Phylogeny and systematics of protodrilidae (annelida) inferred with total evidence analyses

Cladistics

Volumn 31, Issue 3, 2015, Pages 250-276

  Martínez, Alejandro ^a   Di Domenico, Maikon ^a,b   Rouse, Greg W ^c   Worsaae, Katrine ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

^b UNIVERSITY OF CAMPINAS   (Brazil)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANNELIDA; ARCHIANNELIDA; PROTODRILIDAE; PROTODRILUS;

EID: 84928766538     PISSN: 07483007     EISSN: 10960031     Source Type: Journal    
DOI: 10.1111/cla.12089     Document Type: Article

References (108)

1. Aberer, A.J., Krompass, D., Stamatakis, A., 2012. Pruning rogue taxa improves phylogenetic accuracy: an efficient algorithm and webservice. Syst. Biol. 62, 162-166.
2. Agassiz, L., 1845. Nomenclatoris Zoologici Index Universalis: Continens Nomina Systematica Classium, Ordinum, Familiarum et Generum animalium Omnium, Tam Viventium Quam Fossilium, Secundum Ordinem Alphabeticum Unicum Disposita, Adjectis Homonymiis Plantarum. Jent et Gassmann, Paris, pp. 1134.
3. Aguado, M.T., San Martín, G., 2009. Phylogeny of the Syllidae (Polychaeta) based on morphological data. Zool. Scripta 38, 379-402.
4. Aguado, M.T., San Martín, G., Siddall, M.E., 2012. Systematics and evolution of syllids (Annelida, Syllidae). Cladistics 28, 234-250.
5. Aiyar, G., Alikunhi, K.H., 1944. On some archiannelids of Madras coast. Proc. Nat. Inst. Sci. India 10, 113-139.
6. Ax, P., 1966. Die Bedeuting der interstitiellen Sandfauna fuer allgemeine Probleme der Systematik, Oekologie und Biologie. Veröff. Inst. Meeresforsch. Bremerhaven 2, 15-65.
7. Bailey-Brock, J.H., Jouin-Toulmond, C., Brock, R.E., 2010. Protodrilidae (Annelida: Polychaeta) from the Hawaiian Islands and comparison with specimens from French Polynesia 1. Pac. Sci. 64, 463-472.
8. Boaden, P.J.S., 1964. Water movement-a dominant factor in interstitial ecology. Sarsia 34, 125-136.
9. Boyer, S.L., Clouse, R.M., Benavides, L.R., Sharma, P., Schwendinger, P.J., Karunarathna, I., Giribet, G., 2007. Biogeography of the world: a case study from cyphophthalmid Opiliones, a globally distributed group of arachnids. J. Biogeogr. 34, 2070-2085.
10. Capa, M., Hutchings, P., Aguado, M.T., Bott, N.I., 2011. Phylogeny of Sabellidae (Annelida) and relationships with other taxa inferred from morphology and multiple genes. Cladistics 27, 449-469.
11. Capa, M., Parapar, J., Hutchings, P., 2012. Phylogeny of Oweniidae (Polychaeta) based on morphological data and taxonomic revision of Australian fauna. Zool. J. Linnean Soc. 166, 236-278.
12. Castresana, J., 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17, 540-552.
13. Czerniavsky, V., 1881. Material ad zoographiam Ponticam comparatam. Fasc. III Vermes. Bull. Soc. Imp. Nat. Mos. (= Byull. Mosk. Ova Ispyt. Prir.) 55, 211-363.
14. Di Domenico, M., Martínez, A., Lana, P., Worsaae, K., 2013. Protodrilus (Protodrilidae, Annelida) from the southern and southeastern Brazilian coasts. Helgol. Mar. Res. 67, 733-748.
15. Di Domenico, M., Martínez, A., Almeida, T.C.M., Martins, M.O., Worsaae, K., Lana, P.C., 2014a. Response of the meiofaunal annelid Saccocirrus pussicus (Saccocirridae) to sandy beach morphodynamics. Hydrobiologia 734, 1-16.
16. Di Domenico, M., Martínez, A., Lana, P., Worsaae, K., 2014b. Molecular and morphological phylogeny of Saccocirridae (Annelida) reveals two cosmopolitan clades with specific habitat preferences. Mol. Syst. Evol. 75, 202-218.
