scholarly journals Revisiting metazoan phylogeny with genomic sampling of all phyla

2019 ◽  
Vol 286 (1906) ◽  
pp. 20190831 ◽  
Author(s):  
Christopher E. Laumer ◽  
Rosa Fernández ◽  
Sarah Lemer ◽  
David Combosch ◽  
Kevin M. Kocot ◽  
...  

Proper biological interpretation of a phylogeny can sometimes hinge on the placement of key taxa—or fail when such key taxa are not sampled. In this light, we here present the first attempt to investigate (though not conclusively resolve) animal relationships using genome-scale data from all phyla. Results from the site-heterogeneous CAT + GTR model recapitulate many established major clades, and strongly confirm some recent discoveries, such as a monophyletic Lophophorata, and a sister group relationship between Gnathifera and Chaetognatha, raising continued questions on the nature of the spiralian ancestor. We also explore matrix construction with an eye towards testing specific relationships; this approach uniquely recovers support for Panarthropoda, and shows that Lophotrochozoa (a subclade of Spiralia) can be constructed in strongly conflicting ways using different taxon- and/or orthologue sets. Dayhoff-6 recoding sacrifices information, but can also reveal surprising outcomes, e.g. full support for a clade of Lophophorata and Entoprocta + Cycliophora, a clade of Placozoa + Cnidaria, and raising support for Ctenophora as sister group to the remaining Metazoa, in a manner dependent on the gene and/or taxon sampling of the matrix in question. Future work should test the hypothesis that the few remaining uncertainties in animal phylogeny might reflect violations of the various stationarity assumptions used in contemporary inference methods.

2017 ◽  
Author(s):  
Christopher E. Laumer ◽  
Harald Gruber-Vodicka ◽  
Michael G. Hadfield ◽  
Vicki B. Pearse ◽  
Ana Riesgo ◽  
...  

AbstractThe phylogenetic placement of the morphologically simple placozoans is crucial to understanding the evolution of complex animal traits. Here, we examine the influence of adding new genomes from placozoans to a large dataset designed to study the deepest splits in the animal phylogeny. Using site-heterogeneous substitution models, we show that it is possible to obtain strong support, in both amino acid and reduced-alphabet matrices, for either a sister-group relationship between Cnidaria and Placozoa, or for Cnidaria and Bilateria (=Planulozoa), also seen in most published work to date, depending on the orthologues selected to construct the matrix. We demonstrate that a majority of genes show evidence of compositional heterogeneity, and that the support for Planulozoa can be assigned to this source of systematic error. In interpreting this placozoan-cnidarian clade, we caution against a peremptory reading of placozoans as secondarily reduced forms of little relevance to broader discussions of early animal evolution.


eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Christopher E Laumer ◽  
Harald Gruber-Vodicka ◽  
Michael G Hadfield ◽  
Vicki B Pearse ◽  
Ana Riesgo ◽  
...  

The phylogenetic placement of the morphologically simple placozoans is crucial to understanding the evolution of complex animal traits. Here, we examine the influence of adding new genomes from placozoans to a large dataset designed to study the deepest splits in the animal phylogeny. Using site-heterogeneous substitution models, we show that it is possible to obtain strong support, in both amino acid and reduced-alphabet matrices, for either a sister-group relationship between Cnidaria and Placozoa, or for Cnidaria and Bilateria as seen in most published work to date, depending on the orthologues selected to construct the matrix. We demonstrate that a majority of genes show evidence of compositional heterogeneity, and that support for the Cnidaria + Bilateria clade can be assigned to this source of systematic error. In interpreting these results, we caution against a peremptory reading of placozoans as secondarily reduced forms of little relevance to broader discussions of early animal evolution.


2020 ◽  
Author(s):  
Andrew Z. Ontano ◽  
Guilherme Gainett ◽  
Shlomi Aharon ◽  
Jesús A. Ballesteros ◽  
Ligia R. Benavides ◽  
...  

