@article {Nielsen:2002zr,
	title = {Mapping mutations on phylogenies},
	journal = {Systematic Biology},
	volume = {51},
	year = {2002},
	pages = {729-739},
	publisher = {TAYLOR \& FRANCIS INC},
	address = {325 CHESTNUT ST, SUITE 800, PHILADELPHIA, PA 19106 USA},
	abstract = {Mapping of mutations on a phylogeny has been a commonly used analytical tool in phylogenetics and molecular evolution. However, the common approaches for mapping mutations based on parsimony have lacked a solid statistical foundation. Here, I present a Bayesian method for mapping mutations on a phylogeny. I illustrate some of the common problems associated with using parsimony and suggest instead that inferences in molecular evolution can be made on the basis of the posterior distribution of the mappings of mutations. A method for simulating a mapping from the posterior distribution of mappings is also presented, and the utility of the method is illustrated on two previously published data sets. Applications include a method for testing for variation in the substitution rate along the sequence and a method for testing whether the d(N)/d(s) ratio varies among lineages in the phylogeny.},
	keywords = {data augmentation, DNA sequence evolution, Markov chain Monte Carlo, phylogenetics},
	doi = {DOI 10.1080/10635150290102393},
	author = {Nielsen, R}
}
@article {Near2002,
	title = {Acanthocephalan phylogeny and the evolution of parasitism},
	journal = {Integrated and Comparative Biology},
	volume = {42},
	number = {668-677},
	year = {2002},
	author = {Near, Thomas J.}
}
@article {Soetaert:2002tg,
	title = {Size and shape of ocean margin nematodes: morphological diversity and depth-related patterns},
	journal = {Marine Ecology-Progress Series},
	volume = {242},
	year = {2002},
	pages = {179-193},
	publisher = {INTER-RESEARCH},
	address = {NORDBUNTE 23, D-21385 OLDENDORF LUHE, GERMANY},
	abstract = {We studied the composition and variation of nematode body size as a function of nematode depth in the sediment and water depth at 18 stations, ranging from 137 to 4951 m depth, along the Galician margin (NE Atlantic). The analysis is based on more than 10 000 individuals and demonstrates that nematodes have adapted mainly in response to the vertical changing conditions in the sediment. Nematode length and width are similar in the upper 0.5 cm of sediment at all stations, but differ greatly as their depth in the sediment increases. The observed trends are consistent with an adaptation to changing oxygen concentrations in the sediments. In lower slope and abyssal plain stations, oxygen decreases gradually until depletion at about 5 cm depth, and nematode body width decreases concurrently, resulting in higher oxygen absorption efficiency per unit of volume. On the shelf and in the canyons, sediments become anoxic at short distances below the sediment-water interface, and more than 50\% of the nematodes are present in the anoxic part of the sediment. Here, mean nematode length increases as their depth in the sediment increases. This may result in increased mobility, which enables the organisms to migrate between anoxic patches of food and parts of the sediment where oxygen is available and/or the ability to bridge the gap between oxic and anoxic patches with their body. Order of magnitude calculation shows that in shelf sediments, the chemosynthetic bacterial production, which accompanies the oxidation of reduced substances, can not fulfill the feeding requirements of nematodes in the anoxic zone. The different size adaptations with sediment depth in shallow as compared to deep stations combined with deeper penetration of nematodes into the sediment at shallow water depth cause the observed pattern of miniaturization with increasing water depth. We conclude that nematode size distribution is determined by food availability. However, organic matter, as a food source, is not directly responsible,,as a limiting resource, but indirectly because its respiration generates reduced conditions in the sediment. Within the smaller size range (<500 mum length), there are 2 clearly distinct morphological types, which, to a certain extent, impart a taxonomic division. Similar findings at other localities suggest that this is a common feature of nematodes from ocean margin areas. One group consists of corpulent nematodes, which are less than 15 times as long as wide; most prominent in this group are members of the order of the Desmoscolecida. The other group contains significantly more slender nematodes and comprises a large variety of nematode taxa. We hypothesize that this duality in nematode design reflects an ecological adaptation designed to meet the conflicting requirements of either increased mobility (slender) or reduced vulnerability to predation (corpulent) at these small sizes.},
