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Phylogenetic relationships of annelids,molluscs, and arthropods evidenced from molecules and morphology 总被引:10,自引:0,他引:10
Chang Bae Kim Seung Yeo Moon Stuart R. Gelder Won Kim 《Journal of molecular evolution》1996,43(3):207-215
Annelids and arthropods have long been considered each other's closest relatives, as evidenced by similarities in their segmented
body plans. An alternative view, more recently advocated by investigators who have examined partial 18S ribosomal RNA data,
proposes that annelids, molluscs, and certain other minor phyla with trochophore larva stages share a more recent common ancestor
with one another than any do with arthropods. The two hypotheses are mutually exclusive in explaining spiralian relationships.
Cladistic analysis of morphological data does not reveal phylogentic relationships among major spiralian taxa but does suggest
monophyly for both the annelids and molluscs. Distance and maximum-likelihood analyses of 18S rRNA gene sequences from major
spiralian taxa suggest a sister relationship between annelids and molluscs and provide a clear resolution within the major
groups of the spiralians. The parsimonious tree based on molecular data, however, indicates a sister relationship of the Annelida
and Bivalvia, and an earlier divergence of the Gastropoda than the Annelida–Bivalvia clade. To test further hypotheses on
the phylogenetic relationships among annelids, molluscs, and arthropods, and the ingroup relationships within the major spiralian
taxa, we combine the molecular and morphological data sets and subject the combined data matrix to parsimony analysis. The
resulting tree suggests that the molluscs and annelids form a monophyletic lineage and unites the molluscan taxa to a monophyletic
group. Therefore, the result supports the Eutrochozoa hypothesis and the monophyly of molluscs, and indicates early acquisition
of segmented body plans in arthropods.
Received: 25 September 1995 / Accepted: 15 March 1996 相似文献
3.
In this study we constructed a bootstrapped distance tree of 500 small subunit ribosomal RNA sequences from organisms belonging
to the so-called crown of eukaryote evolution. Taking into account the substitution rate of the individual nucleotides of
the rRNA sequence alignment, our results suggest that (1) animals, true fungi, and choanoflagellates share a common origin:
The branch joining these taxa is highly supported by bootstrap analysis (bootstrap support [BS] > 90%), (2) stramenopiles
and alveolates are sister groups (BS = 75%), (3) within the alveolates, dinoflagellates and apicomplexans share a common ancestor
BS > 95%), while in turn they both share a common origin with the ciliates (BS > 80%), and (4) within the stramenopiles, heterokont
algae, hyphochytriomycetes, and oomycetes form a monophyletic grouping well supported by bootstrap analysis (BS > 85%), preceded
by the well-supported successive divergence of labyrinthulomycetes and bicosoecids.
On the other hand, many evolutionary relationships between crown taxa are still obscure on the basis of 18S rRNA. The branching
order between the animal-fungal-choanoflagellates clade and the chlorobionts, the alveolates and stramenopiles, red algae,
and several smaller groups of organisms remains largely unresolved.
When among-site rate variation is not considered, the inferred tree topologies are inferior to those where the substitution
rate spectrum for the 18S rRNA is taken into account. This is primarily indicated by the erroneous branching of fast-evolving
sequences. Moreover, when different substitution rates among sites are not considered, the animals no longer appear as a monophyletic
grouping in most distance trees.
Received: 11 June 1997 / Accepted: 21 July 1997 相似文献
4.
Molecular clocks, molecular phylogenies and the origin of phyla 总被引:3,自引:0,他引:3
DOUGLAS H. ERWIN 《Lethaia: An International Journal of Palaeontology and Stratigraphy》1989,22(3):251-257
Erwin, Douglas H. 1989 07 15: Molecular clocks, molecular phylogenies and the origin of phyla. Lethaia , Vol. 22, pp. 251–257. Oslo. ISSN 0024–1164.
Protein, RNA and DNA sequences have been widely used to construct phylogenies and to calculate divergence times using a molecular clock. Reliance on molecular information is particularly attractive when fossil evidence is missing or equivocal, as in the Cambrian metazoan radiation. I consider the applicability of molecular clocks and phylogenetic analysis of molecular data to the origin of metazoan phyla, and conclude that molecular information is often ambiguous or misleading. Amino acid sequences are of limited use because the redundancy of the genetic code masks patterns of descent, while in a nucleotide sequence only four potential states exist at each site (the four nucleotide bases). In each case, homoplasy may often go undetected. The application of a molecular clock to resolve the timing of the metazoan radiation is unwarranted, while molecular phylogenetic reconstruction should be approached with care. A potentially more useful technique for phylogenetic reconstruction would be the use of patterns of genome structure and organization as characters. * Molecular clock, phylogenetics, metazoan radiation, origin of phyla . 相似文献
Protein, RNA and DNA sequences have been widely used to construct phylogenies and to calculate divergence times using a molecular clock. Reliance on molecular information is particularly attractive when fossil evidence is missing or equivocal, as in the Cambrian metazoan radiation. I consider the applicability of molecular clocks and phylogenetic analysis of molecular data to the origin of metazoan phyla, and conclude that molecular information is often ambiguous or misleading. Amino acid sequences are of limited use because the redundancy of the genetic code masks patterns of descent, while in a nucleotide sequence only four potential states exist at each site (the four nucleotide bases). In each case, homoplasy may often go undetected. The application of a molecular clock to resolve the timing of the metazoan radiation is unwarranted, while molecular phylogenetic reconstruction should be approached with care. A potentially more useful technique for phylogenetic reconstruction would be the use of patterns of genome structure and organization as characters. * Molecular clock, phylogenetics, metazoan radiation, origin of phyla . 相似文献
5.
