.; Adkison, M.A.; Way, K.; Willits, N.H.; Bercovier, H.; Hedrick, R.P. Molecular Comparison of Isolates of an Emerging Fish Pathogen, Koi Herpesvirus, and the Effect of Water Temperature on Mortality of Experimentally Infected Koi. J. Gen. Virol. 2003, 84, 2661–2667. [CrossRef] [PubMed]
Groff, J.M.; LaPatra, S.E.; Munn, R.J.; Zin, J.G. A Viral Epizootic in Cultured Populations of Juvenile Goldfish Due to a Putative Herpesvirus Etiology. J. Vet. Diagn. Investig. 1998, 10, 375–378. [CrossRef] [PubMed]
Jeffery, K.R.; Bateman, K.; Bayley, A.; Feist, S.W.; Hulland, J.; Longshaw, C.; Stone, D.; Woolford, G.; Way, K. Isolation of a Cyprinid Herpesvirus 2 from Goldfish, Carassius Auratus (L.), in the UK. J. Fish Dis. 2007, 30, 649–656. [CrossRef] [PubMed]
Sano, N.; Moriwake, M.; Sano, T. Herpesvirus Cyprini: Thermal Effects on Pathogenicity and Oncogenicity. Fish Pathol. 1993, 28, 171–175. [CrossRef]
Aiewsakun, P.; Katzourakis, A. Time-Dependent Rate Phenomenon in Viruses. J. Virol. 2016, 90, 7184–7195. [CrossRef] [PubMed]
McGeoch, D.J.; Dolan, A.; Ralph, A.C. Toward a Comprehensive Phylogeny for Mammalian and Avian Herpesviruses. J. Virol. 2000, 74, 10401–10406. [CrossRef]
Aoki, T.; Hirono, I.; Kurokawa, K.; Fukuda, H.; Nahary, R.; Eldar, A.; Davison, A.J.; Waltzek, T.B.; Bercovier, H.; Hedrick, R.P. Genome Sequences of Three Koi Herpesvirus Isolates Representing the Expanding Distribution of an Emerging Disease Threatening Koi and Common Carp Worldwide. J. Virol. 2007, 81, 5058–5065. [CrossRef]
McGeoch, D.J.; Cook, S.; Dolan, A.; Jamieson, F.E.; Telford, E.A. Molecular Phylogeny and Evolutionary Timescale for the Family of Mammalian Herpesviruses. J. Mol. Biol. 1995, 247, 443–458. [CrossRef]
Murray, A.G. Epidemiology of the Spread of Viral Diseases under Aquaculture. Curr. Opin. Virol. 2013, 3, 74–78. [CrossRef]
Murray, A.G.; Peeler, E.J. A Framework for Understanding the Potential for Emerging Diseases in Aquaculture. Prev. Vet. Med. 2005, 67, 223–235. [CrossRef]
Pulkkinen, K.; Suomalainen, L.-R.; Read, A.F.; Ebert, D.; Rintamäki, P.; Valtonen, E.T. Intensive Fish Farming and the Evolution of Pathogen Virulence: The Case of Columnaris Disease in Finland. Proc. R. Soc. B Biol. Sci. 2010, 277, 593–600. [CrossRef] [PubMed]
Sundberg, L.-R.; Ketola, T.; Laanto, E.; Kinnula, H.; Bamford, J.K.H.; Penttinen, R.; Mappes, J. Intensive Aquaculture Selects for Increased Virulence and Interference Competition in Bacteria. Proc. Biol. Sci. 2016, 283, 20153069. [CrossRef] [PubMed]
Nakajima, T.; Hudson, M.J.; Uchiyama, J.; Makibayashi, K.; Zhang, J. Common Carp Aquaculture in Neolithic China Dates Back 8000 Years. Nat. Ecol. Evol. 2019, 3, 1415–1418. [CrossRef]
Aiewsakun, P.; Katzourakis, A. Time Dependency of Foamy Virus Evolutionary Rate Estimates. BMC Evol. Biol. 2015, 15. [CrossRef]
Duchêne, S.; Holmes, E.C.; Ho, S.Y.W. Analyses of Evolutionary Dynamics in Viruses Are Hindered by a Time-Dependent Bias in Rate Estimates. Proc. R. Soc. B Biol. Sci. 2014, 281. [CrossRef] [PubMed]
Ho, S.Y.W.; Duchêne, S.; Molak, M.; Shapiro, B. Time-Dependent Estimates of Molecular Evolutionary Rates: Evidence and Causes. Mol. Ecol. 2015, 24, 6007–6012. [CrossRef] [PubMed]
Simmonds, P.; Aiewsakun, P.; Katzourakis, A. Prisoners of War—Host Adaptation and Its Constraints on Virus Evolution. Nat. Rev. Microbiol. 2019, 17, 321–328. [CrossRef] [PubMed]
