Dicyemida and Orthonectida: Two Stories of Body Plan Simplification

Zverkov, Oleg A.; Mikhailov, Kirill V.; Isaev, Sergey; Rusin, L.Y.; Popova, Olga V.; Logacheva, Maria D.; Penin, Aleksey A.; Moroz, Leonid L.; Panchin, Yu. V.; Lyubetsky, Vassily; Aleoshin, Vladimir V.

doi:10.3389/fgene.2019.00443

Cited by 46 publications

(57 citation statements)

References 96 publications

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“…Organismal scope or featured taxon Cunha & Giribet (2019) yes Gastropods Laumer et al (2019) yes Animals Lemer et al (2019) yes Bivalves Lozano-Fernandez et al (2019) yes Chelicerates Marlétaz et al (2019) yes Spiralia Philippe et al (2019) yes Bilateria Narayanan Kutty et al (2019) no Calyptratae Uribe et al (2019) no Gastropods Wolfe et al (2019) no Decapod crustaceans Zverkov et al (2019) no Dicyemida and Orthonectida Aouad et al (2018) yes Archaea Laumer et al (2018) yes Placozoa Otero-Bravo et al (2018) yes Pantoea Puttick et al (2018) yes Land plants Schwentner et al (2018) yes Pancrustacea Sousa et al (2018) yes Land plants Bennett & Mao (2018) no Fulgoroidea symbionts Eitel et al (2018) no Placozoa Manzano-Marín et al (2018) no Cinara strobi symbionts Feuda et al (2017) yes Animals Szabó et al (2017) yes Pseudococcidae symbionts Williams et al (2017) yes Archaea Schwentner et al (2017) no Pancrustacea Shin et al (2017) no Curculionoidea Simion et al (2017) no Animals Yoshida et al (2017) no Tardigrades Leliaert et al (2016) yes Viridiplantae Zhang et al (2016) yes Roseobacter CHAB-I-5 lineage He et al (2016) no Rhizaria Song et al (2016) no Holometabola Domman et al (2015) yes Plastids Luo (2015) yes SAR11 Petitjean et al (2015) yes Archaea Borowiec et al (2015) no Animals Derelle et al (2015) no Eukaryotes Wang & Wu (2015) no Mitochondria…”

Section: Citationmentioning

confidence: 99%

Six-state amino acid recoding is not an effective strategy to offset the effects of compositional heterogeneity and saturation in phylogenetic analyses

Hernandez

Ryan

2019

Preprint

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Six-state amino acid recoding strategies are commonly applied to combat the effects of compositional heterogeneity and substitution saturation in phylogenetic analyses. While these methods have been endorsed from a theoretical perspective, their performance has never been extensively tested. Here, we test the effectiveness of 6-state recoding approaches by comparing the performance of analyses on recoded and non-recoded datasets that have been simulated under gradients of compositional heterogeneity or saturation. In all of our simulation analyses, non-recoding approaches greatly outperformed 6-state recoding approaches. Our results suggest that 6-state recoding strategies are not effective in the face of high saturation. Further, while recoding strategies do buffer the effects of compositional heterogeneity, the loss of information that accompanies 6-state recoding outweighs its benefits, even in the most compositionally heterogeneous datasets. In addition, we evaluate recoding schemes with 9, 12, 15, and 18 states and show that these all outperform 6-state recoding. Our results have important implications for the more than 70 published papers that have incorporated 6-state recoding, many of which have significant bearing on relationships across the tree of life.

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Section: Citationmentioning

confidence: 99%

Six-state amino acid recoding is not an effective strategy to offset the effects of compositional heterogeneity and saturation in phylogenetic analyses

Hernandez

Ryan

2019

Preprint

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“…This indicates that lox2 evolved only after split of the common ancestor of those clades from remaining Spiralia and does not belong to the ancestral hox complement of all Spiralia (16). Whether absence of lox2 in lophophorates is plesiomorphic or represents evolutionary reversal depends on the position of Lophophorata within Spiralia, which is still debatable and not fully resolved (52)(53)(54)(55)94).…”