	keywords = {nematodes, ocean margin, sediment biogeochemistry, size-depth hypothesis},
	author = {Soetaert, K. and Muthumbi, A and HEIP, C}
}
@article {Bleidorn:2002zl,
	title = {Systematic relationships of Nematomorpha based on molecular and morphological data},
	journal = {Invertebrate Biology},
	volume = {121},
	year = {2002},
	pages = {357-364},
	publisher = {AMER MICROSCOPICAL SOC},
	address = {810 EAST 10TH ST, LAWRENCE, KS 66044-8897 USA},
	abstract = {We sequenced the 18S rRNA gene from 11 nematomorph species from 9 genera and derived hypotheses concerning the sister group of Nematomorpha and relationships within this taxon. The molecular and morphological data are consistent with the monophyly of Nematomorpha, a sister-group relationship between Nematomorpha and Nematoda, and a sister-group relationship between the marine genus Nectonema and all of the freshwater taxa, Gordiida. Hypotheses of relationships within Gordiida support the traditional taxa Gordiidae, Chordodidae, and Chordodinae but reject Paracbordodinae and Spinochordodidae. The molecular results differ from those of previous morphological studies by suggesting a reduction of the two tail lobes at the posterior end of males in Chordodinae, monophyly of the genus Paragordionus, and paraphyly of the genus Chordodes.},
	keywords = {Gordiida, Nectonema, Nematoda, phylogeny},
	author = {Bleidorn, C and Schmidt-Rhaesa, A and Garey, JR}
}
@booklet {Sanderson:2002ta,
	title = {Troubleshooting molecular phylogenetic analyses},
	volume = {33},
	year = {2002},
	note = {Annual Review of Ecology and Systematics},
	pages = {49-72},
	publisher = {ANNUAL REVIEWS},
	address = {4139 EL CAMINO WAY, PO BOX 10139, PALO ALTO, CA 94303-0139 USA},
	abstract = {The number, size, and scope of phylogenetic analyses using molecular data has increased steadily in recent years. This has simultaneously led to a dramatic improvement in our understanding of phylogenetic relationships and a better appreciation for an array of methodological problems that continue to hinder progress in phylogenetic studies of certain data sets and/or particular parts of the tree of life. This review focuses on several persistent problems, including rooting, conflict among data sets, weak support in trees, strong but evidently incorrect support, and the computational issues arising when methods are applied to the large data sets that are becoming increasingly commonplace. We frame each of these issues as a specific problem to be overcome, review the relevant theoretical and empirical literature, and suggest solutions, or at least strategies, for further investigation of the issues involved.},
	keywords = {algorithm, data partition, long-branch attraction, model, rooting},
	doi = {DOI 10.1146/annurev.ecolysis.33.010802.150509},
	author = {Sanderson, MJ and Shaffer, HB}
}
@article {BlairEtAl2002,
	title = {The evolutionary position of nematodes},
	journal = {BMC Evolutionary Biology},
	volume = {2},
	number = {1},
	year = {2002},
	pages = {1-7},
	abstract = {BACKGROUND:The complete genomes of three animals have been sequenced by global research efforts: a nematode worm (Caenorhabditis elegans), an insect (Drosophila melanogaster), and a vertebrate (Homo sapiens). Remarkably, their relationships have yet to be clarified. The confusion concerns the enigmatic position of nematodes. Traditionally, nematodes have occupied a basal position, in part because they lack a true body cavity. However, the leading hypothesis now joins nematodes with arthropods in a molting clade, Ecdysozoa, based on data from several genes.RESULTS:We tested the Ecdysozoa hypothesis with analyses of more than 100 nuclear protein alignments, under conditions that would expose biases, and found that it was not supported. Instead, we found significant support for the traditional hypothesis, Coelomata. Our result is robust to different rates of sequence change among genes and lineages, different numbers of taxa, and different species of nematodes.CONCLUSION:We conclude that insects (arthropods) are genetically and evolutionarily closer to humans than to nematode worms.},
	issn = {1471-2148},
	doi = {10.1186/1471-2148-2-7},
