Bibliographic references for the synthetic tree
The following studies (listed alphabetically by first author) have contributed to the current synthetic tree.
A. Bucklin, B. Frost, J. Bradford-Grieve, L. Allen, N. Copley, 2003, 'Molecular systematic and phylogenetic assessment of 34 calanoid copepod species of the Calanidae and Clausocalanidae', Marine Biology, vol. 142, no. 2, pp. 333-343
https://doi.org/10.1007/s00227-002-0943-1
Quintero, Esther, Camila C. Ribas, Joel Cracraft. 2012. The Andean Hapalopsittaca parrots (Psittacidae, Aves): an example of montane-tropical lowland vicariance. Zoologica Scripta 42 (1): 28-43.
https://doi.org/10.1111/j.1463-6409.2012.00567.x
1987 Schaefer, S.A. Osteology of Hypostomus plecostomus (Linnaeus), with a phylogenetic analysis of the loricariid subfamilies (Pisces: Siluroidei). Contributions in Science, Natural History Museum of Los Angeles County, no. 394, 31 p
http://www.nhm.org/site/sites/default/files/pdf/contrib_science/CS394.pdf
A. A. Crowl, N. W. Miles, C. J. Visger, K. Hansen, T. Ayers, R. Haberle, N. Cellinese, 2016, 'A global perspective on Campanulaceae: Biogeographic, genomic, and floral evolution', American Journal of Botany
https://doi.org/10.3732/ajb.1500450
A. C. Schneider, W. A. Freyman, C. M. Guilliams, Y. P. Springer, B. G. Baldwin, 2016, 'Pleistocene radiation of the serpentine-adapted genus Hesperolinon and other divergence times in Linaceae (Malpighiales)', American Journal of Botany, vol. 103, no. 2, pp. 221-232
https://doi.org/10.3732/ajb.1500379
A. Delgado-Salinas, M. Thulin, R. Pasquet, N. Weeden, M. Lavin. 2011. Vigna (Leguminosae) sensu lato: The names and identities of the American segregate genera. American Journal of Botany 98(10):1694-1715.
https://doi.org/10.3732/ajb.1100069
A. E. Syme, T. H. Oakley, 2011, 'Dispersal between Shallow and Abyssal Seas and Evolutionary Loss and Regain of Compound Eyes in Cylindroleberidid Ostracods: Conflicting Conclusions from Different Comparative Methods', Systematic Biology, vol. 61, no. 2, pp. 314-336
https://doi.org/10.1093/sysbio/syr085
A. Leuchtmann, C. W. Bacon, C. L. Schardl, J. F. White, M. Tadych, 2014, 'Nomenclatural realignment of Neotyphodium species with genus Epichloe', Mycologia, vol. 106, no. 2, pp. 202-215
https://doi.org/10.3852/106.2.202
A. Manegold, 2008, 'Composition and phylogenetic affinities of vangas (Vangidae, Oscines, Passeriformes) based on morphological characters', Journal of Zoological Systematics and Evolutionary Research, vol. 46, no. 3, pp. 267-277
https://doi.org/10.1111/j.1439-0469.2008.00458.x
A. da Marcela Vasco-Palacios, C. Lopez-Quintero, A. E. Franco-Molano, T. Boekhout, 2014, 'Austroboletus amazonicus sp. nov. and Fistulinella campinaranae var. scrobiculata, two commonly occurring boletes from a forest dominated by Pseudomonotes tropenbosii (Dipterocarpaceae) in Colombian Amazonia', Mycologia, vol. 106, no. 5, pp. 1004-1014
https://doi.org/10.3852/13-324
ALAN H. BORNBUSCH, 1995, 'Phylogenetic relationships within the Eurasian catfish family Siluridae (Pisces: Siluriformes), with comments on generic validities and biogeography', Zoological Journal of the Linnean Society, vol. 115, no. 1, pp. 1-46
https://doi.org/10.1111/j.1096-3642.1995.tb02322.x
ALICE CIBOIS, JEAN-CLAUDE THIBAULT, ERIC PASQUET, 2008, 'Systematics of the extinct reed warblers Acrocephalus of the Society Islands of eastern Polynesia', Ibis, vol. 150, no. 2, pp. 365-376
https://doi.org/10.1111/j.1474-919x.2008.00800.x
Abalde S., Tenorio M.J., Afonso C.M., Uribe J.E., Echeverry A.M., & Zardoya R. 2017. Phylogenetic relationships of cone snails endemic to Cabo Verde based on mitochondrial genomes. BMC Evolutionary Biology, 17: 231.
