A phylogenomic framework and timescale for comparative studies of tunicates

Delsuc, Frédéric; Piégay, Hervé; Tsagkogeorga, Georgia; Simion, Paul; Tilak, Marie‐Ka; Turon, Xavier; López‐Legentil, Susanna; Piette, Jacques; Lemaire, Patrick; Douzery, Emmanuel J. P.

doi:10.1186/s12915-018-0499-2

Cited by 168 publications

(169 citation statements)

References 76 publications

(119 reference statements)

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“…On the higher taxonomic levels within Tunicata, the position of Appendicularia as the sister taxon to the remaining Tunicata has been found in several molecular phylogenetic analyses before (e.g. Wada, ; Swalla et al., ; Delsuc et al., ; Kocot et al., ) and has been discussed based on morphological data as well (Ax, ; Wada, ; see detailed discussion below). The support for this positioning of Appendicularia is low.…”

Section: Discussionmentioning

confidence: 88%

“…Molecular analyses over the last decades have included an increasing number of taxa (Swalla et al., ; Stach and Turbeville, ; Delsuc et al., ; Tsagkogeorga et al., ; Govindarajan et al., ), concentrated on the usage of slowly evolving genes (Tsagkogeorga et al., ) or applied “phylogenomic” methods (Delsuc et al., ; Kocot et al., ) to resolve phylogenetic inter‐relationships between higher tunicate taxa (see review in Giribet, ). Although these studies seemingly approach a more stable framework regarding some contentious points of tunicate phylogeny, it has been pointed out that phylogenetic analysis of tunicate DNA sequences is difficult due to generally increased mutation rates (Tsagkogeorga et al., ) and that phylogenetic information might not be as solid as suggested by statistical support values in published phylogenies (Stach, ).…”

Section: Discussionmentioning

confidence: 99%

“…Moreover, the Olfactores hypothesis is in conflict with the interpretation of numerous characters shared by Cephalochordata and Craniota, which had been interpreted as synapomorphies (Stach, ). Nevertheless, subsequent molecular studies supported the position of Tunicata as the sister group to vertebrates and this is currently the dominant hypothesis (Delsuc et al., ; Giribet, ; Kocot et al., ).…”

Section: Introductionmentioning

confidence: 99%

“…Phlebobranchiata, for example, was found monophyletic in some analyses but paraphyletic with respect to Aplousobranchiata in others. In most analyses, “Pyuridae”, traditionally considered to be a “family” within Stolidobranchiata, was recovered to be paraphyletic with Styelidae nested within “Pyuridae.” Although the number of molecular markers has increased considerably with two recently published studies that in parallel supported the phylogenies just outlined (Delsuc et al., ; Kocot et al., ), the number of species studied remains low considering the diversity found within Tunicata.…”

Section: Introductionmentioning

confidence: 99%

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Phylogenetic analysis of phenotypic characters of Tunicata supports basal Appendicularia and monophyletic Ascidiacea

2019

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With approximately 3000 marine species, Tunicata represents the most disparate subtaxon of Chordata. Molecular phylogenetic studies support Tunicata as sister taxon to Craniota, rendering it pivotal to understanding craniate evolution. Although successively more molecular data have become available to resolve internal tunicate phylogenetic relationships, phenotypic data have not been utilized consistently. Herein these shortcomings are addressed by cladistically analyzing 117 phenotypic characters for 49 tunicate species comprising all higher tunicate taxa, and five craniate and cephalochordate outgroup species. In addition, a combined analysis of the phenotypic characters with 18S rDNA-sequence data is performed in 32 OTUs. The analysis of the combined data is congruent with published molecular analyses. Successively up-weighting phenotypic characters indicates that phenotypic data contribute disproportionally more to the resulting phylogenetic hypothesis. The strict consensus tree from the analysis of the phenotypic characters as well as the single most parsimonious tree found in the analysis of the combined dataset recover monophyletic Appendicularia as sister taxon to the remaining tunicate taxa. Thus, both datasets support the hypothesis that the last common ancestor of Tunicata was free-living and that ascidian sessility is a derived trait within Tunicata. "Thaliacea" is found to be paraphyletic with Pyrosomatida as sister taxon to monophyletic Ascidiacea and the relationship between Doliolida and Salpida is unresolved in the analysis of morphological characters; however, the analysis of the combined data reconstructs Thaliacea as monophyletic nested within paraphyletic "Ascidiacea". Therefore, both datasets differ in the interpretation of the evolution of the complex holoplanktonic life history of thaliacean taxa. According to the phenotypic data, this evolution occurred in the plankton, whereas from the combined dataset a secondary transition into the plankton from a sessile ascidian is inferred. Besides these major differences, both analyses are in accord on many phylogenetic groupings, although both phylogenetic reconstructions invoke a high degree of homoplasy. In conclusion, this study represents the first serious attempt to utilize the potential phylogenetic information present in phenotypic characters to elucidate the inter-relationships of this diverse marine taxon in a consistent cladistic framework.

