@article {Jorgensen:2004oz,
	title = {Molecular phylogeny of Tardigrada - investigation of the monophyly of Heterotardigrada},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {32},
	year = {2004},
	pages = {666-670},
	publisher = {ACADEMIC PRESS INC ELSEVIER SCIENCE},
	address = {525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA},
	doi = {DOI 10.1016/j.ympev.2004.04.017},
	author = {Jorgensen, A and Kristensen, R. M.}
}
@article {Meldal:2007qp,
	title = {An improved molecular phylogeny of the Nematoda with special emphasis on marine taxa},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {42},
	year = {2007},
	pages = {622-636},
	publisher = {ACADEMIC PRESS INC ELSEVIER SCIENCE},
	address = {525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA},
	abstract = {Phylogenetic reconstructions of relations within the phylum Nematoda are inherently difficult but have been advanced with the introduction of large-scale molecular-based techniques. However, the most recent revisions were heavily biased towards terrestrial and parasitic species and greater representation of clades containing marine species (e.g. Araeolaimida, Chromadorida, Desmodorida, Desmoscolecida, Enoplida, and Monhysterida) is needed for accurate coverage of known taxonomic diversity. We now add small subunit ribosomal DNA (SSU rDNA) sequences for 100 previously un-sequenced species of nematodes, including 46 marine taxa. SSU rDNA sequences for > 200 taxa have been analysed based on Bayesian inference and LogDet-transformed distances. The resulting phylogenies provide support for (i) the re-classification of the Secernentea as the order Rhabditida that derived from a common ancestor of chromadorean orders Araeolaimida, Chromadorida, Desmodorida, Desmoscolecida, and Monhysterida and (ii) the position of Bunonema close to the Diplogasteroidea in the Rhabditina. Other, previously controversial relationships can now be resolved more clearly: (a) Alaimus, Campydora, and Trischistoma belong in the Enoplida, (b) Isolaimium is placed basally to a big clade containing the Axonolaimidae, Plectidae, and Rhabditida, (c) Xyzzors belongs in the Desmodoridae, (d) Comesomatidae and Cyartonema belongs in the Monhysterida, (e) Globodera belongs in the Hoplolaimidae and (0 Paratylenchus dianeae belongs in the Criconematoidea. However, the SSU gene did not provide significant support for the class Chromadoria or clear evidence for the relationship between the three classes, Enoplia, Dorylaimia, and Chromadoria. Furthermore, across the whole phylum, the phylogenetically informative characters of the SSU gene are not informative in a parsimony analysis, highlighting the short-comings of the parsimony method for large-scale phylogenetic modelling. (c) 2006 Elsevier Inc. All rights reserved.},
	keywords = {Adenophorea, Bayesian inference, Chromadorea, Enoplea, evolution, LogDet transformation, Marine nematodes, Nematoda, parsimony, phylogenetic reconstruction, Rhabditida, Secernentea, SSU rDNA, systematics, taxonomy},
	doi = {DOI 10.1016/j.ympev.2006.08.025},
	author = {Meldal, Birgit H. M. and Debenham, Nicola J. and De Ley, Paul and De Ley, Irma Tandingan and Vanfleteren, Jacques R. and Vierstraete, Andy R. and Bert, Wim and Borgonie, Gaetan and Moens, Tom and Tyler, Paul A. and Austen, Melanie C. and Blaxter, Mark L. and Rogers, Alex D. and Lambshead, P. J. D.}
}
@article {Roe:2007rp,
	title = {Patterns of evolution of mitochondrial cytochrome c oxidase I and II DNA and implications for DNA barcoding},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {44},
	year = {2007},
	pages = {325-345},
	publisher = {ACADEMIC PRESS INC ELSEVIER SCIENCE},
	address = {525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA},
	abstract = {DNA barcoding has focused increasing attention on the use of specific regions of mitochondrial cytochrome c oxidase I and 11 genes (COI-COII) to diagnose and delimit species. However, our understanding of patterns of molecular evolution within these genes is limited. Here we examine patterns of nucleotide divergence in COI-COII within species and between species pairs of Lepidoptera and Diptera using a sliding window analysis. We found that: (1) locations of maximum divergence within COI-COII were highly variable among taxa surveyed in this study; (2) there was major overlap in divergence within versus between species, including within individual COI-CoII profiles; (3) graphical DNA saturation analysis showed variation in percent nucleotide transitions throughout COI-COII and only limited association with levels of DNA divergence. Ultimately, no single optimally informative 600 bp location was found within the 2.3kb of COI-COII, and the DNA barcoding region was no better than other regions downstream in Col. Consequently, we recommend that researchers should maximize sequence length to increase the probability of sampling regions of high phylogenetic informativeness, and to minimize stochastic variation in estimating total divergence. (c) 2007 Elsevier Inc. All rights reserved.},