Joachim Schütze Alexander Skorokhod Isabel M. Müller Werner E.G. Müller 《Journal of molecular evolution》2001,53(4-5):402-415
One crucial event during evolution to multicellularity was the development of either direct cell–cell contact or indirect
interaction via extracellular matrix (ECM) molecules. The identification of those polypeptides provides conclusive data on
the phylogenetic relationship of metazoan phyla and helps us to understand the position of the Metazoa among the other kingdoms.
Recently it became evident that the ECM of sponges is amazingly complex; it is composed of fibrous molecules, e.g., collagen,
and their corresponding receptors, which are highly similar to those existing in other metazoan phyla. While these data already
support the view of monophyly of Metazoa, additional studies are required to understand whether these molecules, which are
similar in their primary sequence, also have the same function throughout the metazoan kingdom. In the present study we identified
the ligand for one of the autopomorphic characters of Metazoa, the single-transmembrane receptor protein with the receptor
tyrosine kinase (RTK) from G. cydonium, as an example: the putative mucus-like protein from G. cydonium. This protein was upregulated during autograft fusion in the homologous system with kinetics similar to those of the RTK.
Additionally, a cDNA was isolated from S. domuncula whose deduced polypeptide displays a high sequence similarity to dermatopontin, an ECM molecule found exclusively in Metazoa.
Furthermore, it is documented that expression of the fibrous ECM molecule collagen is regulated by the characteristic metazoan
morphogens myotrophin and endothelial monocyte-activating polypeptide. These data indicate that the ECM of sponges is not
an unstructured ground substance but provides the basis for integrated cell communication.
Received: 26 October 2000 / Accepted: 1 February 2001 相似文献
6.
Nuclear and Nucleomorph SSU rDNA Phylogeny in the Cryptophyta and the Evolution of Cryptophyte Diversity 总被引:5,自引:0,他引:5
The plastid-bearing members of the Cryptophyta contain two functional eukaryotic genomes of different phylogenetic origin,
residing in the nucleus and in the nucleomorph, respectively. These widespread and diverse protists thus offer a unique opportunity
to study the coevolution of two different eukaryotic genomes within one group of organisms. In this study, the SSU rRNA genes
of both genomes were PCR-amplified with specific primers and phylogenetic analyses were performed on different data sets using
different evolutionary models. The results show that the composition of the principal clades obtained from the phylogenetic
analyses of both genes was largely congruent, but striking differences in evolutionary rates were observed. These affected
the topologies of the nuclear and nucleomorph phylogenies differently, resulting in long-branch attraction artifacts when
simple evolutionary models were applied. Deletion of long-branch taxa stabilized the internal branching order in both phylogenies
and resulted in a completely resolved topology in the nucleomorph phylogeny. A comparison of the tree topologies derived from
SSU rDNA sequences with characters previously used in cryptophyte systematics revealed that the biliprotein type was congruent,
but the type of inner periplast component incongruent, with the molecular trees. The latter is indicative of a hidden cellular
dimorphism (cells with two periplast types present in a single clonal strain) of presumably widespread occurrence throughout
cryptophyte diversity, which, in consequence, has far-reaching implications for cryptophyte systematics as it is practiced
today. 相似文献
7.
Aurora M. Nedelcu 《Journal of molecular evolution》2001,53(6):670-679
This study provides a phylogenetic/comparative approach to deciphering the processes underlying the evolution of plastid
rRNA genes in genomes under relaxed functional constraints. Nonphotosynthetic green algal taxa that belong to two distinct
classes, Chlorophyceae (Polytoma) and Trebouxiophyceae (Prototheca), were investigated. Similar to the situation described previously for plastid 16S rRNA genes in nonphotosynthetic land plants,
nucleotide substitution levels, extent of structural variations, and percentage AT values are increased in nonphotosynthetic
green algae compared to their closest photosynthetic relatives. However, the mutational processes appear to be different in
many respects. First, with the increase in AT content, more transversions are noted in Polytoma and holoparasite angiosperms, while more transitions characterize the evolution of the 16S rDNA sequences in Prototheca. Second, although structural variations do accumulate in both Polytoma and Prototheca (as well as holoparasitic plastid 16S rRNAs), insertions as large as 1.6 kb characterize the plastid 16S rRNA genes in the
former, whereas significantly smaller indels (not exceeding 24 bp) seem to be more prevalent in the latter group. The differences
in evolutionary rates and patterns within and between lineages might be due to mutations in replication/repair-related genes;
slipped-strand mispairing is likely the mechanism responsible for the expansion of insertions in Polytoma plastid 16S rRNA genes.
