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Contributions Cladistic analyses of molecular characters: The 71 Zoology, to SPB Academic (1/3) 93-100 (2002) The Hague Publishing bv, and the good, the bad ugly Maximilian+J. Telford Museum University email: of Zoology, Department of Zoology, Downing Street, Cambridge Keywords: molecular synapomorphy, phylogeny, rare Abstract heritable that racter. molecular is a traditional Taxa that an other than point they out problems are that molecular treat derived specific to other taxa as more and illustrate a treated characters are which in molecular closely genomic change, RGC, Metazoa, cladistics susceptible as Herein, to the The same morphological towards a from the Metazoa. genetic ods of Contents ing. Mitochondrial acoel in gene the EF1 94 apparent Mitochondrial genetic Indels codes order in alpha gene 94 birds 95 and the position of the flatworms gene fusions with 96 due to secondary loss of a novel domain combinations aligned approach and a genetic codes: 96 the - the in the gene signatures: Conclusions that is Rather, complemen- heritable characteristics variety of characters way that same a deal amino acids or this not of the used is cladist would morphological character. In such molecular cladistic studies, character (synapomorphies) sharing taxa closely related lacking this novel a to each other than As character. in derived or inferred are they to be are more to taxa morphology-based plesiomorphy) close be cannot as indicator of an relationship. tics used to date have been covered in Rokas and by Holland touched on some of their 97 the taken an excellent who also (2000), echinoderms hemichordates the priapulids does appreciated manner. treats and - steadily improv- of nucleotides sequences in the customary review Mitochondrial are phylogenetics Examples of the diverse molecular characteris- charac- Polarity Hox increasingly ever cladistics, the sharing of a primitive character (sym95 Introns Apparent homoplasy Molecular faster and meth- 95 Contradictory stories from and accumulating 93 and steady expansion phylogenetics. One strand of molecular becoming use real the seen phylogenetic analysis impressive Introduction years have data are genome Homoplasy: 15 past of the field of molecular tary ter: UK; cha- characters characters. polarity any same related to each these problems (and point general solution) using examples the morphological without these of homoplasy and uncertain characters be can cladist would share in emerging discipline characteristic (synapomorphies) are recognized I 3EJ, Introduction cladistics Molecular way CB2 [email protected] dicyemid examine in more shortcomings. detail the mesozoans 98 using Molecular Synapomorphies 99 Rare Acknowledgments 99 References 99 Genomic Holland). some I will suffer Changes show from the - 1 want potential pitfalls RGCs (referred - assessment as by that, perhaps unsurprisingly, same problems as morphological characters, lies in homology to Rokas and morpho- logical characteristics but that their strength, tive to to when the rela- ease of molecular characters. of 94 M.J. real and Homoplasy: 1 would like to distinction between real and apparent a ho- moplasy. Homoplasy entails the parallel evolution of a character state in particular through eages sion. In truth, because most in arise ters unrelated lin- two parallelism convergence, type, it is highly unlikely that but fact pheno- in moplasy. The homoplasy problem arises because we can rarely know enough about character (for molecular tic bristle example developmental basis for on fly’s leg) a morphological a investigate cannot we phological analyses generally have identity. rely to the diagnos- every ascertain to on Mor- overall strength of phylogenetic signal within the totality of the data the set to reveal homoplasy in (hopefully) minority of characters. Traditional molecular analysis of molecular characters genetic code, a of the genome significant It event. the hundreds (or in the of case of specificity the anticodon of or a small hugely for happen suddenly, cannot example by changing synthetase that of the even eukaryotic mitochondrion, is a tRNA, tRNA a tens as or nuclear genome many a thousands) of amino acids would be swapped and this would affect almost every be lethal. The protein and would likely mechanism for more change is, rather, the gradual, apparent ho- to Changing certainly mor- appear identical leading unrelated a independently character could arise in are to truly identical a lineages. Characters only separate fashion to alterations developmental pathways and finally phological rever- morphological charac- involving genotypic changes leading in or immensely complicated an Cladistic Mitochondrial genetic codes apparent For the purposes of this discussion make - Telford certain codon followed Castresana et al., its by in gradual reintroduction complete loss of its Even 1998). happen guise (see the so, clearly immensely complex and potential less to likely, there can be of 19 others (or likely, equally happened, there is only change would a from to changes that