17. Di Domenico, M., Martínez, A., Lana, P., Worsaae, K., 2014c. Saccocirrus (Saccocirridae, Annelida) from the southern and southeastern Brazilian coasts. Mar. Biodivers. 1-13.
18. Edgar, R.C., 2004a. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinform. 5, 113.
19. Edgar, R.C., 2004b. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797.
20. Fauchald, K., Rouse, G.W., 1997. Polychaete systematics: past and present. Zool. Scripta 26, 71-138.
21. Felsenstein, J., 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791.
22. Giere, O., 2009. Meiobenthology. The Microscopic Motile Fauna of Aquatic Sediments. Springer, Berlin.
23. Giere, O., Nieser, C., Windoffer, R., Erseus, C., 1995. A comparative structural study on bacterial symbioses of Caribbean gutless Tubificidae (Annelida, Oligochaeta). Acta Zool. 76, 281-290.
24. Giribet, G., 2003. Stability in phylogenetic formulations and its relationship to nodal support. Syst. Biol. 52, 554-564.
25. Giribet, G., 2007. Efficient tree searches with available algorithms. Evol. Bioinform. 3, 341-356.
26. Giribet, G., Sharma, P.P., Benavides, L.R., Boyer, S.L., Clouse, R.M., De Bivort, B.L., Dimitrov, D., Kawauchi, G.Y., Murienne, J., Schwendinger, P.J., 2012. Evolutionary and biogeographical history of an ancient and global group of arachnids (Arachnida: Opiliones: Cyphophthalmi) with a new taxonomic arrangement. Biol. J. Linnean Soc. 105, 92-130.
27. Goodrich, E.S., 1901. On the structure and affinities of the genus Saccocirrus. Q. J. Microsc. Sci. 44, 413-427.
28. Hall, T.A., 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41, 95-98.
29. Hatschek, B., 1881. Protodrilus leuckartii. Eine neue Gattung Archianneliden. Arb. Zool. Inst. Univ. Wien Zool. Triest 3, 79-93.
30. Hatschek, B., 1888. Lehrbuch der Zoologie. Gustav Fischer, Jena, 1. Lieferung, 144pp.
31. Hermans, C.O., 1969. The systematic position of the Archiannelida. Syst. Zool. 18, 85-102.
32. Higgins, R.P., Thiel, H., 1988. Introduction to the Study of Meiofauna. Smithsonian Institution Press, Washington, DC.
33. Jägersten, G., 1940. Zur Kenntnis der äusseren Morphologie, Entwicklung und Ökologie von Protodrilus rubropharyngeus n. sp. Ark. Zool. 32, 1-19.
34. Jägersten, G., 1952. Studies on the morphology, larval development and biology of Protodrilus. Zool. Bijd. Upps. 29, 425-512.
35. Jägersten, G., 1954. On the locomotion and attachment of Protodrilus, with remarks on the function of locomotory cilia. Zool. Bijd. Upps. 25, 5-320.
36. Johannes, R.E., 1967. Ecology of organic aggregates in the vicinity of a coral reef. Limnol. Oceanogr. 12, 189-195.
37. Jouin, C., 1966. Morphologie et anatomie comparée de Protodrilus chaetifer Remane et Protodrilus symbioticus Giard; création du nouveau genre Protodriloides (Archiannélides). Cah. Biol. Mar. 7, 139-155.
38. Jouin, C., 1970. Recherches sur les Protodrilidae (Archiannélides): 1. Étude morphologique et systématique du genre Protodrilus. Cah. Biol. Mar. 11, 367-434.
39. Jouin, C., 1971. Status of the knowledge of Archiannelida. In: Hulings, N.C. (Ed.), Proceedings of the First International Conference of Meiofauna. Smithson. Contrib. Zool. 76, 47-56.
40. Jouin, C., 1978. Anatomical and ultrastructural study of the pharyngeal bulb in Protodrilus (Polychaeta, Archiannelida). I. Muscles and myo-epithelial junctions. Tissue Cell 10, 269-287.
41. Jouin, C., 1979. Description of a free-living Polychaete without gut: Astomus taenioides n. gen., n. sp. (Protodrilidae, Archiannelida). Can. J. Zool. 57, 2448-2456.
