Should we be worried about long-branch attraction in real data sets? Investigations using metazoan 18S rDNA

Anderson, Frank E.; Swofford, David L.

doi:10.1016/j.ympev.2004.06.015

Cited by 183 publications

(130 citation statements)

References 45 publications

Supporting

Mentioning

121

Contrasting

Order By: Relevance

“…Inclusion of additional bilaterian taxa in the analysis did not change this topology (data not shown). This result is consistent with that reported by Lavrov et al (15) and may be due to long branch attraction that is known to affect analyses of fast evolving metazoan sequences (57). A relative-rates test comparing bilaterians to diploblasts using Monosiga and Monoblepharella as outgroups was performed by using RRTREE (58).…”

Section: Resultssupporting

confidence: 88%

Mitochondrial genome of Trichoplax adhaerens supports Placozoa as the basal lower metazoan phylum

Dellaporta

Sagasser

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

234

186

View full text Add to dashboard Cite

Mitochondrial genomes of multicellular animals are typically 15-to 24-kb circular molecules that encode a nearly identical set of 12-14 proteins for oxidative phosphorylation and 24 -25 structural RNAs (16S rRNA, 12S rRNA, and tRNAs). These genomes lack significant intragenic spacers and are generally without introns. Here, we report the complete mitochondrial genome sequence of the placozoan Trichoplax adhaerens, a metazoan with the simplest known body plan of any animal, possessing no organs, no basal membrane, and only four different somatic cell types. Our analysis shows that the Trichoplax mitochondrion contains the largest known metazoan mtDNA genome at 43,079 bp, more than twice the size of the typical metazoan mtDNA. The mitochondrion's size is due to numerous intragenic spacers, several introns and ORFs of unknown function, and protein-coding regions that are generally larger than those found in other animals. Not only does the Trichoplax mtDNA have characteristics of the mitochondrial genomes of known metazoan outgroups, such as chytrid fungi and choanoflagellates, but, more importantly, it shares derived features unique to the Metazoa. Phylogenetic analyses of mitochondrial proteins provide strong support for the placement of the phylum Placozoa at the root of the Metazoa.animal evolution ͉ phylogenetics T richoplax adhaerens [Shulze 1883] is a marine invertebrate distributed in tropical waters worldwide (1-3). It is the simplest known free-living animal, displaying no axis of symmetry, lacking a basal membrane, possessing only four somatic cell types (4-6), and having one of the smallest known animal genomes (7-9). Until recently, T. adhaerens was the sole representative of the phylum Placozoa, but recent field studies and molecular analyses indicate genetic diversity underlying apparent morphological uniformity within the Placozoa (3, 10). In the laboratory, placozoans reproduce asexually by either binary fission or budding dispersive propagules called swarmers. Eggs have been observed, and recent DNA polymorphism analysis has provided evidence for sexual reproduction within the Placozoa (10).The phylogenetic placement of Placozoa among the metazoans, i.e., the animals, remains unresolved. In particular, its placement among lower metazoans, that is, the phyla Cnidaria, Ctenophora, and Porifera, has been controversial. Most studies place Porifera at the base of the metazoan tree of life (11-15), but others support placozoans as one of the earliest branching lineages of . Conflicting data, including 18S, 28S, and 16S analysis, have suggested that Placozoa form a sister clade to all bilaterians or a sister clade to both cnidarians and bilaterians (14,(21)(22)(23)(24)(25)(26)(27).Comparative mitochondrial genomics is becoming an effective tool to resolve phylogenetic placements because of several unique properties of mitochondrial genomes, including uniparental inheritance, orthologous genes, and lack of substantial intermolecular recombination (reviewed in refs. 28-30). Although some have questioned th...

show abstract

Section: Resultssupporting

confidence: 88%

Mitochondrial genome of Trichoplax adhaerens supports Placozoa as the basal lower metazoan phylum

Dellaporta

Sagasser

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

234

186

View full text Add to dashboard Cite

show abstract

“…Strong molecular and morphological evidence supports a magnoliid clade that includes Piperales and excludes Ceratophyllum (21,30,38). The relatively long branches leading to Ceratophyllum and Piper, the occurrence of each of these taxa in different parts of the tree in the absence of the other taxon in MP analyses, the increasing support for the erroneous Ceratophyllum/Piper topology in MP with increasing sequence length, and the fact that ML never unites these taxa suggest this is almost certainly a case of long-branch attraction (35,39,40). Although breaking up the long branch to Ceratophyllum is impossible, the addition of unsampled Piperales may resolve this problem.…”

