Phylogenetic Pattern, Evolutionary Processes and Species Delimitation in the Genus Echinococcus

Alvarez Rojas, 2014, Echinococcus granulosus sensu lato genotypes infecting humans – review of current knowledge, Int. J. Parasitol., 44, 9, 10.1016/j.ijpara.2013.08.008 Alvarez Rojas, 2016, Microdiversity of Echinococcus granulosus in Australia, Parasitology, 143, 1026, 10.1017/S0031182016000445 Badaraco, 2008, Using mitochondrial and nuclear markers to evaluate the degree of genetic cohesion among Echinococcus populations, Exp. Parasitol., 119, 453, 10.1016/j.exppara.2008.02.004 Barnett, 2014, Revealing the maternal demographic history of Panthera leo using ancient DNA and a spatially explicit genealogical analysis, BMC Evol. Biol., 14, 70, 10.1186/1471-2148-14-70 Bart, 2006, EmsB, a tandem repeated multi-loci microsatellite, new tool to investigate the genetic diversity of Echinococcus multilocularis, Infect. Genet. Evol., 6, 390, 10.1016/j.meegid.2006.01.006 Bowles, 1993, Molecular variation in Echinococcus, Acta Trop., 53, 291, 10.1016/0001-706X(93)90035-A Bowles, 1992, Genetic variants within the genus Echinococcus identified by mitochondrial DNA sequencing, Mol. Biochem. Parasitol., 54, 165, 10.1016/0166-6851(92)90109-W Bowles, 1994, Molecular genetic characterization of the cervid strain (‘northern form’) of Echinococcus granulosus, Parasitology, 109, 215, 10.1017/S0031182000076332 Bowles, 1995, A molecular phylogeny of the genus Echinococcus, Parasitology, 110, 317, 10.1017/S0031182000080902 Bryant, 1986, Biochemical strain variation in parasitic helminths, Adv. Parasitol., 25, 275, 10.1016/S0065-308X(08)60345-0 Camargo, 2012, Species delimitation with ABC and other coalescent-based methods: a test of accuracy with simulations and an empirical example with lizards of the Liolaemus darwinii complex (Squamata: Liolaemidae), Evolution, 66, 2834, 10.1111/j.1558-5646.2012.01640.x Cameron, 1926, Observations on the genus Echinococcus Rudolphi, 1801, J. Helminthol., 4, 13, 10.1017/S0022149X0000211X Casulli, 2012, Genetic variability of Echinococcus granulosus sensu stricto in Europe inferred by mitochondrial DNA sequences, Infect. Genet. Evol., 12, 377, 10.1016/j.meegid.2011.12.014 Coyne, 2004 Crandall, 2000, Considering evolutionary processes in conservation biology, Trends Ecol. Evol., 15, 290, 10.1016/S0169-5347(00)01876-0 Crisp, 2011, Hypothesis testing in biogeography, Trends Ecol. Evol., 26, 66, 10.1016/j.tree.2010.11.005 D'Alessandro, 2008, New aspects of neotropical polycystic (Echinococcus vogeli) and unicystic (Echinococcus oligarthrus) echinococcosis, Clin. Microbiol. Rev., 21, 380, 10.1128/CMR.00050-07 de Meeûs, 1998, Santa Rosalia revisited: or why are there so many kinds of parasites in ‘the garden of earthly delights’?, Parasitol. Today, 14, 10, 10.1016/S0169-4758(97)01163-0 de Queiroz, 1990, Phylogenetic systematics or Nelson's version of cladistics?, Cladistics, 6, 61, 10.1111/j.1096-0031.1990.tb00525.x de Queiroz, 1999, The general lineage concept of species and the defining properties of the species category, 49 de Queiroz, 2007, Species concepts and species delimitation, Syst. Biol., 56, 879, 10.1080/10635150701701083 Degnan, 2009, Gene tree discordance, phylogenetic inference and the multispecies coalescent, Trends Ecol. Evol., 24, 332, 10.1016/j.tree.2009.01.009 Emerson, 2001, Revealing the demographic histories of species using DNA sequences, Trends Ecol. Evol., 16, 707, 