42. Jouin, C., 1992. The ultrastructure of a gutless annelid, Parenterodrilus gen. nov. taenioides (= Astomus taenioides) (Polychaeta, Protodrilidae). Can. J. Zool. 70, 1833-1848.
43. Jouin-Toulmond, C., Purschke, G., 2004. Ultrastructure of the spermatozoa of Parenterodrilus taenioides (Protodrilida: "Polychaeta") and its phylogenetic significance. Zoomorphology 123, 139-146.
44. Katoh, K., Misawa, K., Kuma, K.I., Miyata, T., 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30, 3059-3066.
45. Katoh, K., Asimenos, G., Toh, H., 2010. Multiple alignment of DNA sequences with MAFFT. In: Posada, D. (Ed.) Bioinformatics for DNA Sequence Analysis. Humana Press, Totawa, NJ, pp. 39-64.
46. Kirsteuer, E., 1966. Zur Kenntnis der Archianneliden des Roten Meeres. Zool. Anz. 177, 288-296.
47. Kvist, S., Siddall, M.E., 2013. Phylogenomics of Annelida revisited: a cladistic approach using genome-wide expressed sequence tag data mining and examining the effects of missing data. Cladistics 29, 1-14.
48. Lam, H.J., 1922. Über den Bau und die Verwandschaft der Protoannelis meyeri, nov. gen., nov. spec., eine neue Archiannelide. Tijds. Ned. Dierkd. Ver. Leiden 18, 44-84.
49. Lewis, P.O., 2001. A likelihood approach to estimating phylogeny from discrete morphological character data. Syst. Biol. 50, 913-925.
50. Maddison, D.R., Maddison, W.P., 2001. MacClade 4. Sinauer Associates, Sunderland, MA.
51. Maddison, W.P., Maddison, D.R., 2007. Mesquite: a modular system for evolutionary analysis. Version 2.75. 2011. http://mesquiteproject.org.
52. Martínez, A., Palmero, A.M., Brito, M.d.C., Núñez, J., Worsaae, K., 2009. Anchialine fauna of the Corona lava tube (Lanzarote, Canary Islands): diversity, endemism and distribution. Mar. Biodivers. 39, 169-187.
53. Martínez, A., Di Domenico, M., Jörger, K., Norenburg, J., Worsaae, K., 2013. Description of three new species of Protodrilus (Annelida, Protodrilidae) from Central America. Mar. Biol. Res. 9, 676-691.
54. Miller, M.A., Pfeiffer, W., Schwartz, T., 2010. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. Proceedings of the Gateway Computing Environments Workshop (GCE), New Orleans, LA, pp. 1-8.
55. Pierantoni, U., 1903. Sopra un nuovo Protodrilus d'acqua dolce. Monit. Zool. Ital. 14(12), 324-327.
56. Pierantoni, U., 1908. Protodrilus. Fauna Flora Golf. Neapel 31, 1-226.
57. Pleijel, F., 1995. On character coding for phylogeny reconstruction. Cladistics 11, 309-315.
58. Posada, D., 2008. jModelTest: phylogenetic model averaging. Mol. Biol. Evol. 25, 1253-1256.
59. Purschke, G., 1993. Structure of the prostomial appendages and the central nervous system in the Protodrilida (Polychaeta). Zoomorphology 113, 1-20.
60. Purschke, G., Jouin, C., 1988. Anatomy and ultrastructure of the ventral pharyngeal organs of Saccocirrus (Saccocirridae) and Protodriloides (Protodriloidae fam. n.) with remarks on the phylogenetic relationships within Protodrilida (Annelida: Polychaeta). J. Zool. 215, 405-432.
61. Purschke, G., Jouin-Toulmond, C., 1993. Ultrastructure of presumed ocelli in Astomus taenioides (Polychaeta, Protodrilidae) and their phylogenetic significance. Acta Zool. Stock. 74, 247-256.
62. Purschke, G., Jouin-Toulmond, C., 1994. Ultrastructure of sense organs and the central nervous system in Astomus taenioides and their phylogenetic significance in the taxon Protodrilida (Annelida, Polychaeta). Mém. Mus. Nat. Hist. Natur. Actes Conf. Int. Polychètes 162, 119-128.