AbstractLong-branch attraction is a systematic artifact that results in erroneous groupings of fast-evolving taxa. The combination of short, deep internodes in tandem with LBA artifacts has produced empirically intractable parts of the Tree of Life. One such group is the arthropod subphylum Chelicerata, whose backbone phylogeny has remained unstable despite improvements in phylogenetic methods and genome-scale datasets. Pseudoscorpion placement is particularly variable across datasets and analytical frameworks, with this group either clustering with other long-branch orders or with Arachnopulmonata (scorpions and tetrapulmonates). To surmount LBA, we investigated the effect of taxonomic sampling via sequential deletion of basally branching pseudoscorpion superfamilies, as well as varying gene occupancy thresholds in supermatrices. We show that concatenated supermatrices and coalescent-based summary species tree approaches support a sister group relationship of pseudoscorpions and scorpions, when more of the basally branching taxa are sampled. Matrix completeness had demonstrably less influence on tree topology. As an external arbiter of phylogenetic placement, we leveraged the recent discovery of an ancient genome duplication in the common ancestor of Arachnopulmonata as a litmus test for competing hypotheses of pseudoscorpion relationships. We generated a high-quality developmental transcriptome and the first genome for pseudoscorpions to assess the incidence of arachnopulmonate-specific duplications (e.g., homeobox genes and miRNAs). Our results support the inclusion of pseudoscorpions in Arachnopulmonata, as the sister group of scorpions. Panscorpiones (new name) is proposed for the clade uniting Scorpiones and Pseudoscorpiones.


Author(s):  
Andrew Z Ontano ◽  
Guilherme Gainett ◽  
Shlomi Aharon ◽  
Jesús A Ballesteros ◽  
Ligia R Benavides ◽  
...  

Abstract Long-branch attraction is a systematic artifact that results in erroneous groupings of fast-evolving taxa. The combination of short, deep internodes in tandem with LBA artifacts has produced empirically intractable parts of the Tree of Life. One such group is the arthropod subphylum Chelicerata, whose backbone phylogeny has remained unstable despite improvements in phylogenetic methods and genome-scale datasets. Pseudoscorpion placement is particularly variable across datasets and analytical frameworks, with this group either clustering with other long-branch orders or with Arachnopulmonata (scorpions and tetrapulmonates). To surmount LBA, we investigated the effect of taxonomic sampling via sequential deletion of basally branching pseudoscorpion superfamilies, as well as varying gene occupancy thresholds in supermatrices. We show that concatenated supermatrices and coalescent-based summary species tree approaches support a sister group relationship of pseudoscorpions and scorpions, when more of the basally branching taxa are sampled. Matrix completeness had demonstrably less influence on tree topology. As an external arbiter of phylogenetic placement, we leveraged the recent discovery of an ancient genome duplication in the common ancestor of Arachnopulmonata as a litmus test for competing hypotheses of pseudoscorpion relationships. We generated a high-quality developmental transcriptome and the first genome for pseudoscorpions to assess the incidence of arachnopulmonate-specific duplications (e.g., homeobox genes and miRNAs). Our results support the inclusion of pseudoscorpions in Arachnopulmonata (new definition), as the sister group of scorpions. Panscorpiones (new name) is proposed for the clade uniting Scorpiones and Pseudoscorpiones.


Zootaxa ◽  
2019 ◽  
Vol 4674 (4) ◽  
pp. 482-490 ◽  
Author(s):  
HONGYU LI ◽  
BO WANG ◽  
XINGYUE LIU

The male of Cretaconiopteryx grandis Liu & Lu, 2017, which is the only representative species of the extinct dustywing subfamily Cretaconiopteryginae, is described for the first time from the Upper Cretaceous Burmese amber. The male genitalia, well preserved in the examined specimen, show a number of plesiomorphic characters, which support the sister group relationship between Coniopterygidae and the rest of extant lacewing families. 


