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1.
The large subunit ribosomal RNA sequences from the heterokont algae Ochromonas danica, Nannochloropsis salina, and Tribonema aequale were determined. These sequences were combined with small subunit ribosomal RNA sequences in order to carry out a phylogenetic
analysis based on neighbor-joining, maximum parsimony, and maximum likelihood methods. Our results indicate that heterokont
fungi and heterokont algae each are monophyletic, and confirm that they together form a monophyletic group called ``stramenopiles.'
Within the heterokont algae, the eustigmatophyte Nannochloropsis salina either clusters with the chrysophyte Ochromonas danica or forms a sister group to a cluster comprising the phaeophyte Scytosiphon lomentaria and the xanthophyte Tribonema aequale. The alveolates were identified as the closest relatives of the stramenopiles, but the exact order of divergence between the
eukaryotic crown taxa could not be established with confidence.
Received: 22 November 1996 / Accepted: 14 February 1997 相似文献
2.
Complete chloroplast 23S rRNA and psbA genes from five peridinin-containing dinoflagellates (Heterocapsa pygmaea, Heterocapsa niei, Heterocapsa rotun-data, Amphidinium carterae, and Protoceratium reticulatum) were amplified by PCR and sequenced; partial sequences were obtained from Thoracosphaera heimii and Scrippsiella trochoidea. Comparison with chloroplast 23S rRNA and psbA genes of other organisms shows that dinoflagellate chloroplast genes are the most divergent and rapidly evolving of all.
Quartet puzzling, maximum likelihood, maximum parsimony, neighbor joining, and LogDet trees were constructed. Intersite rate
variation and invariant sites were allowed for with quartet puzzling and neighbor joining. All psbA and 23S rRNA trees showed peridinin-containing dinoflagellate chloroplasts as monophyletic. In psbA trees they are related to those of chromists and red algae. In 23S rRNA trees, dinoflagellates are always the sisters of
Sporozoa (apicomplexans); maximum likelihood analysis of Heterocapsa triquetra 16S rRNA also groups the dinoflagellate and sporozoan sequences, but the other methods were inconsistent. Thus, dinoflagellate
chloroplasts may actually be related to sporozoan plastids, but the possibility of reproducible long-branch artifacts cannot
be strongly ruled out. The results for all three genes fit the idea that dinoflagellate chloroplasts originated from red algae
by a secondary endosymbiosis, possibly the same one as for chromists and Sporozoa. The marked disagreement between 16S rRNA
trees using different phylogenetic algorithms indicates that this is a rather poor molecule for elucidating overall chloroplast
phylogeny. We discuss possible reasons why both plastid and mitochondrial genomes of alveolates (Dinozoa, Sporozoa and Ciliophora)
have ultra-rapid substitution rates and a proneness to unique genomic rearrangements.
Received: 27 December 1999 / Accepted: 24 March 2000 相似文献
3.
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
4.
Julius Lukeš Milan Jirků David Doležel Ivica Kral'ová Laura Hollar Dmitri A. Maslov 《Journal of molecular evolution》1997,44(5):521-527
To further investigate the phylogeny of protozoa from the order Kinetoplastida we have sequenced the small subunit (SSU)
and a portion of the large subunit (LSU) nuclear rRNA genes. The SSU and LSU sequences were determined from a lizard trypanosome,
Trypanosoma scelopori and a bodonid, Rhynchobodo sp., and the LSU sequences were determined from an insect trypanosomatid, Crithidia oncopelti, and a bodonid, Dimastigella trypaniformis. Contrary to previous results, in which trypanosomes were found to be paraphyletic, with Trypanosoma brucei representing the earliest-diverging lineage, we have now found evidence for the monophyly of trypanosomes. Addition of new
taxa which subdivide long branches (such as that of T. brucei) have helped to identify homoplasies responsible for the paraphyletic trees in previous studies. Although the monophyly of
the trypanosome clade is supported in the bootstrap analyses for maximum likelihood at 97% and maximum parsimony at 92%, there
is only a small difference in ln-likelihood value or tree length between the most optimal monophyletic tree and the best suboptimal
paraphyletic tree. Within the trypanosomatid subtree, the clade of trypanosomes is a sister group to the monophyletic clade
of the nontrypanosome genera. Different groups of trypanosomes group on the tree according to their mode of transmission.