63. R Development Core Team, 2008. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna.
64. Rambaut, A., Drummond, A.J. 2007. Tracer v1.4. http://tree.bio.ed.ac.uk/software/tracer/
65. Read, G., 2014. Protoannelis Lam, 1922. In: Read, G., Fauchald, K. (Eds.), World Polychaeta Database. http://www.marinespecies.org/polychaeta/aphia.php?p=taxdetails&id=324624on 2014-02-08
66. Remane, A. 1932. Archiannelida. Tierwelt Nord- und Ostsee 22, 1-36.
67. Richards, K.S., Fleming, T.P., Jamieson, B.G.M., 1982. An ultrastructural study of the distal epidermis and the occurence of subcuticular bacteria in the gutless tubificid Phallodrilus albidus (Oligochaeta: Annelida). Aust. J. Zool. 30, 327-336.
68. Riser, N.W., 1997. Protodrilus gelderi, a new species of infralittoral, interstitial polychaete from Massachusetts Bay. Proc. Biol. Soc. Washington 110, 552-557.
69. Ronquist, F., Huelsenbeck, J.P., 2003. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572-1574.
70. Rouse, G.W., 2001. A cladistic analysis of Siboglinidae Caullery, 1914 (Polychaeta, Annelida): formerly the phyla Pogonophora and Vestimentifera. Zool. J. Linnean Soc. 132, 55-80.
71. Rouse, G.W., Fauchald, K., 1997. Cladistics and polychaetes. Zool. Scripta 26, 139-204.
72. Rousset, V., Pleijel, F., Rouse, G.W., Erséus, C., Siddall, M.E., 2007. A molecular phylogeny of annelids. Cladistics 23, 41-63.
73. Schmidt, P., Westheide, W., 1977. Interstitielle Fauna von Galapagos. XVII. Polygordiidae, Saccocirridae, Protodrilidae, Nerillidae, Dinophilidae (Polychaeta). Mikrofauna Meeresbodens 62, 1-36.
74. Sharma, P.P., Vahtera, V., Kawauchi, G.Y., Giribet, G., 2011. Running WILD: the case for exploring mixed parameter sets in sensitivity analysis. Cladistics 27, 538-549.
75. Sournia, A., Ricard, M., 1976. Phytoplankton and its contribution to primary productivity in two coral reef areas of French Polynesia. J. Exp. Mar. Biol. Ecol. 21, 129-140.
76. Southward, E.C., 1993. Pogonophora. In: Harrison, F.W., Rice, M.E. (Eds.), Microscopic Anatomy of Invertebrates, Vol. 12, Onychophora, Chilopoda and lesser Protostomata. Wiley-Liss, New York, pp. 327-369.
77. Stamatakis, A., 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688-2690.
78. Strong, E., Lipscomb, D., 1999. Character coding and inapplicable data. Cladistics 15, 363-371.
79. Struck, T.H., Paul, C., Hill, N., Hartmann, S., Hosel, C., Kube, M., Lieb, B., Meyer, A., Tiedemann, R., Purschke, G., Bleidorn, C., 2011. Phylogenomic analyses unravel annelid evolution. Nature 471, 95-98.
80. Swedmark, B., 1964. The interstitial fauna of marine sand. Biol. Rev. 39, 1-42.
81. Thorley, J.L., Wilkinson, M., 1999. Testing the phylogenetic stability of early tetrapods. J. Theor. Biol. 200, 2-2.
82. Uljanin, B., 1877. Observations on Polygordius. Bull. Soc. Imp. Nat. Mos. (= Byull. Mosk. Ova Ispyt. Prir.) 52, 53-96. (In Russian)
83. Vaidya, G., Lohman, D.J., Meier, R., 2011. SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information. Cladistics 27, 171-180.
84. Varón, A., Vinh, L.S., Wheeler, W.C., 2010. POY version 4: phylogenetic analysis using dynamic homologies. Cladistics 26, 72-85.
85. Von Nordheim, H., 1983. Systematics and ecology of Protodrilus helgolandicus sp. n., an interstitial polychaete (Protodrilidae) from subtidal sands off Helgoland, German Bight. Zool. Scripta 12, 171-177.
86. Von Nordheim, H., 1989. Six new species of Protodrilus (Annelida, Polychaeta) from Europe and New Zealand, with a concise presentation of the genus. Zool. Scripta 18, 245-268.