Van Tuinen, M.; Torres, C.R. Potential for Bias and Low Precision in Molecular Divergence Time Estimation of the Canopy of Life: An Example from Aquatic Bird Families. Front. Genet. 2015, 6. [CrossRef]
Firth, C.; Kitchen, A.; Shapiro, B.; Suchard, M.A.; Holmes, E.C.; Rambaut, A. Using Time-Structured Data to Estimate Evolutionary Rates of Double-Stranded DNA Viruses. Mol. Biol. Evol. 2010, 27, 2038–2051. [CrossRef]
Forni, D.; Pontremoli, C.; Clerici, M.; Pozzoli, U.; Cagliani, R.; Sironi, M. Recent Out-of-Africa Migration of Human Herpes Simplex Viruses. Mol. Biol. Evol. 2020. [CrossRef]
Bogani, F.; Corredeira, I.; Fernandez, V.; Sattler, U.; Rutvisuttinunt, W.; Defais, M.; Boehmer, P.E. Association between the Herpes Simplex Virus-1 DNA Polymerase and Uracil DNA Glycosylase. J. Biol. Chem. 2010, 285, 27664–27672. [CrossRef] [PubMed]
Su, M.-T.; Liu, I.-H.; Wu, C.-W.; Chang, S.-M.; Tsai, C.-H.; Yang, P.-W.; Chuang, Y.-C.; Lee, C.-P.; Chen, M.-R. Uracil DNA Glycosylase BKRF3 Contributes to Epstein-Barr Virus DNA Replication through Physical Interactions with Proteins in Viral DNA Replication Complex. J. Virol. 2014, 88, 8883–8899. [CrossRef] [PubMed]
Savva, R. The Essential Co-Option of Uracil-DNA Glycosylases by Herpesviruses Invites Novel Antiviral Design. Microorganisms 2020, 8, 461. [CrossRef] [PubMed]
Weller, S.K.; Coen, D.M. Herpes Simplex Viruses: Mechanisms of DNA Replication. Cold Spring Harb. Perspect. Biol. 2012, 4. [CrossRef]
Haenen, O.L.M.; Way, K.; Bergmann, S.M.; Ariel, E. The Emergence of Koi Herpesvirus and Its Significance to European Aquaculture. Bull. Eur. Assoc. Fish Pathol. 2004, 24, 293–307.
Ito, T.; Kurita, J.; Haenen, O.L.M. Importation of CyHV-2-Infected Goldfish into the Netherlands. Dis. Aquat. Organ. 2017, 126, 51–62. [CrossRef]
Kempter, J.; Hofsoe, P.; Panicz, R.; Bergmann, S. First Detection of Anguillid Herpesvirus 1 (AngHV1) in European Eel (Anguilla Anguilla) and Imported American Eel (Anguilla Rostrata) in Poland. Bull. Eur. Assoc. Fish Pathol. 2014, 34, 87–94.
Kullmann, B.; Adamek, M.; Steinhagen, D.; Thiel, R. Anthropogenic Spreading of Anguillid Herpesvirus 1 by Stocking of Infected Farmed European Eels, Anguilla Anguilla (L.), in the Schlei Fjord in Northern Germany. J. Fish Dis. 2017, 40, 1695–1706. [CrossRef]
Panicz, R.; Sadowski, J.; Eljasik, P. Detection of Cyprinid Herpesvirus 2 (CyHV-2) in Symptomatic Ornamental Types of Goldfish (Carassius Auratus) and Asymptomatic Common Carp (Cyprinus Carpio) Reared in Warm-Water Cage Culture. Aquaculture 2019. [CrossRef]
Pearson, H. Carp Virus Crisis Prompts Moves to Avert Global Spread. Nature 2004, 427, 577. [CrossRef] [PubMed]
Pokorova, D.; Vesely, T.; Piackova, V. Current Knowledge on Koi Herpesvirus—A Review. Veterinární Med. 2005, 50, 139–147. [CrossRef]
Boutier, M.; Donohoe, O.; Kopf, R.K.; Humphries, P.; Becker, J.A.; Marshall, J.; Vanderplasschen, A. Biocontrol of Carp: The Australian Plan Does Not Stand Up to a Rational Analysis of Safety and Efficacy. Front. Microbiol. 2019, 10. [CrossRef] [PubMed]
Kopf, R.K.; Boutier, M.; Finlayson, C.M.; Hodges, K.; Humphries, P.; King, A.; Kingsford, R.T.; Marshall, J.; McGinness, H.M.; Thresher, R.; et al. Biocontrol in Australia: Can a Carp Herpesvirus (CyHV-3) Deliver Safe and Effective Ecological Restoration? Biol. Invasions 2019, 21, 1857–1870. [CrossRef]
Marshall, J.; Davison, A.J.; Kopf, R.K.; Boutier, M.; Stevenson, P.; Vanderplasschen, A. Biocontrol of Invasive Carp: Risks Abound. Science 2018, 359, 877. [CrossRef]