This suggests that the adaptation to invertebrate vectors plays a more important role in the trypanosome evolution than the
adaptation to vertebrate hosts.
Received: 5 July 1996 / Accepted: 26 September 1996 相似文献
5.
Bocchetta M Gribaldo S Sanangelantoni A Cammarano P 《Journal of molecular evolution》2000,50(4):366-380
The phylogenetic placement of the Aquifex and Thermotoga lineages has been inferred from (i) the concatenated ribosomal proteins S10, L3, L4, L23, L2, S19, L22, and S3 encoded in
the S10 operon (833 aa positions); (ii) the joint sequences of the elongation factors Tu(1α) and G(2) coded by the str operon tuf and fus genes (733 aa positions); and (iii) the joint RNA polymerase β- and β′-type subunits encoded in the rpoBC operon (1130 aa positions). Phylogenies of r-protein and EF sequences support with moderate (r-proteins) to high statistical confidence (EFs) the placement of the two hyperthermophiles at the base of the bacterial clade
in agreement with phylogenies of rRNA sequences. In the more robust EF-based phylogenies, the branching of Aquifex and Thermotoga below the successive bacterial lineages is given at bootstrap proportions of 82% (maximum likelihood; ML) and 85% (maximum
parsimony; MP), in contrast to the trees inferred from the separate EF-Tu(1α) and EF-G(2) data sets, which lack both resolution
and statistical robustness. In the EF analysis MP outperforms ML in discriminating (at the 0.05 level) trees having A. pyrophilus and T. maritima as the most basal lineages from competing alternatives that have (i) mesophiles, or the Thermus genus, as the deepest bacterial radiation and (ii) a monophyletic A. pyrophilus–T. maritima cluster situated at the base of the bacterial clade. RNAP-based phylogenies are equivocal with respect to the Aquifex and Thermotoga placements. The two hyperthermophiles fall basal to all other bacterial phyla when potential artifacts contributed by the
compositionally biased and fast-evolving Mycoplasma genitalium and Mycoplasma pneumoniae sequences are eschewed. However, the branching order of the phyla is tenuously supported in ML trees inferred by the exhaustive
search method and is unresolved in ML trees inferred by the quartet puzzling algorithm. A rooting of the RNA polymerase-subunit
tree at the mycoplasma level seen in both the MP trees and the ML trees reconstructed with suboptimal amino acid substitution
models is not supported by the EF-based phylogenies which robustly affiliate mycoplasmas with low-G+C gram-positives and,
most probably, reflects a ``long branch attraction' artifact.
Received: 22 September 1999 / Accepted: 11 January 2000 相似文献
6.
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
7.
Megumi Ehara Yasuko Hayashi-Ishimaru Yuji Inagaki Takeshi Ohama 《Journal of molecular evolution》1997,45(2):119-124
Several algae that were previously classified in the phylum Xanthophyta (yellow-green algae) were assigned in 1971 to a new
phylum, Eustigmatophyta. It was anticipated that the number of algae reclassified to Eustigmatophyta would increase. However,
due to the fact that the morphological characteristics that segregate eustigmatophytes from other closely related algae can
be only obtained through laborious electron microscopic techniques, the number of members in this phylum have increased rather
slowly. We attempted, therefore, to segregate two closely related groups of algae, eustigmatophytes and yellow-green algae,
on the basis of a molecular phylogenetic tree as a means of providing an alternative method of distinguishing these phyla.
We analyzed the mitochondrial cytochrome oxidase subunit I (COXI) gene sequences of eight algae classified as xanthophyceans and found that six manifested the expected deviant genetic code
where AUA codes for methionine (AUA/Met), but not for isoleucine (AUA/Ile) as in the universal genetic code. The other two,
Monodus sp. (CCMP 505) and Ophiocytium majus (CCAP 855/1), which were presumed to be yellow-green algae, and all the examined eustigmatophytes utilized AUA for Ile. In
addition, the phylogenetic tree of COXI gene sequences showed that the six yellow-green algae bearing the AUA/Met deviant code composed a tight clade with a bootstrap
value of 100%. The phylogenetic tree of the corresponding sequences from Monodus sp. and Ophiocytium majus and the eustigmatophytes also composed a tight cluster, but with a bootstrap value of 92%. These results strongly suggest
that two previously classified members of yellow-green algae belong to the phylum Eustigmatophyta. Therefore, examination
of the mitochondrial genetic code in algae appears to be a potentially very useful genetic marker for classifying these organisms,
especially when it is considered with the results obtained through a molecular phylogenetic tree.