10.1016/S0169-5347(01)02305-9 Ence, 2010, SpedeSTEM: a rapid and accurate method for species delimitation, Mol. Ecol. Resour., 24, 473 Fujita, 2012, Coalescent-based species delimitation in an integrative taxonomy, Trends Ecol. Evol., 27, 480, 10.1016/j.tree.2012.04.012 Goodwillie, 2005, The evolutionary enigma of mixed mating systems in plants: occurrence, theoretical explanations, and empirical evidence, Ann. Rev. Ecol. Evol. Syst., 47, 10.1146/annurev.ecolsys.36.091704.175539 Haag, 1999, Breeding systems in Echinococcus granulosus (Cestoda; Taeniidae): selfing or outcrossing?, Parasitology, 118, 63, 10.1017/S0031182098003485 Haag, 2004, Livestock trade history, geography, and parasite strains: the mitochondrial genetic structure of Echinococcus granulosus in Argentina, J. Parasitol., 90, 234, 10.1645/GE-173R Haag, 2008, Taeniid history, natural selection and antigenic diversity: evolutionary theory meets helminthology, Trends Parasitol., 24, 96, 10.1016/j.pt.2007.11.004 Haag, 2011, Reappraising the theme of breeding systems in Echinococcus: is outcrossing a rare phenomenon?, Parasitology, 138, 298, 10.1017/S0031182010001307 Harrington, 2012, Phylogenetic and coalescent strategies of species delimitation in snubnose darters (Percidae: Etheostoma), Syst. Biol., 61, 63, 10.1093/sysbio/syr077 Hey, 2006, On the failure of modern species concepts, Trends Ecol. Evol., 21, 447, 10.1016/j.tree.2006.05.011 Hoberg, 2008, A macroevolutionary mosaic: episodic host-switching, geographical colonization and diversification in complex host-parasite systems, J. Biogeogr., 35, 1533, 10.1111/j.1365-2699.2008.01951.x Hoberg, 2010, Beyond vicariance: integrating taxon pulses, ecological fitting, and oscillation in evolution and historical biogeography Hoberg, 2006, Phylogeny of Taenia: species definitions and origins of human parasites, Parasitol. Int., 55, S23, 10.1016/j.parint.2005.11.049 Holsinger, 1996, Pollination biology and the evolution of mating systems in flowering plants, Evol. Biol., 29, 107 Hüttner, 2009, Echinococcus species in African wildlife, Parasitology, 136, 1089, 10.1017/S0031182009990461 Hüttner, 2008, Genetic characterization and phylogenetic position of Echinococcus felidis Ortlepp, 1937 (Cestoda: Taeniidae) from the African lion, Int. J. Parasitol., 38, 861, 10.1016/j.ijpara.2007.10.013 Huyse, 2005, Speciation in parasites: a population genetics approach, Trends Parasitol., 21, 469, 10.1016/j.pt.2005.08.009 Jarne, 2006, Animals mix it up too: the distribution of self-fertilization among hermaphroditic animals, Evolution, 60, 1816 Jiang, 2012, Specific detection of Echinococcus spp. from the Tibetan fox (Vulpes ferrilata) and the red fox (V.vulpes) using copro-DNA PCR analysis, Parasitol. Res., 111, 1531, 10.1007/s00436-012-2993-8 Johnson, 2006, The Late Miocene radiation of modern Felidae: a genetic assessment, Science, 311, 73, 10.1126/science.1122277 Kagendo, 2014, A survey for Echinococcus spp. of carnivores in six wildlife conservation areas in Kenya, Parasitol. Int., 63, 604, 10.1016/j.parint.2014.04.001 Knapp, 2007, Assessment of use of microsatellite polymorphism analysis for improving spatial distribution tracking of Echinococcus multilocularis, J. Clin. Microbiol., 45, 2943, 10.1128/JCM.02107-06 Knapp, 2008, Genetic diversity of Echinococcus multilocularis on a local scale, Infect. Genet. Evol., 8, 367, 10.1016/j.meegid.2008.02.010 Knapp, 2009, Genetic diversity of the cestode Echinococcus