[1] | Berney C, Pawlowski J (2006) A molecular time-scale for eukaryote evolution recalibrated with the continuous microfossil record. Proceedings of the Royal Society B-Biological Sciences 273: 1867–1872 doi:10.1098/rspb.2006.3537.
|
[2] | Parfrey LW, Lahr DJG, Knoll AH, Katz LA (2011) Estimating the timing of early eukaryotic diversification with multigene molecular clocks. Proceedings of the National Academy of Sciences of the United States of America 108: 13624–13629 doi:10.1073/pnas. 1110633108. PubMed: 21810989.
|
[3] | Adl SM, Simpson AGB, Lane CE, Luke? J, Bass D, et al. (2012) The revised classification of eukaryotes. Journal of Eukaryotic Microbiology 59: 429–493.
|
[4] | Lahr DJG, Grant JR, Katz LA (2013) Multigene phylogenetic reconstruction of the Tubulinea (Amoebozoa) corroborates four of the six major lineages, while additionally revealing that shell composition does not predict phylogeny in the Arcellinida. Protist 164: 323–339.
|
[5] | Smirnov AV, Chao E, Nassonova ES, Cavalier-Smith T (2011) A revised classification of naked lobose amoebae (Amoebozoa: Lobosa). Protist 162: 545–570.
|
[6] | Pawlowski J, Audic S, Adl S, Bass D, Belbahri L, et al. (2012) CBOL protist working group: barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms. PloS Biology 10(11): e1001419 doi:10.1371/journal.pbio.1001419.
|
[7] | Golemansky V (2007) Testate Amoebas and Monothalamous Foraminifera (Protozoa) from the Bulgarian Black Sea Coast. In: Fet V, Popov A, editors. Biogeography and Ecology of Bulgaria. pp. 555–570.
|
[8] | Meisterfeld R (2002) Order Arcellinida Kent, 1880. In: Lee JJ, Leedale GF, Bradbury P, editors. The illustrated guide to the protozoa. Second edition ed. Lawrence, Kansas, USA: Society of protozoologists. pp. 827–860.
|
[9] | Booth RK, Zygmunt JR (2005) Biogeography and comparative ecology of testate amoebae inhabiting Sphagnum-dominated peatlands in the Great Lakes and Rocky Mountain regions of North America. Diversity and Distributions 11: 577–590.
|
[10] | Deflandre G (1936) Etude monographique sur le genre Nebela Leidy. Annales de Protistologie 5: 201–286.
|
[11] | Mitchell EAD, Gilbert D, Buttler A, Amblard C, Grosvernier P, et al. (2003) Structure of microbial communities in Sphagnum peatlands and effect of atmospheric carbon dioxide enrichment. Microbial Ecology 46: 187–199.
|
[12] | Mitchell EAD, Charman DJ, Warner BG (2008) Testate amoebae analysis in ecological and paleoecological studies of wetlands: past, present and future. Biodiversity and Conservation 17: 2115–2137.
|
[13] | Charret R (1964) Contribution à l'étude cytologique et biologique de Hyalosphenia papilio (Leidy), Rhizopode Testacé. Bulletin Biologique de la France et de la Belgique XCVIII(2): 369–390.
|
[14] | Hubers M, Kerp H (2012) Oldest known mosses discovered in Mississippian (late Visean) strata of Germany. Geology 40: 755–758.
|
[15] | Porter SM, Knoll AH (2000) Testate amoebae in the Neoproterozoic Era: evidence from vase-shaped microfossils in the Chuar Group, Grand Canyon. Paleobiology 26: 360–385.
|
[16] | Shaw AJ, Devos N, Cox CJ, Boles SB, Shaw B, et al. (2010) Peatmoss (Sphagnum) diversification associated with Miocene Northern Hemisphere climatic cooling? Molecular Phylogenetics and Evolution 55: 1139–1145.