allowing I codon) If all stop codon). even to reassign- reassigned the incumbent amino acid (or stop same unlikely seems 64 codons with the are and each change e.g. process is often. To make convergent codon ment even and reassignment new a any were change has a in 1280 chance that the in two occur independent lin- phylogenetic efforts suffer eages. from the with opposite problem; it is usually certainty character - a that one is easy with dealing to know Considering the unlikeliness reassignment, particular amino acid at a particular are within position due the low to for protein, a diversity of However, example. potential character multiple is or amino 20 prevalent because, independent a I or specific position in in 20 chance, two 1 a ment of two codons The that the novel state ought identical. synapomorphies' of molecular great strength to be that they avoid both of these Being molecularly based it is identity between characters easy to genotypic See layers, “What You Is and What moreover, because these characters order of tween complexity nucleotides should not be are various a than or simple species problem. What surprising cases we a higher be- homoplasy find, however, homoplasy af- fecting these molecular characters and of these below. of substitutions of real (Telford et and the al., 2000). reassignments are seen: In the codon reassigned from coding for Lysine from 1 discuss include UAA and UAG codons STOP to being Glutamine - You Get” amino acids, real echinoderms independently reassigned from development- are of the coding for Asparagine and AUA reassigned convergence in al one problems. morphological cha- racters with their hidden eukaryotic Perhaps Methionine to Isoleucine. Other clear instances of to be certain of in different with molecular characters, unlike in the flatworms same AAA has been will be nuclei. even in 4 both taxa the respectively, of this within striking examples is the convergent reassign- changes taxa, there is surprising instances rhabditophoran at convergent codon to discover that there states acids) real homoplasy given it is mitochondria and most (4 nucleotides of identical an some the nuclear genomes of ciliates and the green diplomonads, several alga Acetabularia acetabu- lum and UGA reassigned from STOP to Tryptophan five separate times in the mitochondria of various eukaryotic groups (Knight Fortunately, thanks netic information, we are example, are eration of mitochondrial sources of not mislead into that the echinoderms and the for worms, al., 2001). et to other phylogebelieving rhabditophoran sister-groups, flat- but consid- genetic codes highlights Contributions 71 Zoology, to the need to understand how it to use changes ever as in a molecular certain changes are 95 trait evolves if one is a equal; due not are for whatever or 2002 - synapomorphy. Clearly genetic code constraint (1/3) more likely adaptive all what- to reasons, than others. to occur discussed above instead vertebrate code with of the sence the Rhabditophora. result, Berney Mitochondrial gene order in birds is arrangements event. There in the are circular which also, 13 the face of it, on 2 proteins, ferent ways. the Despite genome, in 2*10 52 dif- vanishingly small prob- ability of independent adoption of any specific novel it arrangement, ment of three contiguous and Glutamic drial control occasions al., has been shown that region has occurred at on 1994). Of from least 4 separate inversions of sections of genomes have also been and Palmer, ment to the mitochon- the evolution of birds (Mindell 1998). Parallel chloroplast rearrange- (Proline-tRNA, ND6, genes acid-tRNA) relative during a course, position A to et plant reported (Hoot shifting position a B single frag- has et In al. direct contradiction of this found (2000) alpha rhabditophoran flatworms and thors Based Once able the again, gene shared on an a short by one acoel, group these au- Rhabditophora. it turns that wider out sampling again was showed importance of understanding the evolution the character. the Littlewood region of same cies of acoel and peptide motif. of in fact derived are resolve this contradiction and to peptide Convoluta this observation that the acoels suggested from within the and 22 tRN As rRNAs, theoretically be arranged can unlikely an mitochondrial metazoan gene in- The ab- derived from within not are motif in the EFI roscoffensis. Convergent evolution of novel mitochondrial other animals. rhabditophoran novelties demonstrates that the acocls clearly sharing the standard most EF1 et al. alpha from 3 further spe- found that all three On of (2001) sequenced the other hand, lacked the menagerie of a other metazoans (molluscs, annelids, nematodes and chordates) did have the character mation. This persuasive of phoran or a close approxi- particular character, although initially a link between acoels and rhabdito- flatworms, proved unreliable due ho- to moplasy. much a higher likelihood of convergence than suggested by the probability quoted above, but the tendency for repeated evolution of ment might also point a particular novel to an some dense prior