multilocularis in red foxes at a continental scale in Europe, PLoS Negl. Trop. D, 3, e452, 10.1371/journal.pntd.0000452 Knapp, 2011, Phylogenetic relationships within Echinococcus and Taenia tapeworms (Cestoda: Taeniidae): an inference from nuclear protein-coding genes, Mol. Phylogenet. Evol., 61, 628, 10.1016/j.ympev.2011.07.022 Knapp, 2015, Taxonomy, phylogeny and molecular epidemiology of Echinococcus multiocularis: from fundamental knowledge to health ecology, Vet. Parasitol., 213, 85, 10.1016/j.vetpar.2015.07.030 Knowles, 2007, Delimiting species without monophyletic gene trees, Syst. Biol., 56, 887, 10.1080/10635150701701091 Konyaev, 2013, Genetic diversity of Echinococcus spp. in Russia, Parasitology, 140, 1637, 10.1017/S0031182013001340 Kubatko, 2007, Inconsistency of phylogenetic estimates from concatenated data under coalescence, Syst. Biol., 56, 17, 10.1080/10635150601146041 Kumaratilake, 1982, A review of the taxonomy and speciation of the genus Echinococcus. Rudolphi 1801, Z. Parasitenkd., 68, 121, 10.1007/BF00935054 Kumaratilake, 1986, Sperm transfer in Echinococcus (Cestoda: Taeniidae), Z. Parasitenkd., 72, 265, 10.1007/BF00931153 Kunz, 2002, Species concepts versus species criteria, Trends Parasitol., 18, 440, 10.1016/S1471-4922(02)02320-6 Kutschera, 2013, A range-wide synthesis and timeline for phylogeographic events in the red fox (Vulpes vulpes), BMC Evol. Biol., 13, 114, 10.1186/1471-2148-13-114 Lahmar, 2001, Frequency distributions of Echinococcus granulosus and other helminths in stray dogs in Tunisia, Ann. Trop. Med. Parasitol., 95, 69, 10.1080/00034983.2001.11813616 Lande, 1985, The evolution of self-fertilization and inbreeding depression in plants. I. Genetic models, Evolution, 39, 24 Lavikainen, 2003, Molecular genetic characterization of the Fennoscandian cervid strain, a new genotypic group (G10) of Echinococcus granulosus, Parasitology, 127, 207, 10.1017/S0031182003003780 Lavikainen, 2006, Molecular characterization of Echinococcus isolates of cervid origin from Finland and Sweden, Parasitology, 133, 565, 10.1017/S0031182006000667 Le, 2002, Complete mitochondrial genomes confirm the distinctiveness of the horse-dog and sheep-dog strains of Echinococcus granulosus, Parasitology, 124, 97, 10.1017/S0031182001008976 Lymbery, 1992, Inbreeding, monophyly and the genetic yardstick: species concepts in parasites, Parasitol. Today, 8, 208, 10.1016/0169-4758(92)90266-5 Lymbery, 1995, Genetic diversity, genetic differentiation and speciation, 51 Lymbery, 1998, Combining data from morphological traits and genetic markers to determine transmission cycles in the tapeworm, Echinococcus granulosus, Parasitology, 117, 185, 10.1017/S0031182098002911 Lymbery, 1988, Electrophoretic analysis of genetic variation in Echinococcus granulosus from domestic hosts in Australia, Int. J. Parasitol., 18, 803, 10.1016/0020-7519(88)90122-1 Lymbery, 2012, The molecular epidemiology of parasite infections: tools and applications, Mol. Biochem. Parasitol., 181, 102, 10.1016/j.molbiopara.2011.10.006 Lymbery, 1989, The dispersion of Echinococcus granulosus in the intestine of dogs, J. Parasitol., 75, 562, 10.2307/3282907 Lymbery, 1990, Genetic diversity and genetic differentiation in Echinococcus granulosus (Batsch, 1786) from domestic and sylvatic hosts on the mainland of Australia, Parasitology, 101, 283, 10.1017/S0031182000063344 Lymbery, 1997, Self-fertilization without genomic or population structuring in