	keywords = {COI, divergence, insects, mtDNA, saturation, species delimitation},
	doi = {DOI 10.1016/j.ympev.2006.12.005},
	author = {Roe, Amanda D. and Sperling, Felix A. H.}
}
@article {Strandberg:2004fy,
	title = {A comparison of methods for estimating the transition: transversion ratio from DNA sequences},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {32},
	year = {2004},
	pages = {495-503},
	publisher = {ACADEMIC PRESS INC ELSEVIER SCIENCE},
	address = {525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA},
	abstract = {Estimation of the ratio of the rates of transitions to transversions (TI:TV ratio) for a collection of aligned nucleotide sequences is important because it provides insight into the process of molecular evolution and because such estimates may be used to further model the evolutionary process for the sequences under consideration. In this paper, we compare several methods for estimating the TI:TV ratio, including the pairwise method [TREE 11 (1996) 158], a modification of the pairwise method due to Ina [J. Mol. Evol. 46 (1998) 521], a method based on parsimony (TREE 11 (1996) 158), a method due to Purvis and Bromham [J. Mol. Evol. 44 (1997) 112] that uses phylogenetically independent pairs of sequences, the maximum likelihood method, and a Bayesian method [Bioinformatics 17 (2001) 754]. We examine the performance of each estimator under several conditions using both simulated and real data. (C) 2004 Elsevier Inc. All rights reserved.},
	keywords = {Bayesian estimation, independent contrasts, maximum likelihood, rate variation, transition bias, transition/transversion ratio},
	doi = {DOI 10.1016/j.ympev.2004.01.013},
	author = {Strandberg, AKK and Salter, LA}
}
@article {Holterman:2008fx,
	title = {Small subunit ribosomal DNA-based phylogeny of basal Chromadoria (Nematoda) suggests that transitions from marine to terrestrial habitats (and vice versa) require relatively simple adaptations},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {48},
	year = {2008},
	pages = {758-763},
	publisher = {ACADEMIC PRESS INC ELSEVIER SCIENCE},
	address = {525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA},
	doi = {DOI 10.1016/j.ympev.2008.04.033},
	author = {Holterman, Martijn and Holovachov, Oleksandr and van den Elsen, Sven and van Megen, Hanny and Bongers, Tom and Bakker, Jaap and Helder, Johannes}
}
@article {Subbotin:2001qm,
	title = {Phylogenetic relationships within the cyst-forming nematodes (Nematoda, Heteroderidae) based on analysis of sequences from the ITS regions of ribosomal DNA},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {21},
	year = {2001},
	pages = {1-16},
	publisher = {ACADEMIC PRESS INC},
	address = {525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA},
	abstract = {The ITS1, ITS2, and 5.8S gene sequences of nuclear ribosomal DNA from 40 taxa of the family Heteroderidae (including the genera Afenestrata, Cactodera, Heterodera, Globodera, Punctodera, Meloidodera, Cryphodera, and Thecavermiculatus) were sequenced and analyzed. The ITS regions displayed high levels of sequence divergence within Heteroderinae and compared to outgroup taxa. Unlike recent findings in root knot nematodes, ITS sequence polymorphism does not appear to complicate phylogenetic analysis of cyst nematodes. Phylogenetic analyses with maximum-parsimony, minimum-evolution, and maximum-likelihood methods were performed with a range of computer alignments, including elision and culled alignments. All multiple alignments and phylogenetic methods yielded similar basic structure for phylogenetic relationships of Heteroderidae. The cyst-forming nematodes are represented by six main clades corresponding to morphological characters and host specialization, with certain clades assuming different positions depending on alignment procedure and/or method of phylogenetic inference. Hypotheses of monophyly of Punctoderinae and Heteroderinae are, respectively, strongly and moderately supported by the ITS data across most alignments. Close relationships were revealed between the Avenae and the Sacchari groups and between the Humuli group and the species H. salixophila within Heteroderinae. The Goettingiana group occupies a basal position within this subfamily. The validity of the genera Afenestrata and Bidera was tested and is discussed based on molecular data. We conclude that ITS sequence data are appropriate for studies of relationships within the different species groups and less so for recovery of more ancient speciations within Heteroderidae. (C) 2001 Academic Press.},