knowledge of bird sampling and through phylogcny. assumption that parallel changes gene order caused us are hugely unlikely to reconstruct an in An a priori mitochondrial could incorrect easily have phylogcny. In the example cally be must (3-thymosin tide in the be gene and the position of the acoel flatworms triplicated years. other flatworms, the plete gut, the two Although, acoels lack a groups share a in lot showed are of contro- coelom and no not com- other obvious suggest unrelated and Telford et al. that the acoels do with common features. Ribosomal RNA phylogenies two groups and we one On as the a have two con- of which logi- the (2000) share the rhabdito- phoran flatworm mitochondrial genetic code changes hand, the one single short pep- of metazoans, has been shown to serially arthropods (Manuel seemingly et linked in nematodes and al., 2000). This unusual char- gives Hypothesis' strong a the to support that postulates clade of moulting animals including nematodes and arthropods. On the other hand, the Glutamyl The acoel flatworms have caused recent homoplastic. majority aminoacyl versy in below, gene, which exists Ecdysozoa EF1alpha I describe molecular characters, tradictory acter Indels in the stories from gene fusions arrange- underlying constraint. Importantly, this constraint could only be inferred through sufficiently Contradictory genes in and the are found including which the yeast plant Arabidopsis and also to tein in both This synthetases, most taxa ces and tRNA be fused into a and are Prolyl separate Saccharomyin nematodes, single, bifunctional pro- arthropods and vertebrates (Bcrthonneau Mirande, finding 2000 and seems to unpublished Ecdysozoa Hypothesis, flies to the vertebrates than observations). suggest that, contrary they are are more closely to the related to the nematodes. 96 M.J. Clearly one of these two characters must be homoand nematodes plastic. Perhaps arthropods deed ecdysozoan nematodes have reverted to the for RNA two in which sister-groups, if the coelomate vertebrates either is the to the and convergently. On or has been then correct share not closely related than todes, then unique domain combinations. lost in secondarily What find is we taxa is needed from worms one of these characters is look for all the Meanwhile, homoplastic. be the result of very rare of them must indeed point is made that, seem the face of it to on genetic events, have occurred one or other convergently. mains a number of domain large combinations of in two out pairs of protein three metazoans by by humans and flies. If humans and worms, by and worms, and Introns Should this 12 destroy We shared our 3 we we look for find shared Ecdysozoa Perhaps less suiprising than the previous examples, Hypothesis? it without closer examination of these results. is becoming or presence absence of synapomorphy (but by is not no means when tors of and than and The molecular some cases less reliable thought (Krzywinski Wada et al., a readily phylogenetic relationship have been as using the adequately sampled, are prove that reliable. In always all) lost and hence intron an becomes clear that introns edly clear increasingly as it probably not, is elegans certainly model a rapidly in the a very species It is laboratory. indica- small and constant cell number and has once mode of Examination 2002). and development an genome associated with these of the genes an Apparent homoplasy due to secondary loss of other taxa, in has evolved atypical its of the joining mains only in a supports (unpublished is Tyrosine a the the and choanoflagellates. in the do- found This presumed link between Metazoa. This work led collaboration with Rob Russell and Aloy, EMBL, Heidelberg) to look for novel combinations of protein domains in the sequenced Kinase combination comprising the Metazoa and their choanoflagellates Patrick the and single protein sister-group; observation the EGF in the clade possible us (2001) have demonstrated that the genomes of human, fly completely and nematode hope that unique domain combinations might it a has been order to make up for in lacks in brainpower. The we of C. are can see elegans derived. The genes (derived) reveals homologs it has are new genes, for probably evolved in hardwiring what the worm upon that the genes and the of this is that many of its to have been secondarily lost and analyses I formative present, unreliable because and, reasonably at of character be ge- highly unusual and highly this fact makes the distribution ex- chemoreception which, were significance likely lost the other hand, it point of these observations is that, reflection, nome on large number of postulated, a atypical genome evolving; and, those associated with ample Caroll fast are several of its Hox genes a character: Novel domain combinations King and most has lifestyle constraints. various oddities. Of its genes with clear in reproduce small, very Besansky, 2002; not derived animal. C. selected to repeat- might least at problem here lies with Caenorhabditis ele- which is gans, none by flies by humans and flies. confidence in the think by flies and