a parasitic tapeworm, Evolution, 51, 289, 10.2307/2410983 Lymbery, 2015, Echinococcus canadensis, E. borealis, and E. intermedius. What's in a name?, Trends Parasitol., 31, 23, 10.1016/j.pt.2014.11.003 Mayden, 1997, A hierarchy of species concepts: the denouement in the saga of the species problem, 381 McCoy, 2003, Sympatric speciation in parasites - what is sympatry?, Trends Parasitol., 19, 400, 10.1016/S1471-4922(03)00194-6 McManus, 1986, Hydatidosis: changing concepts in epidemiology and speciation, Parasitol. Today, 2, 163, 10.1016/0169-4758(86)90147-X McManus, 2002, Molecular genetic characterization of an unusually severe case of hydatid disease in Alaska caused by the cervid strain of Echinococcus granulosus, Am. J. Trop. Med. Hyg., 67, 296, 10.4269/ajtmh.2002.67.296 Moks, 2008, First report of Echinococcus granulosus G8 in Eurasia and a reappraisal of the phylogenetic relationships of ‘genotypes’ G5-G10, Parasitology, 135, 647, 10.1017/S0031182008004198 Moro, 2009, Echinococcosis: a review, Int. J. Infect. Dis., 13, 125, 10.1016/j.ijid.2008.03.037 Moro, 2009, Molecular identification of Echinococcus isolates from Peru, Parasitol. Int., 58, 184, 10.1016/j.parint.2009.01.005 Nakao, 2003, Isolation of polymorphic microsatellite loci from the tapeworm Echinococcus multilocularis, Infect. Genet. Evol., 3, 159, 10.1016/S1567-1348(03)00070-4 Nakao, 2007, A molecular phylogeny of the genus Echinococcus inferred from complete mitochondrial genomes, Parasitology, 134, 713, 10.1017/S0031182006001934 Nakao, 2009, Geographic pattern of genetic variation in the fox tapeworm Echinococcus multilocularis, Parasitol. Int., 58, 384, 10.1016/j.parint.2009.07.010 Nakao, 2010, State-of-the-art Echinococcus and Taenia: phylogenetic taxonomy of human-pathogenic tapeworms and its application to molecular diagnosis, Infect. Genet. Evol., 10, 444, 10.1016/j.meegid.2010.01.011 Nakao, 2010, Genetic polymorphisms of Echinococcus tapeworms in China as determined by mitochondrial and nuclear DNA sequences, Int. J. Parasitol., 40, 379, 10.1016/j.ijpara.2009.09.006 Nakao, 2013, Molecular phylogeny of the genus Taenia (Cestoda: Taeniidae): proposals for the resurrection of Hydatigera Lamarck, 1816 and the creation of the new genus Versteria, Int. J. Parasitol., 43, 427, 10.1016/j.ijpara.2012.11.014 Nakao, 2013, Phylogenetic systematics of the genus Echinococcus (Cestoda: Taeniidae), Int. J. Parasitol., 43, 1017, 10.1016/j.ijpara.2013.06.002 Nakao, 2013, Mitochondrial phylogeny of the genus Echinococcus (Cestoda: Taeniidae) with emphasis on relationships among Echinococcus canadensis genotypes, Parasitology, 140, 1625, 10.1017/S0031182013000565 Nakao, 2015, Is Echinococcus intermedius a valid species?, Trends Parasitol., 8, 342, 10.1016/j.pt.2015.04.012 Niemiller, 2012, Delimiting species using multilocus data: diagnosing cryptic diversity in the southern cavefish, Typhlichthys subterraneus (Teleostei: Amblyopsidae), Evolution, 66, 846, 10.1111/j.1558-5646.2011.01480.x O'Meara, 2010, New heuristic methods for joint species delimitation and species tree inference, Syst. Biol., 59, 59, 10.1093/sysbio/syp077 Obwaller, 2004, Echinococcus granulosus strain differentiation based on sequence heterogeneity in mitochondrial genes of cytochrome c oxidase-1and NADH dehydrogenase-1, Parasitology, 128, 569, 10.1017/S0031182004004871 Ortlepp, 1934, Echinococcus in dogs from Pretoria and vicinity, Onderstepoort J. Vet. Sci. Anim. Ind., 3, 97 