https://doi.org/10.1186/s128620171069x
Abasova L., Aghayeva D., & Takamatsu S. 2018. Notes on powdery mildews of the genus Erysiphe from Azerbaijan. Current Research in Environmental & Applied Mycology, 8(1): 50-53 .
https://doi.org/10.5943/cream/8/1/3
Adam L. Bazinet, Michael P. Cummings, Kim T. Mitter, Charles W. Mitter, 2013, 'Can RNA-Seq Resolve the Rapid Radiation of Advanced Moths and Butterflies (Hexapoda: Lepidoptera: Apoditrysia)? An Exploratory Study', PLoS ONE, vol. 8, no. 12, p. e82615
https://doi.org/10.1371/journal.pone.0082615
Adamcik S., Slovak M., Eberhardt U., Ronikier A., Jairus T., Hampe F., & Verbeken A. 2016. Molecular inference, multivariate morphometrics and ecological assessment are applied in concert to delimit species in the Russula clavipes complex. Mycologia, 108(4): 716-730.
https://doi.org/10.3852/15-194
Adams N.F., Collinson M.E., Smith S.Y., Bamford M.K., Forest F., Malakasi P., Marone F., & Sykes D. 2016. X-rays and virtual taphonomy reveal the first fossil record of Cissus (Vitaceae) in Africa: phylogenetic, biogeographic and paleoenvironmental implications. American Journal of Botany, .
https://doi.org/10.3732/ajb.1600177
Adeljean L.F.C. Ho, Christin L. Pruett, Junda Lin, 2016, 'Phylogeny and biogeography of Poecilia (Cyprinodontiformes: Poeciliinae) across Central and South America based on mitochondrial and nuclear DNA markers', Molecular Phylogenetics and Evolution, vol. 101, pp. 32-45
https://doi.org/10.1016/j.ympev.2016.04.032
Aggerbeck, Marie, Jon Fjeldså, Les Christidis, Pierre-Henri Fabre, Knud Andreas Jønsson. 2014. Resolving deep lineage divergences in core corvoid passerine birds supports a proto-Papuan island origin. Molecular Phylogenetics and Evolution 70: 272-285.
https://doi.org/10.1016/j.ympev.2013.09.027
Agnarsson, I., Zambrana-torrelio C.M., Flores saldaña N.P., & May-collado L.M. 2011. A time-calibrated species-level phylogeny of bats (Chiroptera, Mammalia). PLoS Currents: Tree of Life, Version 44.
https://doi.org/10.1371/currents.RRN1212
Agorreta, Ainhoa, Diego San Mauro, Ulrich Schliewen, James L. Van Tassell, Marcelo Kovačić, Rafael Zardoya, Lukas Rüber. 2013. Molecular phylogenetics of Gobioidei and phylogenetic placement of European gobies. Molecular Phylogenetics and Evolution 69 (3): 619-633.
https://doi.org/10.1016/j.ympev.2013.07.017
Ahyong, S., Lai J., Sharkey D., Colgan D., & Ng P. 2007. Phylogenetics of the brachyuran crabs (Crustacea: Decapoda): the status of Podotremata based on small subunit nuclear ribosomal RNA. Molecular Phylogenetics and Evolution 45 (2): 576-586.
https://doi.org/10.1016/j.ympev.2007.03.022
Ainscough, B. J., Breinholt, J. W., Robison, H. W., & Crandall, K. A. (2013). Molecular phylogenetics of the burrowing crayfish genus Fallicambarus (Decapoda: Cambaridae). Zoologica Scripta.