Section: Discussionmentioning

confidence: 91%

Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms

Moore

Bell²,

Soltis³

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

615

601

View full text Add to dashboard Cite

Although great progress has been made in clarifying deep-level angiosperm relationships, several early nodes in the angiosperm branch of the Tree of Life have proved difficult to resolve. Perhaps the last great question remaining in basal angiosperm phylogeny involves the branching order among the five major clades of mesangiosperms (Ceratophyllum, Chloranthaceae, eudicots, magnoliids, and monocots). Previous analyses have found no consistent support for relationships among these clades. In an effort to resolve these relationships, we performed phylogenetic analyses of 61 plastid genes (Ϸ42,000 bp) for 45 taxa, including members of all major basal angiosperm lineages. We also report the complete plastid genome sequence of Ceratophyllum demersum. Parsimony analyses of combined and partitioned data sets varied in the placement of several taxa, particularly Ceratophyllum, whereas maximum-likelihood (ML) trees were more topologically stable. Total evidence ML analyses recovered a clade of Chloranthaceae ؉ magnoliids as sister to a well supported clade of monocots ؉ (Ceratophyllum ؉ eudicots). ML bootstrap and Bayesian support values for these relationships were generally high, although approximately unbiased topology tests could not reject several alternative topologies. The extremely short branches separating these five lineages imply a rapid diversification estimated to have occurred between 143.8 ؎ 4.8 and 140.3 ؎ 4.8 Mya.

show abstract

“…This surprising Wnd warrants further investigation using additional loci and samples from leptanilline genera such as Anomalomyrma, Noonilla, Phaulomyrma, Protanilla and Yavnella. The inclusion of additional leptanilline genera would likely eliminate any long branch attraction as one potential explanation of this result (Anderson and SwoVord, 2004).…”

Section: Early Branching Lineagesmentioning

confidence: 95%

Molecular systematics of basal subfamilies of ants using 28S rRNA (Hymenoptera: Formicidae)

Ouellette

Fisher

Girman

2006

Molecular Phylogenetics and Evolution

View full text Add to dashboard Cite

For many years, the ant subfamily Ponerinae was hypothesized to contain the basal (early branching) lineages of ants. Recently the Ponerinae were reclassiWed into six poneromorph subfamilies based on morphological analysis. We evaluate this new poneromorph classiWcation using 1240 base pairs of DNA sequence data obtained from 28S rRNA gene sequences of 68 terminal taxa. The molecular tree supported the monophyly of the ant family Formicidae, with 100% parsimony bootstrap (PB) support and posterior probabilities (PP) of 1.00, with the ant subfamily Leptanillinae as a sister group to all other ants (PB D 62, PP D 93). However, our analyses strongly support the polyphyly of the Poneromorph subfamilies (sensu Bolton). The Ectatomminae and Heteroponerinae are more closely related to the Formicoid subfamilies than to the rest of the poneromophs (PB D 96, PP D 100). The Amblyoponinae (PB D 52, PP D 96), Paraponerinae (PB D 100, PP D 100), Ponerinae (PB < 50, PP D 71), and Proceratiinae (PB D 98, PP D 100) appear as distinct lineages at the base of the tree and are identiWed as a poneroid grade. Monophyletic origins for the poneroid subfamilies Amblyoponinae, Paraponerinae, Ponerinae and Proceratiinae are supported in our analysis. However, the genus Platythyrea forms a distinct sister group to the Ponerini within the Ponerinae. The Heteroponerinae, based on our sample of Heteroponera, are associated with the subfamily Ectatomminae (PB D 98, PP D 100). Furthermore, our data indicate the genus Probolomyrmex belongs to the Proceratiinae as suggested by recent morphological analysis (PB 98, PP 100).

show abstract

Should we be worried about long-branch attraction in real data sets? Investigations using metazoan 18S rDNA

Cited by 183 publications

References 45 publications

Mitochondrial genome of Trichoplax adhaerens supports Placozoa as the basal lower metazoan phylum

Mitochondrial genome of Trichoplax adhaerens supports Placozoa as the basal lower metazoan phylum

Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms

Molecular systematics of basal subfamilies of ants using 28S rRNA (Hymenoptera: Formicidae)

Contact Info

Product

Resources

About