Ortlepp, 1937, South African helminths, part I, Onderstepoort J. Vet. Sci. Anim. Ind., 9, 311 Padial, 2010, The integrative future of taxonomy, Front. Zool., 7, 16, 10.1186/1742-9994-7-16 Pons, 2006, Sequence based species delimitation for the DNA taxonomy of undescribed insects, Syst. Biol., 55, 595, 10.1080/10635150600852011 Price, 1980 Rannala, 2003, Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci, Genetics, 164, 1645, 10.1093/genetics/164.4.1645 Rausch, 1953, The taxonomic value and variability of certain structures in the cestode genus Echinococcus (Rud., 1801) and a review of recognised species, Thapar Commem. Vol., 233 Rausch, 1963, A review of the genus Echinococcus Rudolphi, 1801, Ann. Trop. Med. Parasitol., 57, 127, 10.1080/00034983.1963.11686168 Romig, 2011, Echinococcosis in sub-Saharan Africa: emerging complexity, Vet. Parasitol., 181, 43, 10.1016/j.vetpar.2011.04.022 Romig, 2015, Taxonomy and molecular epidemiology of Echinococcus granulosus sensu lato, Vet. Parasitol., 213, 76, 10.1016/j.vetpar.2015.07.035 Saarma, 2009, A novel phylogeny for the genus Echinococcus, based on nuclear data, challenges relationships based on mitochondrial evidence, Parasitology, 136, 317, 10.1017/S0031182008005453 Santos, 2012, Mitochondrial and nuclear sequence polymorphisms reveal geographic structuring in Amazonian populations of Echinococcus vogeli (Cestoda: Taeniidae), Int. J. Parasitol., 42, 1115, 10.1016/j.ijpara.2012.10.010 Schantz, 1976, Sylvatic echinococcosis in Argentina. II. Susceptibility of wild carnivores to Echinococcus granulosus (Batsch, 1786) and host-induced morphological variation, Tropenmed. Parasitol., 27, 70 Schurer, 2014, Echinococcus multilocularis and Echinococcus canadensis in wolves from western Canada, Parasitology, 141, 159, 10.1017/S0031182013001716 Sharma, 2013, Genetic diversity and population genetic structure analysis of Echinococcus granulosus sensu stricto complex based on mitochondrial DNA signature, PLoS One, e82904, 10.1371/journal.pone.0082904 Siles-Lucas, 2001, Comparative analysis of the 14-3-3 gene and its expression in Echinococcus granulosus and Echinococcus multilocularis metacestodes, Parasitology, 122, 281, 10.1017/S0031182001007405 Smyth, 1964, Natural and experimental hosts of Echinococcus granulosus and E. multilocularis, with comments on the genetics of speciation the genus Echinococcus, Parasitology, 54, 493, 10.1017/S0031182000082536 Smyth, 1969, Self insemination in Echinococcus granulosus in vivo, J. Helminthol., 43, 383, 10.1017/S0022149X00004946 Soares, 2013, Anatomo-clinical and molecular description of liver neotropical echinococcosis caused by Echinococcus oligarthrus in human host, Acta Trop., 125, 110, 10.1016/j.actatropica.2012.09.004 Stefanic, 2004, Polymerase chain reaction for detection of patent infections of Echinococcus granulosus (“sheep strain”) in naturally infected dogs, Parasitol. Res., 92, 347, 10.1007/s00436-003-1043-y Templeton, 1989, The meaning of species and speciation: a genetic perspective, 3 Thompson, 1986, Biology and systematics of Echinococcus, 5 Thompson, 1995, Biology and systematics of Echinococcus, 1 Thompson, 2008, The taxonomy, phylogeny and transmission of Echinococcus, Exp. Parasitol., 119, 439, 10.1016/j.exppara.2008.04.016 Thompson, 1988, The nature, extent and significance of variation within the genus Echinococcus, Adv. Parasitol., 27, 209, 10.1016/S0065-308X(08)60356-5 Thompson, 2002, Towards a