	url = {http://www.biomedcentral.com/1471-2148/2/7},
	author = {Blair, Jaime and Ikeo, Kazuho and Gojobori, Takashi and Hedges, S Blair}
}
@article {Blouin2002_52,
	title = {Molecular prospecting for cryptic species of nematodes: Mitochondrial DNA versus internal transcribed spacer},
	journal = {International Journal for Parasitology},
	volume = {32},
	number = {5},
	year = {2002},
	pages = {527{\textendash}531},
	author = {Blouin, Michael S}
}
@article {Bonnet2002,
	title = {zt: a software tool for simple and partial {Mantel} tests},
	journal = {Journal of Statistical Software},
	volume = {7},
	number = {10},
	year = {2002},
	pages = {1{\textendash}12},
	author = {Bonnet, E. and Van de Peer, Y.}
}
@inbook {Bromham2002_60,
	title = {Testing the relationship between morphological and molecular rates of change along phylogenies},
	booktitle = {Evolution},
	volume = {56},
	year = {2002},
	pages = {1921{\textendash}1930},
	author = {Bromham, L. and Woolfit, M. and Lee, M. S. Y. and Rambaut, A.}
}
@article {CannoneEtAl2002,
	title = {The {Comparative RNA Web (CRW) Site}: An Online Database of Comparative Sequence and Structure Information for Ribosomal, Intron, and other {RNA}s. {Available} at http://www.rna.icmb.utexas.edu/},
	journal = {BMC Bioinformatics},
	volume = {3},
	year = {2002},
	pages = {15.},
	author = {Cannonne, J J. and Subramanian, S. and Schnare, M N. and Collett, J R. and D{\textquoteright}Souza, L M. and Du, Y. and Feng, B. and Lin, N. and Madabusi, L V. and Muller, K M. and Pande, N. and Shang, Z. and Yu, N. and Gutell, R R.}
}
@article {DeLey2002,
	title = {Phylogenetic analyses of \emph{Meloidogyne} small subunit r{DNA}},
	journal = {Journal of Nematology},
	volume = {34},
	number = {4},
	year = {2002},
	pages = {319{\textendash}327},
	author = {De Ley, I. T. and De Ley, P and Vierstraete, A and Karssen, G. and Moens, M and Vanfleteren, J.}
}
@article {DeLey2002_128,
	title = {Video capture and editing as a tool for the storage, distribution, and illustration of morphological characters of nematodes},
	journal = {Journal of Nematology},
	volume = {43},
	number = {4},
	year = {2002},
	pages = {296{\textendash}302},
	author = {De Ley, P and Bert, W.}
}
@book {DeLey2002_131,
	title = {Gulf of CA Marine Nematode Bioinventory proposal-unsure of actual project title},
	year = {2002},
	author = {De Ley, P and Baldwin, J.}
}
@inbook {DeLeyandBlaxter2002,
	title = {Systematic Position and Phylogeny},
	booktitle = {The Biology of Nematodes},
	year = {2002},
	pages = {pp. 1{\textendash}30},
	publisher = {Taylor and Francis},
	organization = {Taylor and Francis},
	address = {London},
	author = {De Ley, P and Blaxter, M. L.},
	editor = {Lee, D.L.}
}
@article {Elbadri2002,
	title = {Intraspecific variation in \emph{Radopholus similis} isolates assessed with restriction fragment length polymorphism and {DNA} sequencing of the internal transcribed spacer region of the ribosomal {RNA} cistron},
	journal = {International Journal for Parasitology},
	volume = {32},
	number = {2},
	year = {2002},
	pages = {199{\textendash}205},
	author = {Elbadri, G.A.A. and De Ley, P and Waeyenberge, L and Vierstraete, A and Moens, M and Vanfleteren. J.}
}
@article {Geiger2002_191,
	title = {Stretch coding and block coding: Two new strategies to represent questionably aligned DNA sequences},
	journal = {Journal of Molecular Evolution},
	volume = {54},
	year = {2002},
	pages = {191{\textendash}199},
	author = {Geiger, D. L.}
}
@inbook {GiribetEtAl2002,
	title = {{DNA} multiple sequence alignments},
	booktitle = {Molecular Systematics and Evolution: Theory and Practice},
	year = {2002},
	pages = {107{\textendash}114},
	publisher = {Birkhauser Verlag},
	organization = {Birkhauser Verlag},
	address = {Switzerland},
	author = {Giribet, Gonzalo and Wheeler, Ward C. and Muona, Jyrki},
	editor = {DeSalle, Roberto and Wheeler, Ward C.}
}
@inbook {HopeIA2002,
	title = {Embryology, developmental biology and the genome},
	booktitle = {The Biology of Nematodes},
	year = {2002},
	pages = {121{\textendash}145},
	publisher = {Taylor and Francis},
	organization = {Taylor and Francis},
	address = {London},
	author = {Hope, I.A.},
	editor = {Lee, D.L.}
}
@article {Hudson2002_244,
	title = {Mathematical consequences of the genealogical species concept},
	journal = {Evolution},
	volume = {56},
	number = {8},
	year = {2002},
	pages = {1557{\textendash}1565},
	author = {Hudson, R. R. and Coyne, J. A.}
}
@inbook {Jones2002,
	title = {Nematode sense organs},