worms, all combinations of three domains then shared we do- find 20 shared we humans and worms, 29 shared and 276 shared mentioned. If of the and absent in the out-groups com- humans and absent and the out-groups present nema- might share certain to flies and common to discover two the exclusion of to then flies and humans binations is to worms Hypothesis is correct, which and humans arthropods nematodes, and out-groups (fungi and plants). or If the older, Coelomate sampling of sister although both characters might expect flies we in humans links flies Ecdysozoa Hypoth- Ecdysozoa Hypothesis unique combinations of protein domains some seen test the to If the (see above). vertebrates. Further which analysis of molecular characters provide characters esis (3-thymosin is either convergent worms Cladistic and pseudocoelomate of triplication in flies and more state arthropods or coelomate are either case primitive, unfused a synthetases vertebrates have fused their genes the other hand, are in- - Telford presented above unin- states we observe explained by the secondary the could loss of Contributions to of these many Zoology, 71 (1/3) in the characters 2002 - 97 of ancestry the nematode. What we in all of these see true of equally two factors cases and this is - morphological characters important in order are by homoplasy, real it is desirable to not to be fooled apparent. First and foremost, or sample widely. Only through that certain code a sam- can we changes in mitochondrial genetic sampling of the Metazoa stand where and when these code in this clade. can under- we changes occurred one are expect a certain character unrelated lineages or, genome, The be to evolve to in the as case highlights when performing such studies; further be assessed in both is generally preferable sent to be of or to genes unless in elegans ele- taxa in character that a derived a can it is present in the cause ancient impossible certain character is absent in pointed by Rokas out of evidence is not the The inability clone to a genome and Holland same as a warm the likely can is absent in to see we are the more considering, the a a same rea- derived cha- frog. The use of which character state see bloodedness) is primitive and which derived is procedure known a This is simply an as out- argument from parsimony because, in this example, if warm bloodedness were the primitive once it state would have to and then been lost frogs and once pretation requires in lizards; twice; once the alternative inter- that it has evolved just once in mammals. Character is polarity just important as molecular characters and below I when give two a prove because, (2000), three bloodedness should be it We primitive character be- primitive. Following or warm sequenced to to the rabbit frog which, being than the early diverging frog (cold a the other ab- secondary loss (cases dealing with completely is often all but is racter because using genomes, it lineage assume soning, commonplace) and further- are peculiar on state as seem any of these to bloodedness, Warm derived character a in determin- help of the rabbit quadru- the ancestor and the horse and absent in the lizard. in to particular. hand, is have evolved that is coded one relationship group comparison. important consideration particularly susceptible more, the is in fact all by even of horses. This character cannot (therefore) Molecular characters present. missing of the C. primitive and a might repeatedly lost genes of C. secondarily gcins a we lost? secondarily of the case primitive we underlying molecular reasons why any character that is shared peds: rabbits, lizards, frogs and must understand the charac- ter and its evolution. We should ask whether there bloodedness warm horse. that the five toed foot is Secondly, and hopefully this follows from the first, the Considering first the five-toed foot; this a ing happen relatively frequently, and only through broad on is that - pling many lineages within the eukaryotes see five-toed foot with the lizard and with examples of when this has been problematic. as absence evidence of absence. certain DNA sequence does Mitochondrial genetic codes: The echinoderms and hemichordates not demonstrate it does exist. not The hemichordates, long thought Polarity to be more dates than to the third As emphasised above, only the sharing of derived characters is informative relationships. Shared primitive place those larger clade of all absolutely taxa that have clear to anyone between about which simply them within (or had and those characters. To make this distics there follows lationship phylogenetic characters that possess species sequently lost) regarding we an a know not well sub- point versed in cla- example. Consider the rabbit, a the horse and a only that the rabbit shares a name closely group this close the and sister-group Degnan, position 1999; Halanych, above has been cited in a the chor- of deuterostomes; phylogenies the deny the hemichordates of the echinoderms in mitochondrial changes to were relationship between chordates and hemi- chordates and instead as suggests, related