https://doi.org/10.1111/zsc.12006
Akito Y. Kawahara, Jesse W. Breinholt, Marianne Espeland, Caroline Storer, David Plotkin, Kelly M. Dexter, Emmanuel F.A. Toussaint, Ryan A. St Laurent, Gunnar Brehm, Sergio Vargas, Dimitri Forero, Naomi E. Pierce, David J. Lohman, 2018, 'Phylogenetics of moth-like butterflies (Papilionoidea: Hedylidae) based on a new 13-locus target capture probe set', Molecular Phylogenetics and Evolution, vol. 127, pp. 600-605
https://doi.org/10.1016/j.ympev.2018.06.002
Alencar, Laura R.V., Tiago B. Quental, Felipe G. Grazziotin, Michael L. Alfaro, Marcio Martins, Mericien Venzon, Hussam Zaher. 2016. Diversification in vipers: Phylogenetic relationships, time of divergence and shifts in speciation rates. Molecular Phylogenetics and Evolution 105: 50-62
https://doi.org/10.1016/j.ympev.2016.07.029
Alex Dornburg, Jon Moore, Jeremy M. Beaulieu, Ron I. Eytan, Thomas J. Near, 2014, 'The impact of shifts in marine biodiversity hotspots on patterns of range evolution: Evidence from the Holocentridae (squirrelfishes and soldierfishes)', Evolution, vol. 69, no. 1, pp. 146-161
https://doi.org/10.1111/evo.12562
Alexandrou, M. A., Swartz, B. A., Matzke, N. J., & Oakley, T. H. (2013). Genome duplication and multiple evolutionary origins of complex migratory behavior in Salmonidae. Molecular Phylogenetics and Evolution, 69(3), 514–523. doi:10.1016/j.ympev.2013.07.026
https://doi.org/10.1016/j.ympev.2013.07.026
Aliabadian, Mansour, Mohammad Kaboli, Roger Prodon, Vincent Nijman, Miguel Vences. 2007. Phylogeny of Palaearctic wheatears (genus Oenanthe)—Congruence between morphometric and molecular data. Molecular Phylogenetics and Evolution 42 (3): 665-675
https://doi.org/10.1016/j.ympev.2006.08.018
Allen G. Collins, Bastian Bentlage, Alberto Lindner, Dhugal Lindsay, Steven H.D. Haddock, Gerhard Jarms, Jon L. Norenburg, Thomas Jankowski, Paulyn Cartwright, 2008, 'Phylogenetics of Trachylina (Cnidaria: Hydrozoa) with new insights on the evolution of some problematical taxa', Journal of the Marine Biological Association of the United Kingdom, vol. 88, no. 08, p. 1673
https://doi.org/10.1017/s0025315408001732
Allen G., Soltis D., & Soltis P. 2003. Phylogeny and biogeography of Erythronium (Liliaceae) inferred from chloroplast matK and nuclear rDNA ITS sequences. Systematic Botany, 28(3): 512-523.
https://doi.org/10.1043/02-18.1
Almeida, Francisca C., Norberto P. Giannini, Nancy B. Simmons, Kristofer M. Helgen. 2014. Each flying fox on its own branch: a phylogenetic tree for Pteropus and related genera (Chiroptera: Pteropodidae). Molecular Phylogenetics and Evolution 77: 83-95.
https://doi.org/10.1016/j.ympev.2014.03.009
Alstrom, P., D. M. Hooper, Y. Liu, U. Olsson, D. Mohan, M. Gelang, H. Le Manh, J. Zhao, F. Lei, T. D. Price. 2014. Discovery of a relict lineage and monotypic family of passerine birds. Biology Letters 10 (3): 20131067-20131067.
https://doi.org/10.1098/rsbl.2013.1067
Alström, Per, Keith N. Barnes, Urban Olsson, F. Keith Barker, Paulette Bloomer, Aleem Ahmed Khan, Masood Ahmed Qureshi, Alban Guillaumet, Pierre-André Crochet, Peter G. Ryan. 2013. Multilocus phylogeny of the avian family Alaudidae (larks) reveals complex morphological evolution, non-monophyletic genera and hidden species diversity. Molecular Phylogenetics and Evolution 69 (3): 1043-1056.