	booktitle = {The Biology of Nematodes},
	year = {2002},
	pages = {353{\textendash}368},
	publisher = {Taylor and Francis},
	organization = {Taylor and Francis},
	address = {London},
	author = {Jones, John},
	editor = {Lee, D.L.}
}
@inbook {Justine2002,
	title = {Male and female gametes and fertilisation},
	booktitle = {The Biology of Nematodes},
	year = {2002},
	pages = {73{\textendash}119},
	publisher = {Taylor and Francis},
	organization = {Taylor and Francis},
	address = {London},
	author = {Justine, J.},
	editor = {Lee, D.L.}
}
@inbook {Leroy2002_302,
	title = {Sequence analysis of the GP, NP, VP40 and VP24 genes of Ebola virus isolated from deceased, surviving and asymptomatically infected individuals during the 1996 outbreak in Gabon: comparative studies and phylogenetic characterization},
	booktitle = {Journal of General Virology},
	volume = {83},
	year = {2002},
	pages = {67{\textendash}73},
	author = {Leroy, E. M. and Baize, S. and Mavoungou, E. and Apetrei, C.}
}
@inbook {Machado2002_323,
	title = {Inferring the history of speciation from multilocus DNA sequence data: The case of Drosophila pseudoobscura and close relatives},
	booktitle = {Molecular Biology \&amp; Evolution},
	volume = {19},
	year = {2002},
	pages = {472{\textendash}488},
	author = {Machado, C. A. and Kliman, R. M. and Markert, J. A. and Hey, J.}
}
@article {Nadler2002_373,
	title = {Species delimitation and nematode biodiversity: phylogenies rule},
	journal = {Nematology},
	volume = {4},
	number = {5},
	year = {2002},
	pages = {615{\textendash}625},
	author = {Nadler,S.A.}
}
@booklet {OBrien2002,
	title = {Guide to Python Introspection: How to spy on your python objects},
	year = {2002},
	publisher = {Orbtech},
	author = {O{\textquoteright}Brien, Patrick K.}
}
@article {Poiras2002,
	title = {\emph{Nothacrobeles} \emph{borregi} n. sp. ({Nematoda}: {Cephalobidae}) from {Anza} {Borrego}, {California} and \emph{N.} \emph{laticollaris} ({De Ley} \& {Vandebroek}, 1992) n. comb.},
	journal = {Nematology},
	volume = {4},
	number = {7},
	year = {2002},
	pages = {865{\textendash}874},
	author = {Poiras, L. and Baldwin, J.G. and Mundo-Ocampo, M. and Bumbarger, D.J.}
}
@article {HolovachovEtAl2002,
	title = {Morphology and systematics of the genera \emph{Wilsonema} Cobb, 1913, \emph{Ereptonema} Anderson, 1966 and \emph{Neotylocephalus} Ali, Farooqui \&amp; Tejpal, 1969 ({Leptolaimina: Wilsonematinae})},
	journal = {Journal of Nematode Morphology and Systematics},
	volume = {5},
	number = {1},
	year = {2002},
	pages = {73{\textendash}106},
	author = {Holovachov, O. and Bostr{\"o}m, S. and De Ley, I. Tandingan and De Ley, P and Coomans, A.}
}
@inbook {Slowinski2002_476,
	title = {Snake phylogeny: evidence from nuclear and mitochondrial genes},
	booktitle = {Molecular Phylogenetics \&amp; Evolution},
	volume = {24},
	year = {2002},
	pages = {194{\textendash}202},
	author = {Slowinski, J. B. and Lawson, R.}
}
@inbook {Stock2002_490,
	title = {Panagrobelus stammeri Ruhm, 1956 and Plectonchus hunti n. sp.: implications of new morphological observations for characterisation of these genera (Nematoda : Panagrolaimoidea)},
	booktitle = {Nematology},
	volume = {4},
	year = {2002},
	pages = {403{\textendash}419},
	author = {Stock, S.P. and De Ley, P and De Ley, I. and Mundo-Ocampo, M. and Baldwin, J.G. and Nadler,S.A.}
}
@inbook {Stothard2002_491,
	title = {Evolution of the PP2C family in Caenorhabditis: Rapid divergence of the sex-determining protein FEM-2},
	booktitle = {Journal of Molecular Evolution},
	volume = {54},
	year = {2002},
	pages = {267{\textendash}282},
	author = {Stothard, P. and Hansen, D. and Pilgrim, D.}
}
@inbook {Vollmer2002_526,
	title = {Hybridization and the evolution of reef coral diversity},
	booktitle = {Science},
	volume = {296},
	year = {2002},
	pages = {2023{\textendash}2025},
	author = {Vollmer, S. V. and Palumbi, S. R.}
}
@inbook {deBono2002_113,
	title = {Social feeding in Caenorhabditis elegans is induced by neurons that detect aversive stimuli},
	booktitle = {Nature},
	volume = {419},
	year = {2002},
	pages = {899{\textendash}903},
	author = {de Bono, M. and Tobin, D. M. and Davis, M. W. and Avery, L. and Bargmann, C. I.}
}
@article {deSkowronskiAndCorbisier2002,
	title = {Meiofauna distribution in {Martel Inlet, King George Island (Antarctica)}: sediment features versus food availability},
	journal = {Polar Biology},
	volume = {25},
	year = {2002},
	pages = {126-134},
	author = {de Skowronski,R.S.P. and Corbisier, T.N.}
}