	keywords = {coevolution, cyst-forming nematodes, Heteroderidae, phylogeny, sequence alignments},
	author = {Subbotin, SA and Vierstraete, A and De Ley, P and Rowe, J and Waeyenberge, L and Moens, M and Vanfleteren, JR}
}
@article {Baldwin1997,
	title = {An evolutionary framework for the study of developmental evolution in a set of nematodes related to \emph{Caenorhabditis} \emph{elegans}},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {8},
	number = {2},
	year = {1997},
	pages = {249{\textendash}259},
	author = {Baldwin, J.G. and Frisse, L.M. and Vida, J.T. and Eddleman, C.D. and Thomas, W. K.}
}
@article {Bininda-Emonds2000_37,
	title = {Factors influencing phylogenetic inference: A case study using the mammalian carnivores},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {16},
	number = {1},
	year = {2000},
	pages = {113{\textendash}126},
	author = {Bininda-Emonds, Olaf R. P.}
}
@inbook {Dewey1997_142,
	title = {Cladistic analysis of Tospovirus using molecular characters},
	booktitle = {Molecular Phylogenetics and Evolution},
	volume = {8},
	year = {1997},
	pages = {11{\textendash}32},
	author = {Dewey, R. A. and Semorile, L. C. and Grau, O. and Crisci, J. V.}
}
@article {Gatesy1993_188,
	title = {Alignment ambiguous nucleotide sites and the exclusion of systematic data},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {2},
	number = {2},
	year = {1993},
	pages = {152{\textendash}157},
	author = {Gatesy, J. and DeSalle, R. and Wheeler, W.}
}
@article {GoertzenEtAl2003,
	title = {{ITS} secondary structure derived from comparative analysis: Implications for sequence alignement and phylogeny of the {Asteraceae}},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {29},
	year = {2003},
	pages = {216{\textendash}234},
	author = {Goertzen, L.R. and Cannone, J.J. and Gutell, R R. and Jansen, R.K.}
}
@article {Hudelot03,
	title = {{RNA}-based phylogenetic methods: Application to mammalian mitochondrial {RNA} sequences},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {28},
	year = {2003},
	pages = {241{\textendash}252},
	author = {Hudelot, C. and Gowri-Shankar, V. and Jow, H. and Rattray, M.and Higgs, P.G.}
}
@article {Kjer1995,
	title = {Use of r{RNA} secondary structure in phylogenetic studies to identify homologous positions: an example of alignment and data presentationfrom the frogs},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {4},
	number = {3},
	year = {1995},
	pages = {314{\textendash}330},
	author = {Kjer, K.M.}
}
@article {Nadler1998_368,
	title = {Ribosomal {DNA} and phylogeny of the {Ascaridoidea (Nemata: Secernentea}): Implications for morphological evolution and classification},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {10},
	number = {2},
	year = {1998},
	pages = {221{\textendash}236},
	author = {Nadler, Steven A. and Hudspeth, Deborah S. S.}
}
@article {NadlerEtal2006,
	title = {Phylogeny of {Cephalobina ({Nematoda})}: Molecular evidence for recurrent evolution of probolae and incongruence with traditional classifications},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {40},
	year = {2006},
	pages = {696{\textendash}711},
	author = {Nadler,S.A. and De Ley, P and Mundo-Ocampo, M. and Smythe, AB and Stock, S.P. and Bumbarger, D. and Adams, B.J. and De Ley, I. T. and Holovachov, A. and Baldwin, J.G.}
}
@article {Near1998_376,
	title = {Phylogenetic relationships of the Acanthocephala inferred from 18S ribosomal DNA sequences},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {10},
	year = {1998},
	pages = {287{\textendash}298},
	author = {Near, Thomas J. and Garey, James R. and Nadler, Steven A.}
}
@article {Slowinski1998,
	title = {The number of multiple alignments},
	journal = {Molecular phylogenetics and evolution},
	volume = {10},
	number = {2},
	year = {1998},
	pages = {264{\textendash}266},
	author = {Slowinski, Joseph B.}
}
@inbook {Slowinski2001_475,
	title = {Molecular polytomies},
	booktitle = {Molecular Phylogenetics and Evolution},
	volume = {19},
	year = {2001},
	pages = {114{\textendash}120},
	author = {Slowinski, Joseph B.}
}
@inbook {Tarrio2000_502,
	title = {Tree rooting with outgroups when they differ in their nucleotide composition from the ingroup: The Drosophila saltans and willistoni groups, a case study.},
	booktitle = {Molecular Phylogenetics and Evolution},
	volume = {16},
	year = {2000},
	pages = {344{\textendash}349},
	author = {Tarrio, Rosa and Rodriguez-Trelles, Francisco and Ayala, Francisco J.}
}