Section: Hox Gene Complement In Phoronidamentioning

confidence: 99%

“…Brachiopoda -into the group called Lophophorata (50,51), which recently gained support as a valid clade from several transcriptomic and phylogenomic studies (52)(53)(54)(55). Although originally the Lophophorata were considered as deuterostomes (50,51), molecular data showed their protostome affinity (56) and currently the lophophorates occupy a wellsupported position within the clade of Spiralia (52)(53)(54)(55)57). Phoronids develop through a distinctive planktotrophic larval stage, called actinotrocha (58)(59)(60)(61).…”

Section: Introductionmentioning

confidence: 99%

“…ancestor of all phoronids. Recent studies are favoring a sister group relationship between phoronids and ectoprocts(52)(53)(54)(55)94), the latter of which possesses a mineralized external shell similarly as brachiopods. However, the Hox gene survey using degenerate polymerase chain reaction primers in ectoproct Crisularia (Bugula) turrita did not retrieve neither scr nor post1 sequences(95), which questions the possible correlation between loss of scr and post1 and the reduction of shell secreting tissues in phoronid lineage.…”

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confidence: 99%

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Hox gene expression during the development of the phoronidPhoronopsis harmeri

Gąsiorowski

Hejnol

2019

Preprint

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“…1a). Due to the presence of lophophore, Phoronida have been traditionally united with two other clades-Ectoprocta (Bryozoa) and Brachiopoda-into the group called Lophophorata [50,51], which recently gained support as a valid clade from several transcriptomic and phylogenomic studies [52][53][54][55]. Although originally the Lophophorata were considered as deuterostomes [50,51], molecular data showed their protostome affinity [56] and currently the lophophorates Fig.…”

Section: Introductionmentioning

confidence: 99%

Hox gene expression during development of the phoronid Phoronopsis harmeri

Gąsiorowski

Hejnol

2020

EvoDevo

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Background: Phoronida is a small group of marine worm-like suspension feeders, which together with brachiopods and bryozoans form the clade Lophophorata. Although their development is well studied on the morphological level, data regarding gene expression during this process are scarce and restricted to the analysis of relatively few transcription factors. Here, we present a description of the expression patterns of Hox genes during the embryonic and larval development of the phoronid Phoronopsis harmeri. Results:We identified sequences of eight Hox genes in the transcriptome of Ph. harmeri and determined their expression pattern during embryonic and larval development using whole mount in situ hybridization. We found that none of the Hox genes is expressed during embryonic development. Instead their expression is initiated in the later developmental stages, when the larval body is already formed. In the investigated initial larval stages the Hox genes are expressed in the non-collinear manner in the posterior body of the larvae: in the telotroch and the structures that represent rudiments of the adult worm. Additionally, we found that certain head-specific transcription factors are expressed in the oral hood, apical organ, preoral coelom, digestive system and developing larval tentacles, anterior to the Hox-expressing territories. Conclusions:The lack of Hox gene expression during early development of Ph. harmeri indicates that the larval body develops without positional information from the Hox patterning system. Such phenomenon might be a consequence of the evolutionary intercalation of the larval form into an ancestral life cycle of phoronids. The observed Hox gene expression can also be a consequence of the actinotrocha representing a "head larva", which is composed of the most anterior body region that is devoid of Hox gene expression. Such interpretation is further supported by the expression of head-specific transcription factors. This implies that the Hox patterning system is used for the positional information of the trunk rudiments and is, therefore, delayed to the later larval stages. We propose that a new body form was intercalated to the phoronid life cycle by precocious development of the anterior structures or by delayed development of the trunk rudiment in the ancestral phoronid larva.

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Dicyemida and Orthonectida: Two Stories of Body Plan Simplification

Cited by 46 publications

References 96 publications

Six-state amino acid recoding is not an effective strategy to offset the effects of compositional heterogeneity and saturation in phylogenetic analyses

Six-state amino acid recoding is not an effective strategy to offset the effects of compositional heterogeneity and saturation in phylogenetic analyses

Hox gene expression during the development of the phoronidPhoronopsis harmeri

Hox gene expression during development of the phoronid Phoronopsis harmeri

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