Received: 14 December 1996 / Accepted: 3 April 1997 相似文献
8.
Yuji Inagaki Yasuko Hayashi-Ishimaru Megumi Ehara Ikuo Igarashi Takeshi Ohama 《Journal of molecular evolution》1997,45(3):295-300
The chloroplasts of euglenophytes and dinoflagellates have been suggested to be the vestiges of endosymbiotic algae acquired
during the process of evolution. However, the evolutionary positions of these organisms are still inconclusive, and they have
been tentatively classified as both algae and protozoa. A representative gene of the mitochondrial genome, cytochrome oxidase
subunit I (coxI), was chosen and sequenced to clarify the phylogenetic positions of four dinoflagellates, two euglenophytes and one apicomplexan
protist. This is the first report of mitochondrial DNA sequences for dinoflagellates and euglenophytes. Our COXI tree shows clearly that dinoflagellates are closely linked to apicomplexan parasites but not with algae. Euglenophytes and
algae appear to be only remotely related, with euglenophytes sharing a possible evolutionary link with kinetoplastids. The
COXI tree is in general agreement with the tree based on the nuclear encoded small subunit of ribosomal RNA (SSU rRNA) genes,
but conflicts with that based on plastid genes. These results support the interpretation that chloroplasts present in euglenophytes
and dinoflagellates were captured from algae through endosymbioses, while their mitochondria were inherited from the host
cell. We suggest that dinoflagellates and euglenophytes were originally heterotrophic protists and that their chloroplasts
are remnants of endosymbiotic algae.
Received: 24 March 1997 / Accepted: 21 April 1997 相似文献
9.
The Origin of Chlorarachniophyte Plastids, as Inferred from Phylogenetic Comparisons of Amino Acid Sequences of EF-Tu 总被引:4,自引:0,他引:4
Ken-ichiro Ishida Ying Cao Masami Hasegawa Norihiro Okada Yoshiaki Hara 《Journal of molecular evolution》1997,45(6):682-687
A molecular phylogenetic analysis of elongation factor Tu (EF-Tu) proteins from plastids was performed in an attempt to identify
the origin of chlorarachniophyte plastids, which are considered to have evolved from the endosymbiont of a photosynthetic
eukaryote. Partial sequences of the genes for plastid EF-Tu proteins (1,080–1,089 bp) were determined for three algae that
contain chlorophyll b, namely, Gymnochlora stellata (Chlorarachniophyceae), Bryopsis maxima (Ulvophyceae), and Pyramimonas disomata (Prasinophyceae). The deduced amino acid sequences were used to construct phylogenetic trees of the plastid and bacterial
EF-Tu proteins by the maximum likelihood, the maximum parsimony, and the neighbor joining methods.
The trees obtained in the present analysis suggest that all plastids that contain chlorophyll b are monophyletic and that the chlorarachniophyte plastids are closely related to those of the Ulvophyceae. The phylogenetic
trees also suggest that euglenophyte plastids are closely related to prasinophycean plastids. The results indicate that the
chlorarachniophyte plastids evolved from a green algal endosymbiont that was closely related to the Ulvophyceae and that at
least two secondary endosymbiotic events have occurred in the lineage of algae with plastids that contain chlorophyll b.
Received: 10 March 1997 / Accepted: 28 July 1997 相似文献
10.
Molecular evolution of nitrate reductase genes 总被引:9,自引:0,他引:9
To understand the evolutionary mechanisms and relationships of nitrate reductases (NRs), the nucleotide sequences encoding
19 nitrate reductase (NR) genes from 16 species of fungi, algae, and higher plants were analyzed. The NR genes examined show
substantial sequence similarity, particularly within functional domains, and large variations in GC content at the third codon
position and intron number. The intron positions were different between the fungi and plants, but conserved within these groups.