|
[17] | Lara E, Heger TJ, Ekelund F, Lamentowicz M, Mitchell EAD (2008) Ribosomal RNA genes challenge the monophyly of the Hyalospheniidae (Amoebozoa: Arcellinida). Protist 159: 165–176.
|
[18] | Cavalier-Smith T (2009) Megaphylogeny, cell body plans, adaptive zones: causes and timing of eukaryote basal radiations. Journal of Eukaryotic Microbiology 56: 26–33.
|
[19] | Fiz-Palacios O, Romeralo M, Ahmadzadeh A, Weststrand S, Ahlberg PE, et al. (2013) Did terrestrial diversification of amoebas (Amoebozoa) occur in synchrony with Land plants? Plos One 8(9): e74374 doi:10.1371/journal.pone.0074374.
|
[20] | Pons J, Barraclough TG, Gomez-Zurita J, Cardoso A, Duran DP, et al. (2006) Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Systematic Biology 55: 595–609.
|
[21] | Fontaneto D, Herniou EA, Boschetti C, Caprioli M, Melone G, et al. (2007) Independently evolving species in asexual bdelloid rotifers. Plos Biology 5(4): e87 doi:10.1371/journal.pbio.0050087.
|
[22] | Heger TJ, Mitchell EAD, Leander BS (2013) Holarctic phylogeography of the testate amoeba Hyalosphenia papilio (Amoebozoa: Arcellinida) reveals extensive genetic diversity explained more by environment than dispersal limitation. Molecular Ecology 22: 5172–5184.
|
[23] | Kosakyan A, Gomaa F, Mitchell EAD, Heger TJ, Lara E (2013) Using DNA-barcoding for sorting out protist species complexes: A case study of the Nebela tincta-collaris-bohemica group (Amoebozoa; Arcellinida, Hyalospheniidae). European Journal of Protistology 49: 222–237.
|
[24] | Kosakyan A, Heger TJ, Leander BS, Todorov M, Mitchell EAD, et al. (2012) COI barcoding of Nebelid testate amoebae (Amoebozoa: Arcellinida): extensive cryptic diversity and redefinition of the Hyalospheniidae Schultze. Protist 163: 415–434.
|
[25] | Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41: 95–98.
|
[26] | Jobb G, von Haeseler A, Strimmer K (2004) TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. BMC Evolutionary Biology 4.
|
[27] | Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572–1574.
|
[28] | Posada D, Crandall KA (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14: 817–818.
|
[29] | Lahr DJG, Grant J, Nguyen T, Lin JH, Katz LA (2011) Comprehensive phylogenetic reconstruction of amoebozoa based on concatenated analyses of SSU-rDNA and actin genes. Plos One 6(7): e22780 doi:10.1371/journal.pone.0022780.
|
[30] | Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide-sequences. Journal of Molecular Evolution 16: 111–120.
|
[31] | R Development Core Team (2010) R: A Language and Environment for Statistical Computing. Foundation for Statistical Computing, Version 2.8.0. R Development Core Team, Vienna, Austria. Available: http://wwwR-projectorg.
|
[32] | Fujisawa T, Barraclough TG (2013) Delimiting Species Using Single-Locus Data and the Generalized Mixed Yule Coalescent Approach: A Revised Method and Evaluation on Simulated Data Sets. Systematic Biology 62: 707–724.
|
[33] | Monaghan MT, Wild R, Elliot M, Fujisawa T, Balke M, et al. (2009) Accelerated species inventory on Madagascar using coalescent-based models of species delineation. Systematic Biology 58: 298–311.
|
[34] | Drummond AJ, Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees. Bmc Evolutionary Biology 7.
|
[35] | Bosak T, Lahr DJG, Pruss SB, Macdonald FA, Dalton L, et al. (2011) Agglutinated tests in post-Sturtian cap carbonates of Namibia and Mongolia. Earth and Planetary Science Letters 308: 29–40.
|
[36] | Girard V, Neraudeau D, Adl SM, Breton G (2011) Protist-like inclusions in amber, as evidenced by Charentes amber. European Journal of Protistology 47: 59–66.