Received: 29 December 2000 / Accepted: 18 May 2001 相似文献
8.
Geneviàve Pont-Kingdon Norichika A. Okada Jane L. Macfarlane C. Timothy Beagley Cristi D. Watkins-Sims Thomas Cavalier-Smith G. Desmond Clark-Walker David R. Wolstenholme 《Journal of molecular evolution》1998,46(4):419-431
The nucleotide sequences of two segments of 6,737 ntp and 258 ntp of the 18.4-kb circular mitochondrial (mt) DNA molecule
of the soft coral Sarcophyton glaucum (phylum Cnidaria, class Anthozoa, subclass Octocorallia, order Alcyonacea) have been determined. The larger segment contains
the 3′ 191 ntp of the gene for subunit 1 of the respiratory chain NADH dehydrogenase (ND1), complete genes for cytochrome
b (Cyt b), ND6, ND3, ND4L, and a bacterial MutS homologue (MSH), and the 5′ terminal 1,124 ntp of the gene for the large subunit rRNA (l-rRNA). These genes are arranged in the order given
and all are transcribed from the same strand of the molecule. The smaller segment contains the 3′ terminal 134 ntp of the
ND4 gene and a complete tRNAf-Met gene, and these genes are transcribed in opposite directions. As in the hexacorallian anthozoan, Metridium senile, the mt-genetic code of S. glaucum is near standard: that is, in contrast to the situation in mt-genetic codes of other invertebrate phyla, AGA and AGG specify
arginine, and ATA specifies isoleucine. However, as appears to be universal for metazoan mt-genetic codes, TGA specifies tryptophan
rather than termination. Also, as in M. senile the mt-tRNAf-Met gene has primary and secondary structural features resembling those of Escherichia coli initiator tRNA, including standard dihydrouridine and TψC loop sequences, and a mismatched nucleotide pair at the top of
the amino-acyl stem. The presence of a mutS gene homologue, which has not been reported to occur in any other known mtDNA, suggests that there is mismatch repair activity
in S. glaucum mitochondria. In support of this, phylogenetic analysis of MutS family protein sequences indicates that the S. glaucum mtMSH protein is more closely related to the nuclear DNA-encoded mitochondrial mismatch repair protein (MSH1) of the yeast
Saccharomyces cerevisiae than to eukaryotic homologues involved in nuclear function, or to bacterial homologues. Regarding the possible origin of
the S. glaucum mtMSH gene, the phylogenetic analysis results, together with comparative base composition considerations, and the absence of an
MSH gene in any other known mtDNA best support the hypothesis that S. glaucum mtDNA acquired the mtMSH gene from nuclear DNA early in the evolution of octocorals. The presence of mismatch repair activity in S. glaucum mitochondria might be expected to influence the rate of evolution of this organism's mtDNA.
Received: 13 January 1997 / Accepted: 23 September 1997 相似文献
9.
A 2550-bp portion of the mitochondrial genome of a Demosponge, genus Tetilla, was amplified from whole genomic DNA extract and sequenced. The sequence was found to code for the 3′ end of the 16S rRNA
gene, cytochrome c oxidase subunit II, a lysine tRNA, ATPase subunit 8, and a 5′ portion of ATPase subunit 6. The Porifera cluster distinctly
within the eumetazoan radiation, as a sister group to the Cnidaria. Also, the mitochondrial genetic code of this sponge is
likely identical to that found in the Cnidaria. Both the full COII DNA and protein sequences and a portion of the 16S rRNA
gene were found to possess a striking similarity to published Cnidarian mtDNA sequences, allying the Porifera more closely
to the Cnidaria than to any other metazoan phylum. The gene arrangement, COII—tRNALys—ATP8—ATP6, is observed in many Eumetazoan phyla and is apparently ancestral in the metazoa.
Received: 24 November 1997 / Accepted: 14 September 1998 相似文献
10.
Birgitta M.H. Winnepenninckx David G. Reid Thierry Backeljau 《Journal of molecular evolution》1998,47(5):586-596
In the past, 18S rRNA sequences have proved to be very useful for tracing ancient divergences but were rarely used for resolving
more recent ones. Moreover, it was suggested that the molecule does not contain useful information to resolve divergences
which took place during less than 40 Myr. The present paper takes littorinid phylogeny as a case study to reevaluate the utility
of the molecule for resolving recent divergences. Two data sets for nine species of the snail family Littorinidae were analyzed,
both separately and combined. One data set comprised 7 new complete 18S rRNA sequences aligned with 2 published littorinid
sequences; the other comprised 12 morphological, 1 biochemical, and 2 18S rRNA secondary structure characters. On the basis
of its ability to confirm generally accepted relationships and the congruence of results derived from the different data sets,
it is concluded that 18S rRNA sequences do contain information to resolve ``rapid' cladogenetic events, provided that they
occurred in the not too distant past. 18S rRNA sequences yielded support for (1) the branching order (L. littorea, (L. obtusata, (L. saxatilis, L. compressa))) and (2) the basal position of L. striata in the Littorina clade.
Received: 6 February 1998 / Accepted: 20 March 1998 相似文献