The overall and nonsynonymous substitution rates among fungi, algae, and higher plants were estimated to be 4.33 × 10−10 and 3.29 × 10−10 substitutions per site per year. The three functional domains of NR genes evolved at about one-third of the rate of the N-terminal
and the two hinge regions connecting the functional domains. Relative rate tests suggested that the nonsynonymous substitution
rates were constant among different lineages, while the overall nucleotide substitution rates varied between some lineages.
The phylogenetic trees based on NR genes correspond well with the phylogeny of the organisms determined from systematics and
other molecular studies. Based on the nonsynonymous substitution rate, the divergence time of monocots and dicots was estimated
to be about 340 Myr when the fungi–plant or algae–higher plant divergence times were used as reference points and 191 Myr
when the rice–barley divergence time was used as a reference point. These two estimates are consistent with other estimates
of divergence times based on these reference points. The lack of consistency between these two values appears to be due to
the uncertainty of the reference times.
Received: 10 April 1995 / Accepted: 10 September 1995 相似文献
11.
12.
Conflict Among Individual Mitochondrial Proteins in Resolving the Phylogeny of Eutherian Orders 总被引:19,自引:0,他引:19
Ying Cao Axel Janke Peter J. Waddell Michael Westerman Osamu Takenaka Shigenori Murata Norihiro Okada Svante Pääbo Masami Hasegawa 《Journal of molecular evolution》1998,47(3):307-322
The phylogenetic relationship among primates, ferungulates (artiodactyls + cetaceans + perissodactyls + carnivores), and
rodents was examined using proteins encoded by the H strand of mtDNA, with marsupials and monotremes as the outgroup. Trees
estimated from individual proteins were compared in detail with the tree estimated from all 12 proteins (either concatenated
or summing up log-likelihood scores for each gene). Although the overall evidence strongly suggests ((primates, ferungulates),
rodents), the ND1 data clearly support another tree, ((primates, rodents), ferungulates). To clarify whether this contradiction
is due to (1) a stochastic (sampling) error; (2) minor model-based errors (e.g., ignoring site rate variability), or (3) convergent
and parallel evolution (specifically between either primates and rodents or ferungulates and the outgroup), the ND1 genes
from many additional species of primates, rodents, other eutherian orders, and the outgroup (marsupials + monotremes) were
sequenced. The phylogenetic analyses were extensive and aimed to eliminate the following artifacts as possible causes of the
aberrant result: base composition biases, unequal site substitution rates, or the cumulative effects of both. Neither more
sophisticated evolutionary analyses nor the addition of species changed the previous conclusion. That is, the statistical
support for grouping rodents and primates to the exclusion of all other taxa fluctuates upward or downward in quite a tight
range centered near 95% confidence. These results and a site-by-site examination of the sequences clearly suggest that convergent
or parallel evolution has occurred in ND1 between primates and rodents and/or between ferungulates and the outgroup. While
the primate/rodent grouping is strange, ND1 also throws some interesting light on the relationships of some eutherian orders,
marsupials, and montremes. In these parts of the tree, ND1 shows no apparent tendency for unexplained convergences.
Received: 5 December 1997 / Accepted: 24 February 1998 相似文献
13.
Genomic trees have been constructed based on the presence and absence of families of protein-encoding genes observed in 27
complete genomes, including genomes of 15 free-living organisms. This method does not rely on the identification of suspected
orthologs in each genome, nor the specific alignment used to compare gene sequences because the protein-encoding gene families
are formed by grouping any protein with a pairwise similarity score greater than a preset value. Because of this all inclusive
grouping, this method is resilient to some effects of lateral gene transfer because transfers of genes are masked when the
recipient genome already has a homolog (not necessarily an ortholog) of the incoming gene. Of 71 genes suspected to have been
laterally transferred to the genome of Aeropyrum pernix, only approximately 7 to 15 represent genes where a lateral gene transfer appears to have generated homoplasy in our character
dataset. The genomic tree of the 15 free-living taxa includes six different bacterial orders, six different archaeal orders,
and two different eukaryotic kingdoms. The results are remarkably similar to results obtained by analysis of rRNA. Inclusion
of the other 12 genomes resulted in a tree only broadly similar to that suggested by rRNA with at least some of the differences
due to artifacts caused by the small genome size of many of these species. Very small genomes, such as those of the two Mycoplasma genomes included, fall to the base of the Bacterial domain, a result expected due to the substantial gene loss inherent to
these lineages. Finally, artificial ``partial genomes' were generated by randomly selecting ORFs from the complete genomes
in order to test our ability to recover the tree generated by the whole genome sequences when only partial data are available.
