Phylogeny and mitochondrial gene order variation in Lophotrochozoa in the light of new mitogenomic data from Nemertea

Podsiadłowski, Lars; Braband, Anke; Struck, Torsten H.; Döhren, Jörn von; Bartolomaeus, Thomas

doi:10.1186/1471-2164-10-364

Cited by 52 publications

(33 citation statements)

References 58 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, none of several approaches accounting for this bias supported a sister group relationship between Ectoprocta and Brachiopoda or between Phoronida and Entoprocta [34] as did some of the phylogenetic analyses of mitochondrial data ([19,37-39]; Table 4). …”

Section: Discussionmentioning

confidence: 99%

The complete mitochondrial genome of Flustra foliacea (Ectoprocta, Cheilostomata) - compositional bias affects phylogenetic analyses of lophotrochozoan relationships

et al. 2011

View full text Add to dashboard Cite

BackgroundThe phylogenetic relationships of the lophophorate lineages, ectoprocts, brachiopods and phoronids, within Lophotrochozoa are still controversial. We sequenced an additional mitochondrial genome of the most species-rich lophophorate lineage, the ectoprocts. Although it is known that there are large differences in the nucleotide composition of mitochondrial sequences of different lineages as well as in the amino acid composition of the encoded proteins, this bias is often not considered in phylogenetic analyses. We applied several approaches for reducing compositional bias and saturation in the phylogenetic analyses of the mitochondrial sequences.ResultsThe complete mitochondrial genome (16,089 bp) of Flustra foliacea (Ectoprocta, Gymnolaemata, Cheilostomata) was sequenced. All protein-encoding, rRNA and tRNA genes are transcribed from the same strand. Flustra shares long intergenic sequences with the cheilostomate ectoproct Bugula, which might be a synapomorphy of these taxa. Further synapomorphies might be the loss of the DHU arm of the tRNA L(UUR), the loss of the DHU arm of the tRNA S(UCN) and the unique anticodon sequence GAG of the tRNA L(CUN). The gene order of the mitochondrial genome of Flustra differs strongly from that of the other known ectoprocts. Phylogenetic analyses of mitochondrial nucleotide and amino acid data sets show that the lophophorate lineages are more closely related to trochozoan phyla than to deuterostomes or ecdysozoans confirming the Lophotrochozoa hypothesis. Furthermore, they support the monophyly of Cheilostomata and Ectoprocta. However, the relationships of the lophophorate lineages within Lophotrochozoa differ strongly depending on the data set and the used method. Different approaches for reducing heterogeneity in nucleotide and amino acid data sets and saturation did not result in a more robust resolution of lophotrochozoan relationships.ConclusionThe contradictory and usually weakly supported phylogenetic reconstructions of the relationships among lophotrochozoan phyla based on mitochondrial sequences indicate that these alone do not contain enough information for a robust resolution of the relations of the lophotrochozoan phyla. The mitochondrial gene order is also not useful for inferring their phylogenetic relationships, because it is highly variable in ectoprocts, brachiopods and some other lophotrochozoan phyla. However, our study revealed several rare genomic changes like the evolution of long intergenic sequences and changes in the structure of tRNAs, which may be helpful for reconstructing ectoproct phylogeny.

show abstract

Section: Discussionmentioning

confidence: 99%

The complete mitochondrial genome of Flustra foliacea (Ectoprocta, Cheilostomata) - compositional bias affects phylogenetic analyses of lophotrochozoan relationships

et al. 2011

View full text Add to dashboard Cite

show abstract

“…As a result, mitogenomes have become popular tools for reconstructing phylogeny, particularly among basal metazoan groups (Kan et al, 2010;Kayal et al, 2013;Lavrov et al, 2008;Podsiadlowski et al, 2009;Rota-Stabelli et al, 2010), the evolutionary histories of which are otherwise difficult to infer. This is particularly true for sea anemones, which possess a paucity of diagnostic morphological characters and exhibit low rates of nucleotide substitution at the single gene level, with interspecific variation often exceeding intraspecific variation (Shearer et al, 2002).…”