|
[37] | Schmidt AR, Ragazzi E, Coppellotti O, Roghi G (2006) A microworld in Triassic amber. Nature 444: 835–835.
|
[38] | Schmidt AR, Schonborn W, Schafer U (2004) Diverse fossil amoebae in German Mesozoic amber. Palaeontology 47: 185–197.
|
[39] | van Hengstum PJ, Reinhardt EG, Medioli FS, Grocke DR (2007) Exceptionally preserved late albian (cretaceous) arcellaceans (thecamoebians) from the Dakota formation near Lincoln, Nebraska,USA. Journal of Foraminiferal Research 37: 300–308.
|
[40] | Medioli FS, Scott DB, Collins ES, McCarthy FMG (1990) Fossil thecamoebians: Present status and prospects for the future. In: Hemleben C, Kaminski MA, Kuhnt W, Scott DB, editors. Proceedings of the NATO Advanced Study Institute on paleoecology, biostratigraphy, paleoceanography and taxonomy of agglutinated foraminifera. Dordrecht-Boston, International: D. Reidel Publishing Company. pp. 813–839.
|
[41] | Gomaa F, Todorov M, Heger TJ, Mitchell EAD, Lara E (2012) SSU rRNA phylogeny of Arcellinida (Amoebozoa) reveals that the largest Arcellinida genus, Difflugia Leclerc 1815, is not monophyletic. Protist 163: 389–399.
|
[42] | Kumar A (2011) Acid-resistant Cretaceous thecamoebian tests from the Arabian Peninsula: a suggestion for study of agglutinated rhizopods in palynological slides. Journal of Micropalaeontology 30: 1–5.
|
[43] | Rabosky DL (2006) LASER: a maximum likelihood toolkit for detecting temporal shifts in diversification rates from molecular phylogenies. Evolutionary Bioinformatics 2: 247–250.
|
[44] | Magallon S (2006) Sanderson (2006) Absolute diversification rates in angiosperm clades (vol 55, pg 1762, 2001). Evolution 60: 2411–2411.
|
[45] | Xia X, Xie Z (2001) DAMBE: Software package for data analysis in molecular biology and evolution. Journal of Heredity 92: 371–373.
|
[46] | Fontaneto D, Hortal J (2013) At least some protist species are not ubiquitous. Molecular Ecology 22: 5053–5055.
|
[47] | Knoll AH (2014) Paleobiological Perspectives on Early Eukaryotic Evolution. Cold Spring Harbor Perspectives in Biology 6.
|
[48] | Porter S (2011) The rise of predators. Geology 39: 607–608.
|
[49] | Farooqui A, Kumar AN, Jha N, Pande AC, Bhattacharya DD (2010) A Thecamoebian assemblage from the Manjir Formation (Early Permian) of Northwest Himalaya. Earth Sci India 3: 146–153.
|
[50] | Rubinstein CV, Gerrienne P, de la Puente GS, Astini RA, Steemans P (2010) Early Middle Ordovician evidence for land plants in Argentina (eastern Gondwana). New Phytologist 188: 365–369.
|
[51] | Newton AE, Wikstr?m N, Bell N, Forrest LL, Ignatov MS (2007) Dating the Diversification of the Pleurocarpous mosses. In: Newton AE, Tangney RS, editors. Pleurocarpous mosses: Systematics and Evolution Boca Raton, CRC Press. pp. 337–366.
|
[52] | Fiz-Palacios O, Schneider H, Heinrichs J, Savolainen V (2011) Diversification of land plants: insights from a family-level phylogenetic analysis. Bmc Evolutionary Biology 11.
|
[53] | Brenner GJ (1996) Evidence for the earliest stage of angiosperm pollen evolution: A paleoequatorial section from Israel. In: Taylor DW, Hickey LJ, editors. Flowering plant origin, evolution and phylogeny. New York: Chapman. pp. 91–115.
|