The results indicated that partial genomic data, when sampled randomly, could robustly recover the tree generated by the whole
genome sequences.
Received: 30 May 2001 / Accepted: 10 October 2001 相似文献
14.
In translation, separate aminoacyl-tRNA synthetases attach the 20 different amino acids to their cognate tRNAs, with the
exception of glutamine. Eukaryotes and some bacteria employ a specific glutaminyl-tRNA synthetase (GlnRS) which other Bacteria,
the Archaea (archaebacteria), and organelles apparently lack. Instead, tRNAGln is initially acylated with glutamate by glutamyl-tRNA synthetase (GluRS), then the glutamate moiety is transamidated to glutamine.
Lamour et al. [(1994) Proc Natl Acad Sci USA 91:8670–8674] suggested that an early duplication of the GluRS gene in eukaryotes
gave rise to the gene for GlnRS—a copy of which was subsequently transferred to proteobacteria. However, questions remain
about the occurrence of GlnRS genes among the Eucarya (eukaryotes) outside of the ``crown' taxa (animals, fungi, and plants),
the distribution of GlnRS genes in the Bacteria, and their evolutionary relationships to genes from the Archaea. Here, we
show that GlnRS occurs in the most deeply branching eukaryotes and that putative GluRS genes from the Archaea are more closely
related to GlnRS and GluRS genes of the Eucarya than to those of Bacteria. There is still no evidence for the existence of
GlnRS in the Archaea. We propose that the last common ancestor to contemporary cells, or cenancestor, used transamidation
to synthesize Gln-tRNAGln and that both the Bacteria and the Archaea retained this pathway, while eukaryotes developed a specific GlnRS gene through
the duplication of an existing GluRS gene. In the Bacteria, GlnRS genes have been identified in a total of 10 species from
three highly diverse taxonomic groups: Thermus/Deinococcus, Proteobacteria γ/β subdivision, and Bacteroides/Cytophaga/Flexibacter.
Although all bacterial GlnRS form a monophyletic group, the broad phyletic distribution of this tRNA synthetase suggests that
multiple gene transfers from eukaryotes to bacteria occurred shortly after the Archaea–eukaryote divergence. 相似文献
15.
A.D. Shutov H. Braun Yu.V. Chesnokov Ch. Horstmann I.A. Kakhovskaya H. Bäumlein 《Journal of molecular evolution》1998,47(4):486-492
The development of seeds as a specialized organ for the nutrition, protection, and dispersal of the next generation was an
important step in the evolution of land plants. Seed maturation is accompanied by massive synthesis of storage compounds such
as proteins, starch, and lipids. To study the processes of seed storage protein evolution we have partially sequenced storage
proteins from maturing seeds of representatives from the gymnosperm genera Gnetum, Ephedra, and Welwitschia—morphologically diverse and unusual taxa that are grouped in most formal systems into the common order Gnetales. Based on
partial N-terminal amino acid sequences, oligonucleotide primers were derived and used for PCR amplification and cloning of
the corresponding cDNAs. We also describe the structure of the nuclear gene for legumin of Welwitschia mirabilis. This first gnetalean nuclear gene structure contains introns in only two of the four conserved positions previously characterized
in other spermatophyte legumin genes. The distinct phylogenetic status of the gnetalean taxa is also reflected in a sequence
peculiarity of their legumin genes. A comparative analysis of exon/intron sequences leads to the hypothesis that legumin genes
from Gnetales belong to a monophyletic evolutionary branch clearly distinct from that of legumin genes of extant Ginkgoales
and Coniferales as well as from all angiosperms.
Received: 5 June 1997 / Accepted: 31 March 1998 相似文献
16.
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
17.