87. Von Nordheim, H., 1991a. Ultrastructure and functional morphology of the female reproductive organs in Protodrilus (Polychaeta, Annelida). Helgol. Meer. 45, 465-485.
88. Von Nordheim, H., 1991b. Ultrastructure and functional morphology of the male genital organs and spermatophore formation in Protodrilus (Polychaeta, Annelida). Zoomorphology 111, 81-94.
89. Westheide, W., 1987. Progenesis as a principle in meiofauna evolution. J. Nat. Hist. 21, 843-854.
90. Westheide, W., 2009. Polychaetes: Interstitial Families. Universal Book Services/Dr W. Backhays, Oegstgeest, Netherlands.
91. Wheeler, Q.D., 1995. Systematics, the scientific basis for inventories of biodiversity. Biodivers. Conserv. 4, 476-489.
92. Wheeler, W., 1996. Optimization alignment: the end of multiple sequence alignment in Phylogenetics? Cladistics 12, 1-9.
93. Wheeler, W., Aagesen, L., Arango, C.P., Faivovich, J., Grant, T., D'Haese, C., Janies, D., Smith, W.L., Varón, A., Giribet, G. 2006. Dynamic Homology and Phylogenetic Systematics: A Unified Approach Using POY. American Museum of Natural History, New York.
94. Wiens, J.J., 2001. Character analysis in morphological phylogenetics: problems and solutions. Syst. Biol. 50, 689-699.
95. Wieser, W., 1957. Archiannelids from the intertidal of Puget Sound. Trans. Am. Microsc. Soc. 76, 275-285.
96. Wilkens, H., Iliffe, T.M., Oromí, P., Martínez, A., Tysall, T.N., Koenemann, S., 2009. The Corona lava tube, Lanzarote: geology, habitat diversity and biogeography. Mar. Biodivers. 39, 155-167.
97. Wilkinson, M., 1995. A comparison of two methods of character construction. Cladistics 11, 297-308.
98. Wilkinson, M., 1996. Majority-rule reduced consensus trees and their use in bootstrapping. Mol. Biol. Evol. 13, 437-444.
99. Worsaae, K., 2005. Phylogeny of Nerillidae (Polychaeta, Annelida) as inferred from combined 18S rDNA and morphological data. Cladistics 21, 143-162.
100. Worsaae, K., Kristensen, R.M., 2005. Evolution of interstitial Polychaeta (Annelida). Hydrobiologia 535, 319-340.
101. Worsaae, K., Martínez, A., Núñez, J., 2009. Nerillidae (Annelida) from the Corona lava tube, Lanzarote, with description of Meganerilla cesari n. sp. Mar. Biodivers. 39, 195-207.
102. Worsaae, K., Nygren, A., Rouse, G.W., Giribet, G., Persson, J., Sundberg, P., Pleijel, F., 2005. Phylogenetic position of Nerillidae and Aberranta (Polychaeta, Annelida), analysed by direct optimization of combined molecular and morphological data. Zool. Scripta 34, 313-328.
103. Wu, B.l., Ruiping, S., 1980. On archiannelids of the Yellow Sea I. Protodrilidae. Acta Oceanol. Sin. 2, 132-148.
104. Xia, X., Lemey, P., 2009. Assessing substitution saturation with DAMBE. In: Lemey, P., Salemi, M., Vandamme, A.M. (Eds.), The Phylogenetic Handbook. Cambridge University Press, Cambridge, UK, pp. 611-626.
105. Xia, X., Xie, Z., 2001. DAMBE: software package for data analysis in molecular biology and evolution. J. Heredity 92, 371-373.
106. Xia, X., Xie, Z., Salemi, M., Chen, L., Wang, Y., 2003. An index of substitution saturation and its application. Mol. Phylogenet. Evol. 26, 1-7.
107. Zanol, J., Fauchald, C., Paiva, P.C., 2007. A phylogenetic analysis of the genus Eunice (Eunicidae, Polychaete, Annelida). Zool. J. Linnean Soc. 150, 413-434.
108. Zrzavy, J., Říha, P., Piálek, L., Janouškovec, J., 2009. Phylogeny of Annelida (Lophotrochozoa): total-evidence analysis of morphology and six genes. BMC Evol. Biol. 9, 189.