2003 ◽  
Vol 40 (4) ◽  
pp. 527-556 ◽  
Author(s):  
Michael deBraga

A morphological study of the postcranial skeleton of Procolophon trigoniceps from the Lower Triassic of South Africa and Antarctica is undertaken. Procolophon shares a sister-group relationship with the procolophonid Tichvinskia from the Lower Triassic of Russia and is a basal member of Procolophonidae. This clade also includes the enigmatic taxon Sclerosaurus, believed most recently to be a pareiasaur relative. Owenettids form a separate lineage from Procolophonidae and are predominantly restricted to the Permian of both South Africa and Madagascar. A phylogenetically based assessment is considered, in which specialized modern taxa (sand lizards) are compared to their nonfossorial sister clade, allowing for "key innovations" to be identified. A similar comparison between owenettids and procolophonids reveals a number of apparent "key innovations" within procolophonids that are suggestive of a burrowing lifestyle for Procolophon.


2013 ◽  
Vol 198 ◽  
pp. 633-638 ◽  
Author(s):  
Marek Płaczek

Work presents a proposal of an analysis method of the piezoelectric transducer. The considered system is a longitudinally vibrating single PZT plate. The main aim of this work is to designate characteristics of the considered PZT plate. Using constitutive equations of piezoelectric materials and an equation of the plates motion a matrix of characteristics of the system was obtained. Relations between mechanical and electrical parameters (forces, displacements, electric current and voltage) that describe behaviour of the system are included in the matrix of characteristics. A dynamic flexibility relation between the plates deformation and a force applied to the system is considered. A structural damping of the plates material was being taken into consideration and its influence on the plates dynamic flexibility is analysed. This work is an introduction to a task of analysis of complex systems. In future work the developed model and proposed mathematical algorithm will be used to analyse piezoelectric stacks. Non-classical methods will be used. It is a part of research works of Gliwice research centre related with an analysis and synthesis of mechanical and mechatronic systems [4-7,9,10,16-18]. Passive and active mechanical and mechatronic systems with piezoelectric transducers were analysed [1-3]. Works were also supported by computer-aided methods [8]. Both classical and non-classical methods were being considered. The discussed subject is important due to increasing number of applications of both simple and reverse piezoelectric phenomena in various modern technical devices.


1993 ◽  
Vol 30 (10) ◽  
pp. 2128-2138 ◽  
Author(s):  
Donald B. Brinkman ◽  
Jiang-Hua Peng

Ordosemys leios, n.gen., n.sp., from the Early Cretaceous Luohandong Formation, Zhidan Group, Ordos Basin, Inner Mongolia, is a primitive aquatic turtle with a reduced, fenestrated plastron. It shares with the members of the Centrocryptodira the presence of well-formed articular surfaces on the cervical and caudal vertebrae. Within the Centrocryptodira, characters of the cervical vertebrae suggest it is more closely related to the Polycryptodira than is the Meiolaniidae. Ordosemys shares with the Chelydridae the presence of two procoelous anterior caudals, but this character may be primitive for the Polycryptodira. Characters of the basicranial region of the braincase shared by Ordosemys and the Chelonioidea support a sister-group relationship between these two taxa, but a sister-group relationship between Ordosemys and the Polycryptodira is more strongly supported by characters shared by the Chelonioidea and other members of the Polycryptodira.


2021 ◽  
Author(s):  
Ksenia Juravel ◽  
Luis Porras ◽  
Sebastian Hoehna ◽  
Davide Pisani ◽  
Gert Wörheide