Molecular and morphological evidence points to the ancyromonad Ancyromonas as a plausible candidate for the closest relative to the common ancestor of metazoans, fungi, and choanoflagellates (the
Opisthokonta). Using 18S rDNA sequences from most of the major eukaryotic lineages, maximum-likelihood, minimum-evolution,
and maximum-parsimony analyses yielded congruent phylogenies supporting this hypothesis. Combined with ultrastructural similarities
between Ancyromonas and opisthokonts, the evidence presented here suggests that Ancyromonas may form an independent lineage, the Ancyromonadida Cavalier-Smith 1997, closer in its relationship to the opisthokonts than
is its nearest protist relatives, the Apusomonadida. However, the very low bootstrap support for deep nodes and hypothesis
testing indicate that the resolving power of 18S rDNA sequences is limited for examining this aspect of eukaryotic phylogeny.
Alternate branching positions for the Ancyromonas lineage cannot be robustly rejected, revealing the importance of ultrastructure when examining the origins of multicellularity.
The future use of a multigene approach may additionally be needed to resolve this aspect of eukaryotic phylogeny.
Received: 27 March 2000 / Accepted: 12 June 2000 相似文献
18.
Microeukaryotes in oxygen-depleted environments are among the most diverse, as well as the least studied, organisms. We conducted a cultivation-independent, small-subunit (SSU) rRNA-based survey of microeukaryotes in suboxic waters and anoxic sediments in the great Sippewisset salt marsh, Cape Cod, Mass. We generated two clone libraries and analyzed approximately 300 clones, which contained a large diversity of microeukaryotic SSU rRNA signatures. Only a few of these signatures were closely related (sequence similarity of >97%) to the sequences reported earlier. The bulk of our sequences represented deep novel branches within green algae, fungi, cercozoa, stramenopiles, alveolates, euglenozoa and unclassified flagellates. In addition, a significant number of detected rRNA sequences exhibited no affiliation to known organisms and sequences and thus represent novel lineages of the highest taxonomical order, most of them branching off the base of the global phylogenetic tree. This suggests that oxygen-depleted environments harbor diverse communities of novel organisms, which may provide an interesting window into the early evolution of eukaryotes. 相似文献
19.
Biology and systematics of heterokont and haptophyte algae 总被引:1,自引:0,他引:1
Andersen RA 《American journal of botany》2004,91(10):1508-1522
In this paper, I review what is currently known of phylogenetic relationships of heterokont and haptophyte algae. Heterokont algae are a monophyletic group that is classified into 17 classes and represents a diverse group of marine, freshwater, and terrestrial algae. Classes are distinguished by morphology, chloroplast pigments, ultrastructural features, and gene sequence data. Electron microscopy and molecular biology have contributed significantly to our understanding of their evolutionary relationships, but even today class relationships are poorly understood. Haptophyte algae are a second monophyletic group that consists of two classes of predominately marine phytoplankton. The closest relatives of the haptophytes are currently unknown, but recent evidence indicates they may be part of a large assemblage (chromalveolates) that includes heterokont algae and other stramenopiles, alveolates, and cryptophytes. Heterokont and haptophyte algae are important primary producers in aquatic habitats, and they are probably the primary carbon source for petroleum products (crude oil, natural gas). 相似文献
20.
The aldo-keto reductase enzymes comprise a functionally diverse gene family which catalyze the NADPH-dependant reduction
of a variety of carbonyl compounds. The protein sequences of 45 members of this family were aligned and phylogenetic trees
were deduced from this alignment using the neighbor-joining and Fitch algorithms. The branching order of these trees indicates
that the vertebrate enzymes cluster in three groups, which have a monophyletic origin distinct from the bacterial, plant,
and invertebrate enzymes. A high level of conservation was observed between the vertebrate hydroxysteroid dehydrogenase enzymes,
prostaglandin F synthase, and ρ-crystallin of Xenopus laevis. We infer from the phylogenetic analysis that prostaglandin F synthase may represent a recent recruit to the eicosanoid biosynthetic
pathway from the hydroxysteroid dehydrogenase pathway and furthermore that, in the context of gene recruitment, Xenopus laevisρ-crystallin may represent a shared gene.
Received: 26 August 1996 / Accepted: 5 June 1997 相似文献