echinoderms. Recent molecular idea of re- lizard their as 1996). genetic support (Bromham One of this alternative hemichordate/echinoderm clade: assignment of the code discussed the re- in echinoderms of the codon AUA from coding for Methionine (Met) to coding for Isoleu- 98 MJ. cine (He) has been shown to recently heinichordates (Castresana that this character (AUA ously interpreted as al., et Upon closer inspection, He) is of the that it is Bilateria, parsimonious equally ther AUA Met, = one Knowing AUA or follows: (i) if AUA Bilateria this is the requires Met is = assume He = state. Each of these solutions close a show readily can to clear not that AUA also codes for He in the Cnidaria, out-group that ei- primitive changes 2 as primitive within the requires the change AUA He = its AUA to What had not been considered, In the absence of molog of this like be chozoan Hox primitive evolution of AUA convergent Met twice; in once the chordates and protostomes (Telford of the character AUA derms and in hemichordates has viding To (see update this story, it also that above) dclius et the acoels, character AUA follow be = AUA Met is parsimoniously morphy linking co- these two groups. increasingly likely flatworms branching bilaterians (Jon1999). in that, Met = al., et the suggests = If this basally that It would primitive. that the character AUA most the been conclu- acoelomorph then the observation true, in once = the interpreted as a synapo- hemichordates and echinoderms. fact being derived,) then in the dicyemids are peptide that the the gene signatures; dicyemid mesozoans and, and sozoan deuterostomian metazoan status of genes one or act can as more a is taken, approach properly considered is the the dicyemid mesozoan. shown that certain of specific Hox peptides genes were polarity of case It had a has Hox been not been gene of previously found in the homeoboxes associated with each of also shared by the the Hox genes closely possible to 1999). Kobayashi that a Hox contained one of the Lox5 gene that is clade. et al (1999) found in gene From this a were et al., able to show dicyemid mesozoan peptides characteristic of the specific to the lophotrochozoan they deduced that the mesozoan by arose related Hox out-group. mesozoan gives limited support for from within the When identify this certain ter is the derivation of mesozoans polarity of the charac- emphasise the significance of this approach, can consider the within the worms share are approach established (Telford, 2000). To one This gene. Lophotrochozoa but this result only becomes credible when the a relationship The protostomes. of the priapulid priapulids clearly Ubx/abdA- like gene with other protostomes Lox2 and Lox4 in the priapulid gene is lophotrochozoan clade) one most looks similar for to arthropod Ubx gene, priapulids share only residue with the Hypothesis, the the synapomorphic amino acids within this finds that the arthropods, all a ‘signa- however, group comparison of protostomes, as or other amino acids the By contrast, being present specific same to one single derived being either primitive, i.e., interpreted through the three great clades of bilaterian: deuterostomes, eedysozoans and lophotrochozoans (de Rosa The dispute. derived amino acids within the Lox5 gene that ture’ Another instance where the not in was of the proxy it is meta- crown-groups). mesozoans because Fortunately, duplication, When gene. priapulids meso- (although it does exclude them from the ecdy- but, consistent with the Ecdysozoa The primitive simply (called Hox the zoans then He could indeed in was zoan He in echino- = not linking seems al., 2002; Ruiz-Trillo branching AUA shared derived character pro- a additional evidence indeed the earliest are is to be requires to al., 2000). In short, the et occurrence sively shown He = equally parsimo- (the ecdysozoan and deutero- of the LOX5 shows possible like, ecdysozoan- can character states both discovery ho- a states primitive. If this lophotro- signature state for this character the the considered the was possessing out-group lophotrochozoan-like) or niously stomian within the Bialteria this an character (deuterostome Met to AUA is by (Telford, 2000). of this gene, each of the three Met at base of the Bilateria and the reversal AUA He suggested however, polarity of these Hox signatures = He in the echinoderms, (ii) if AUA metazoan simple morphology. = = analysis of molecular characters derived from within this clade rather than be- was parsimoni- most derived character. a Cladistic - ing the basally branching 1998). however, it is = in co-occur Telford the out- in the ancestor priapulid. comparisons offer over- whelming support (from polarised residues) for the notion that both to be basal Platyhelminthes (previously thought bilaterians) and Brachiopoda (previously widely believed are in fact to be related to the deuterostomes) lophotrochozoans (Telford, 2000). Contributions 71 Zoology, to (1/3) 2002 - 99 Conclusions The theme linking all of these potential problems 1-alpha sequences do not Acoela. Mol. Biol. Evol. Bromham stome with molecular characters is