taxonomic revision of the genus Echinococcus, Trends Parasitol., 18, 452, 10.1016/S1471-4922(02)02358-9 Thompson, 1995, Variation in Echinococcus: towards a taxonomic revision of the genus, Adv. Parasitol., 35, 145, 10.1016/S0065-308X(08)60071-8 Thompson, 2006, Molecular and morphological characterization of Echinococcus in cervids from North America, Parasitology, 132, 439, 10.1017/S0031182005009170 Tigre, 2016, Molecular characterization of Echinococcus granulosus s.l. cysts from cattle, camels, goats and pigs in Ethiopia, Vet. Parasitol., 215, 17, 10.1016/j.vetpar.2015.10.022 Torgerson, 2013, One world health: socioeconomic burden and parasitic disease control priorities, Vet. Parasitol., 195, 223, 10.1016/j.vetpar.2013.04.004 Tsai, 2013, The genomes of four tapeworm species reveal adaptations to parasitism, Nature, 496, 57, 10.1038/nature12031 Turelli, 2001, Theory and speciation, Trends Ecol. Evol., 16, 330, 10.1016/S0169-5347(01)02177-2 Velasco, 2009, When monophyly is not enough: exclusivity as the key to defining a phylogenetic species concept, Biol. Phil., 24, 473, 10.1007/s10539-009-9151-4 Vogel, 1957, Uber den Echinococcus multilocularis Suddeutschlands. I. Das Bandwurmstadium von Stammen menschlicher und tierischer Herkunft. Z. Tropenmed, Parasitology, 8, 404 Wang, 2014, Genetic diversity of Echinococcus granulosus in southwest China determined by the mitochondrial NADH dehydrogenase subunit 2 gene, Sci. World J., 214, e867839 Wang, 1998, A study on morphology of reproductive organs of Echinococcus granulosus by light microscopy, transmission and scanning electron, Endem. Dis. Bull. (China), 3, 31 Wassermann, 2015, A sylvatic lifecycle of Echinococcus equinus in the Etosha National Park, Namibia, Int. J. Parasitol. Parasites Wildl., 4, 97, 10.1016/j.ijppaw.2014.12.002 Wiley, 1978, The evolutionary species concept reconsidered, Syst. Zool., 27, 17, 10.2307/2412809 Wassermann, 2016, A novel zoonotic genotype related to Echinococcus granulosus sensu stricto from southern Ethiopia,, Int. J. Parasitol., 10.1016/j.ijpara.2016.04.005 Xiao, 2005, Echinococcus shiquicus n. sp., a taeniid cestode from Tibetan fox and plateau pika in China, Int. J. Parasitol., 35, 693, 10.1016/j.ijpara.2005.01.003 Xiao, 2006, Dual infection of animal hosts with different Echinococcus species in the eastern Qinhai-Tibet plateau region of China, Am. J. Trop. Med. Hyg., 75, 292, 10.4269/ajtmh.2006.75.292 Yanagida, 2012, Genetic polymorphisms of Echinococcus granulosus sensu stricto in the Middle East, Parasitol. Int., 61, 599, 10.1016/j.parint.2012.05.014 Yang, 2010, Bayesian species delimitation using multilocus sequence data, Proc. Natl. Acad. Sci. U.S.A., 107, 9264, 10.1073/pnas.0913022107 Yeates, 2011, Integrative taxonomy, or iterative taxonomy?, Syst. Entomol., 36, 209, 10.1111/j.1365-3113.2010.00558.x Zhang, 2006, Morphological and molecular characteristics of Echinococcus multilocularis and Echinococcus granulosus mixed infection in a dog from Xinjiang, China, Vet. Parasitol., 148, 384, 10.1016/j.vetpar.2006.05.036 Zhang, 2011, Evaluation of a Bayesian coalescent method of species delimitation, Syst. Biol., 60, 747, 10.1093/sysbio/syr071 Zheng, 2013, The genome of the hydatid tapeworm Echinococcus granulosus, Nat. Genet., 45, 1168, 10.1038/ng.2757 Ziadinov, 2010, Frequency distribution of Echinococcus multilocularis and other helminths of foxes in Kyrgyzstan, Vet. Parasitol., 171, 286, 10.1016/j.vetpar.2010.04.006