An accurate phylogeny of animals is needed to clarify their evolution, ecology, and impact on shaping the biosphere. Although multi-gene alignments of up to several hundred thousand amino acids are nowadays routinely used to test hypotheses of animal relationships, some nodes towards the root of the animal phylogeny are proving hard to resolve. While the relationships of the non-bilaterian lineages, primarily sponges (Porifera) and comb jellies (Ctenophora), have received much attention since more than a decade, controversies about the phylogenetic position of the worm-like bilaterian lineage Xenacoelomorpha and the monophyly of the "Superphylum" Deuterostomia have more recently emerged. Here we independently analyse novel genome gene content and morphological datasets to assess patterns of phylogenetic congruence with previous amino-acid derived phylogenetic hypotheses. Using statistical hypothesis testing, we show that both our datasets very strongly support sponges as the sister group of all the other animals, Xenoacoelomorpha as the sister group of the other Bilateria, and largely support monophyletic Deuterostomia. Based on these results, we conclude that the last common animal ancestor may have been a simple, filter-feeding organism without a nervous system and muscles, while the last common ancestor of Bilateria might have been a small, acoelomate-like worm without a through gut.


1984 ◽  
Vol 15 (2) ◽  
pp. 151-178 ◽  
Author(s):  
Niels P. Kristensen

AbstractThe genital segments and internal genitalia of Agathiphaga vitiensis are described. Sternum VIII is anteriorly produced into blunt paired apophyses and posteriorly into a tongue-shaped lobe. Segment IX is a complete ring, very short in the dorsal and ventral midlines; its anterolateral lobes are largely apodemal. The long and curved gonopod ("valva") consists of a single piece. There is no median sclerite between the gonopod bases, but an open, softwalled "subgenital crypt" below the entrance of the phallocrypt may be homologous with the "median plate" in other primitive homoneurous moths. Tergum X bears a pair of broad "superior lobes" and the postgenital complex terminates in a medially intended, sclerotized "terminal lobe" above the eversible perianal area. The roof of the posterior part of the genital chamber bears a median aggregation of cuticular spines (the "spiny plate"), and a pair of smooth lateral sclerotizations ("presocii") tentatively attributed to venter X: a pair of setose sclerites (socii) are tentatively attributed to the paraprocts. The area bearing the spiny plate and presocii may in repose be folded down behind the phallus, thereby closing the phallocrypt. The phallus comprises a tubular phallotheca and an eversible aedeagus; the thick basal margen of the phallotheca is posteriorly expanded and forms the floor of the greater part of the phallocrypt; there is no ventral aedeagal branch. The musculature comprises two IX/X muscles, a segment IX muscle inserting on the subgenital crypt, phallic pro- and retractors (the former originating in the gonopod), intrinsic phallic muscles, a single segment IX muscle (adductor) to the gonopod and five intrinsic muscles of the postgenital complex. Each testis comprises four large, separate follicles. The spermatozoa do not remain grouped in discrete bundles in the vas deferens. Seminal vesicles are located on the vasa deferentia close to the testis and are doubtfully homologous with the vesicles in other Lepidoptera. The unpaired ejaculatory duct is very short. The evidence bearing on a reconstruction of the ground plan of the lepidopteran male genitalia is reviewed. Segment VIII was similar to the preceding segments. It is tentatively suggested that tergum and sternum IX were fused, that the gonopod was undivided and that a tubular, partly sclerotized aedeagus was present; deviations from these states within the order are therefore considered to be autapomorphic. The base of the aedeagus was probably surrounded by a short, collarlike phallotheca. It is suggested that there was a median sclerite between the gonopod bases, but the presence of discrete, paired and muscular "valvellae" in the lepidopteran ground plan is considered doubtful. It is further suggested that dorsum X bore a pair of lobes and that there were paired sclerotizations in venter X. The X/XI boundary is very difficult to trace. Seventeen muscle sets are ascribed to the lepidopteran ground plan; it is considered an autapomorphy of this ground plan that the phallic protractor originates within the gonopod. The testes presumably had large, separate follicles and there may have been two pairs of tubular accessory glands. The testes and the double set of accessory glands of Agathiphaga could be cited in support of a sistergroup relationship to all other Lepidoptera whereas the phallic structure (and possibly the "spiny plate") might support a sister group relationship to the Heterobathmiina. There is no support in male genital structure for a sistergroup relationship to the Heterobathmiina + Glossata; the latter phylogenetic hypothesis may be preferable on other grounds, however.


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