Section: Mitogenomic Phylogeny Of the Actiniariamentioning

confidence: 99%

Multiplexed pyrosequencing of nine sea anemone (Cnidaria: Anthozoa: Hexacorallia: Actiniaria) mitochondrial genomes

Foox

Brugler

Siddall

et al. 2015

Mitochondrial DNA Part A

View full text Add to dashboard Cite

Six complete and three partial actiniarian mitochondrial genomes were amplified in two semi-circles using long-range PCR and pyrosequenced in a single run on a 454 GS Junior, doubling the number of complete mitogenomes available within the order. Typical metazoan mtDNA features included circularity, 13 protein-coding genes, 2 ribosomal RNA genes, and length ranging from 17,498 to 19,727 bp. Several typical anthozoan mitochondrial genome features were also observed including the presence of only two transfer RNA genes, elevated A + T richness ranging from 54.9 to 62.4%, large intergenic regions, and group 1 introns interrupting NADH dehydrogenase subunit 5 and cytochrome c oxidase subunit I, the latter of which possesses a homing endonuclease gene. Within the sea anemone Alicia sansibarensis, we report the first mitochondrial gene order rearrangement within the Actiniaria, as well as putative novel non-canonical protein-coding genes. Phylogenetic analyses of all 13 protein-coding and 2 ribosomal genes largely corroborated current hypotheses of sea anemone interrelatedness, with a few lower-level differences.

show abstract

“…Relationships among the lophotrochozoans have been difficult to establish (Giribet 2008), but until recently a consensus was beginning to emerge in which brachiopods and phoronids would form a clade more closely related either to molluscs (Mallatt & Winchell 2002, Paps et al 2009, Luo et al 2015 or to annelids (Dunn et al 2008, Podsiadlowski et al 2009, with bryozoans more distantly related, near the base of the lophotrochozoan clade (Nielsen 1995(Nielsen , 2002Hejnol et al 2009;Paps et al 2009) (Figure 3a). More recent phylogenomic studies, however, have recovered a monophyletic Lophophorata (Nesnidal et al 2013) (Figure 3b), which supports a hypothesis proposed initially by Emig (1984) on the basis of morphology.…”

Section: Mesodermmentioning

confidence: 99%

The Evolution of Brachiopoda

Carlson

2016

Annu. Rev. Earth Planet. Sci.

View full text Add to dashboard Cite

Brachiopods are (perhaps all too) familiar to any geology student who has taken an invertebrate paleontology course; they may well be less familiar to biology students. Even though brachiopods are among the most significant components of the marine fossil record by virtue of their considerable diversity, abundance, and long evolutionary history, fewer than 500 species are extant. Reconciling the geological and biological perspectives is necessary in order to test hypotheses, not only about phylogenetic relationships among brachiopods but also about their spectacular decline in diversity in the end-Permian mass extinction, which permanently reset their evolutionary trajectory. Studying brachiopod ontogeny and development, population genetics, ecology, physiology, and biogeography, as well as molecular systematics and phylogenomics, enables us to better understand the context of evolutionary processes over the short term. Investigating brachiopod morphological, taxonomic, and stratigraphic records over the Phanerozoic Eon reveals historical patterns of long-term macroevolutionary change, patterns that are simply unknowable from a biological perspective alone.

show abstract

Phylogeny and mitochondrial gene order variation in Lophotrochozoa in the light of new mitogenomic data from Nemertea

Cited by 52 publications

References 58 publications

The complete mitochondrial genome of Flustra foliacea (Ectoprocta, Cheilostomata) - compositional bias affects phylogenetic analyses of lophotrochozoan relationships

The complete mitochondrial genome of Flustra foliacea (Ectoprocta, Cheilostomata) - compositional bias affects phylogenetic analyses of lophotrochozoan relationships

Multiplexed pyrosequencing of nine sea anemone (Cnidaria: Anthozoa: Hexacorallia: Actiniaria) mitochondrial genomes

The Evolution of Brachiopoda

Contact Info

Product

Resources

About