https://doi.org/10.1016/j.ympev.2013.06.005
Amanda F. Cunha, Allen G. Collins, Antonio C. Marques, 2017, 'Phylogenetic relationships of Proboscoida Broch, 1910 (Cnidaria, Hydrozoa): Are traditional morphological diagnostic characters relevant for the delimitation of lineages at the species, genus, and family levels?', Molecular Phylogenetics and Evolution, vol. 106, pp. 118-135
https://doi.org/10.1016/j.ympev.2016.09.012
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https://doi.org/10.1038/nature12872
Andrea M. Quattrini, Samuel E. Georgian, Luke Byrnes, Alex Stevens, Rosalia Falco, Erik E. Cordes, 2013, 'Niche divergence by deep-sea octocorals in the genusCallogorgiaacross the continental slope of the Gulf of Mexico', Molecular Ecology, vol. 22, no. 15, pp. 4123-4140
https://doi.org/10.1111/mec.12370
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https://doi-org.www2.lib.ku.edu/10.1080/00275514.2017.1354169
Andres B., & Ji Q. 2008. A new pterosaur from the Liaoning Province of China, the phylogeny of the Pterodactyloidea, and convergence in their cervical vertebrae. Palaeontology, 51(2): 453-469.
https://doi.org/10.1111/j.1475-4983.2008.00761.x
Andres B.B., Clark J.M., & Xu X. 2012. A new rhamphorhynchid pterosaur from the Upper Jurassic of Xinjiang, China, and the phylogenetic relationships of basal pterosaurs. Journal of Vertebrate Paleontology, 30(1): 163-187.
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Andrew L. Hipp, Paul S. Manos, Antonio González-Rodríguez, Marlene Hahn, Matthew Kaproth, John D. McVay, Susana Valencia Avalos, Jeannine Cavender-Bares, 2017, 'Sympatric parallel diversification of major oak clades in the Americas and the origins of Mexican species diversity', New Phytologist, vol. 217, no. 1, pp. 439-452
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Anna V. Williams, Joseph T. Miller, Ian Small, Paul G. Nevill, Laura M. Boykin, 2016, 'Integration of complete chloroplast genome sequences with small amplicon datasets improves phylogenetic resolution in Acacia', Molecular Phylogenetics and Evolution, vol. 96, pp. 1-8
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Antoine Simon, Bernard Goffinet, Nicolas Magain, Emmanuël Sérusiaux, 2018, 'High diversity, high insular endemism and recent origin in the lichen genus Sticta (lichenized Ascomycota, Peltigerales) in Madagascar and the Mascarenes', Molecular Phylogenetics and Evolution, vol. 122, pp. 15-28
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Aoki T., O'donnell K., Homma Y., & Lattanzi A. 2003. Sudden death syndrome of soybean is caused by two morphologically and phylogenetically distinct species within the Fusarium solani species complex, F. virguliforme in North America and F. tucumaniae in South America. Mycologia, 95(4): 660-684.
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Aoki T., Suga H., Hyakumachi M., Scandiani M.M., & O'donnell K. 2012. Fusarium azukicola sp. nov., a novel exotic azuki bean root-rot pathogen in Hokkaido, Japan. Mycologia, 104(5): 1068-1084.
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Arbabi, Tayebeh, Javier Gonzalez, Michael Wink. 2014. A re-evaluation of phylogenetic relationships within reed warblers (Aves: Acrocephalidae) based on eight molecular loci and ISSR profiles. Molecular Phylogenetics and Evolution 78: 304-313.
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Arcila, Dahiana, Guillermo Ortí, Richard Vari, Jonathan W. Armbruster, Melanie L. J. Stiassny, Kyung D. Ko, Mark H. Sabaj, John Lundberg, Liam J. Revell, Ricardo Betancur-R., 2017, 'Genome-wide interrogation advances resolution of recalcitrant groups in the tree of life', Nature Ecology & Evolution, vol. 1, p. 0020
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Arora D., & Frank J.L. 2014. Clarifying the Butter Boletes: a new genus, Butyriboletus, is established to accommodate Boletus sect. Appendiculati, and seven new species are described. Mycologia, 106(3): 464-480.
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Arshad, Muhammad, Javier Gonzalez, Abdel Aziz El-Sayed, Tim Osborne, Michael Wink. 2009. Phylogeny and phylogeography of critically endangered Gyps species based on nuclear and mitochondrial markers. Journal of Ornithology 150 (2): 419-430.
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