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Section: Discussionmentioning

confidence: 88%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Phylogenetic analysis of phenotypic characters of Tunicata supports basal Appendicularia and monophyletic Ascidiacea

2019

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“…Ascidian species used in the study. (a) Ascidian phylogeny[27,28]. Species used in this study are bold.…”

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confidence: 99%

Colonial ascidians strongly preyed upon, yet dominate the substrate in a subtropical fouling community

et al. 2019

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Higher diversity and dominance at lower latitudes has been suggested for colonial species. We verified this pattern in species richness of ascidians, finding that higher colonial-to-solitary species ratios occur in the tropics and subtropics. At the latitudinal region with the highest ratio, in southeastern Brazil, we confirmed that colonial species dominate space on artificial plates in two independent studies of five fouling communities. We manipulated settlement plates to measure effects of predation and competition on growth and survivorship of colonial versus solitary ascidians. Eight species were subjected to a predation treatment, i.e. caged versus exposed to predators, and a competition treatment, i.e. leaving versus removing competitors, to assess main and interactive effects. Predation had a greater effect on growth and survivorship of colonial compared to solitary species, whereas competition did not show consistent patterns. We hypothesize that colonial ascidians dominate at this subtropical site despite being highly preyed upon because they regrow when partially consumed and can adjust in shape and space to grow into refuges. We contend that these means of avoiding mortality from predation can have large influences on diversification patterns of colonial species at low latitudes, where predation intensity is greater.

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An evolutionary history of F12 gene: Emergence, loss, and vulnerability with the environment as a driver

Padilla,

Prado,

Anitua

2023

BioEssays

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In the context of macroevolutionary transitions, environmental changes prompted vertebrates already bearing genetic variations to undergo gradual adaptations resulting in profound anatomical, physiological, and behavioral adaptations. The emergence of new genes led to the genetic variation essential in metazoan evolution, just as was gene loss, both sources of genetic variation resulting in adaptive phenotypic diversity. In this context, F12‐coding protein with defense and hemostatic roles emerged some 425 Mya, and it might have contributed in aquatic vertebrates to the transition from water‐to‐land. Conversely, the F12 loss in marine, air‐breathing mammals like cetaceans has been associated with phenotypic adaptations in some terrestrial mammals in their transition to aquatic lifestyle. More recently, the advent of technological innovations in western lifestyle with blood‐contacting devices and harmful environmental nanoparticles, has unfolded new roles of FXII. Environment operates as either a positive or a relaxed selective pressure on genes, and consequently genes are selected or lost. FXII, an old dog facing environmental novelties can learn new tricks and teach us new therapeutic avenues.

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A phylogenomic framework and timescale for comparative studies of tunicates

Cited by 168 publications

References 76 publications

Phylogenetic analysis of phenotypic characters of Tunicata supports basal Appendicularia and monophyletic Ascidiacea

Phylogenetic analysis of phenotypic characters of Tunicata supports basal Appendicularia and monophyletic Ascidiacea

Colonial ascidians strongly preyed upon, yet dominate the substrate in a subtropical fouling community

An evolutionary history of F12 gene: Emergence, loss, and vulnerability with the environment as a driver

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