the need a how they evolve. In particular, sider the potential is vital to con- that homoplasy Rosa plesiomorphy of also are synapomorphy versus easily overlooked as sym- seen. of not want that molecular reliable. On give the impression synapomorphies the contrary, I very valuable their great do is to of source essentially are believe that un- Hoot are RA. ease of certaining homology between features of DNA, and of differing complexity that be can of features used, JD. J. only a Jenner Zool. superiority of molecular morphological studies. What ever, is the great RA, Schram phylogfiny: Jondelius Jenner, to is 1999; Jenner set and become to thanks to the and the quality of morphologi- Schram, an e.g. rules FR. and approach increasingly Platyhelminthes. Carroll King N, tool evolution. SB. Proc. keyboard: tools analysing them. thanks also on to the Chuck Cook, higher animals. Frederick Schram Dr Rob protein Evol. gene: chloroplast genome Evol. 38:274-281. a tool for evolutionary in application. grand Biol. game Rev. of metazoan 74:121-142. Riutort M. 2002. not The members of Scripla 31:201-215. A receptor tyrosine kinase from Sci. USA Landwcber the of 98:15032-15037. LF. 2001. Rewiring the genetic code. Nature Rev. a Holland H, NJ. 2002. cautionary PWH. 1999. Dicyemids 401:762. tale in Frequent intron loss forphylogeneticists. Mol. the Biol. 19:362-366. Littlewood D IM, Olson M. 2001, Elongation assist resolving helpful Russell domain comments on the in an ot PD,Telford MJ, Factor the I -alpha position Evol. Herniou sequences of EA, Riutort alone do not the Acoela within the 18:437-442. Muller WEG, Lc Parco Y. [3-thymosin homologues arthropod-nematode clade. J. 2000. The among Mol. Metazoa Evol. 51:378- and and Dr Patrick combination manuscript. Thanks Aloy for Mindell DP, Sorenson MD, collaboration Work referred independent origins to in Proc. Natl. Acad. Sci. tool Holland for phylogenetics. Ruiz-Trillo Baguna I, J. metazoans Bcrthonncau E, of Mirande M. 2000. A gene fusion aminoacyi-tRNA synthetases. event in FEES the Lett, J, Zaninetti L. 2000. Elongation factor 1999. not Rare T.R.E.E. M, order Multiple in birds. genomic changes flatworms: members of as a 15:454-459. Littlewood DTJ, Acoel 1998. gene 95:10693-10697. PWH. 2000. Riutort DE. Herniou EA, earliest bilaterian Platyhelminthes. Science 283:1919-1923. Telford, MJ. 2000. Turning phies. Evol. Dev. 6:360-364. 470:300-304. Pawlowski Dimcheff mitochondrial USA A, References evolution of this Rokas C, the 381. Jenner for manuscript. Bcrney 190:1-5. bilaterians and Nature Krzywinski J, Bcsansky supports Prof. apparatuses Bull. Mol. Baguna J, Natl. Acad. evolvability comparison Many feeding Molecular insights into early animal Metazoa. Mol. Biot. Dr Ronald I. basal 2001. Manuel M, Kruse M, Acknowledgements Dr in protostome 2:49-58. Genetics White rapidly expanding genomic databases to A, genes for discrepancies 1999. The Knight RD, Freeland SJ, phylogeneuseful Biol. within and Zool. choanoflagellates: are to Hox Structural rearrangements, strategies. Ruiz-Trillo U, Kobayashl M, Furuya 1999). increasingly powerful bioinformatic have for we shifting might well bring rewards (see This molecular cladistic tics emphasise, how- and would suggest that emphasis from quantity characters over advantage of using clearly homo- logous characters cal I will Adoutte CE, 129:245-262. the the 95:3703-3707. 1999. the phylogeny as problems I assert in genera. J. 1999. Metazoan current nemertodermatids are to 1994. and related few of which have been discussed here. Neither do want G. Codon hemichordate as- Belg. secondly in the almost limitless variety USA for 1:166-171. 1998, in implications interpretation. an information, strengths lying firstly in the deutero- pterobranch hemichordates revealed a biology: S. Cook T, Balavoine including parallel inversions, Jenner phylogenetic Dev. Paabo Sci. Convergence and Palmer of Anemone they Evol. composition Andreeva SB, 1996. 18S rDNA: SB, acid priapulids: lophophorates by What 1 do and Hemichordates Nature,399:772-776. Halanych KM. have we and brachiopods evolution. polarity and 1999. Natl. Acad. JK, Carroll JV'l, ensur- amino Proc. the molecular phylogenetic support echinoderm clade. + Grenier R, Akam by ing adequately dense sampling. The closely related issues of robust and mitochondria. de early divergence of an J, Feldmaier-Fuchs G, reassignment highly complex be best achieved always hemichordate Castrcsana are Understanding the evolution of charac- almost can it in what appear to be unexpected characters. ters problems of LD, Degnan BM. evolution: understand to support 17:1032-1039. Telford MJ, Herniou EA, Hox Russell ‘signatures’ into synapomor- RB, Littlewood DTJ. 2000. 100 M.J. Changes in characters: Acad. Sci. Wada mitochondrial genetic two USA examples from the codes as phylogenetic flatworms. Proc. Nall. Telford - Cladistic Shirayama in analysis of molecular characters Y. 2002. deuterostome EFI 97:11359-11364. II, Kobayashi M, Sato R, Satoh N, Miyasaka II, Received: 11 June 2002 Dynamic alpha insertion-deletion genes. J. Mol. Evol. of introns 54:118-128.