scholarly journals Genome-scale approach proves that the lungfish-coelacanth sister group is the closest living relative of tetrapods with the BEST program

2009 ◽  
Author(s):  
Yunfeng Shan ◽  
Robin Gras
Keyword(s):  
Sister Group ◽  
Genome Scale

scholarly journals Genomic data do not support comb jellies as the sister group to all other animals

2015 ◽  
Vol 112 (50) ◽  
pp. 15402-15407 ◽  
Author(s):  
Davide Pisani ◽  
Walker Pett ◽  
Martin Dohrmann ◽  
Roberto Feuda ◽  
Omar Rota-Stabelli ◽  
...  
Keyword(s):  
Complex Traits ◽  
Sister Group ◽  
Last Common Ancestor ◽  
Nervous Systems ◽  
Conventional View ◽  
Evolution Of Complexity ◽  
Genomic Gene ◽  
Choice Of Species ◽  
Genome Scale ◽  
Inappropriate Choice

Understanding how complex traits, such as epithelia, nervous systems, muscles, or guts, originated depends on a well-supported hypothesis about the phylogenetic relationships among major animal lineages. Traditionally, sponges (Porifera) have been interpreted as the sister group to the remaining animals, a hypothesis consistent with the conventional view that the last common animal ancestor was relatively simple and more complex body plans arose later in evolution. However, this premise has recently been challenged by analyses of the genomes of comb jellies (Ctenophora), which, instead, found ctenophores as the sister group to the remaining animals (the “Ctenophora-sister” hypothesis). Because ctenophores are morphologically complex predators with true epithelia, nervous systems, muscles, and guts, this scenario implies these traits were either present in the last common ancestor of all animals and were lost secondarily in sponges and placozoans (Trichoplax) or, alternatively, evolved convergently in comb jellies. Here, we analyze representative datasets from recent studies supporting Ctenophora-sister, including genome-scale alignments of concatenated protein sequences, as well as a genomic gene content dataset. We found no support for Ctenophora-sister and conclude it is an artifact resulting from inadequate methodology, especially the use of simplistic evolutionary models and inappropriate choice of species to root the metazoan tree. Our results reinforce a traditional scenario for the evolution of complexity in animals, and indicate that inferences about the evolution of Metazoa based on the Ctenophora-sister hypothesis are not supported by the currently available data.

scholarly journals Genome-Scale Phylogenetic and Population Genetic Studies Provide Insight Into Introgression and Adaptive Evolution of Takifugu Species in East Asia

2021 ◽  
Vol 12 ◽  
Author(s):  
Bo Liu ◽  
Zhixiong Zhou ◽  
Yulin Bai ◽  
Junyi Yang ◽  
Yue Shi ◽  
...  
Keyword(s):  
Adaptive Evolution ◽  
Incomplete Lineage Sorting ◽  
Morphological Characteristics ◽  
Sister Group ◽  
Natural Hybridization ◽  
Takifugu Rubripes ◽  
Female Reproduction ◽  
Lineage Sorting ◽  
Group Relationships ◽  
Genome Scale

As a typical marine adaptive radiation species, most Takifugu species are widely distributed in East Asian offshore, which have diversified morphological characteristics and different ecological habits. The phylogenetic relationship and population structure of the Takifugu species was complicated because of incomplete lineage sorting, widespread hybridization and introgression. Therefore, to systematically clarify the phylogenetic relationships of Takifugu genus, explore the introgression and natural hybridization between different Takifugu species, and detect the selective signatures in the adaptive evolution of diversified traits, whole-genome resequencing was used in 122 Takifugu samples from 10 species. Phylogenetic analysis showed solid sister-group relationships between Takifugu bimaculatus and Takifugu flavidus, Takifugu oblongus, and Takifugu niphobles, Takifugu rubripes, and Takifugu obscurus, Takifugu xanthoptreus, and Takifugu ocellatus. Further admixture analysis indicated the divergence of T. obscurus population and the bidirectional gene flow between T. bimaculatus and T. flavidus. Using species-specific homozygous genetic variance sites, we detected the asymmetric introgression between T. bimaculatus and T. flavidus at China East sea and southern Taiwan Strait. By genome-scale genetic diversity scanning, we detected two copies of syt1, zar1 and tgfbr1 related to the semilunar reproduction rhythm in T. niphobles, involved in memory formation, embryo maturation and female reproduction. Furthermore, we also found lots of T. niphobles specific mutations in CDS region of circadian rhythm related genes and endocrine hormone genes. For Takifugu species, our research provides reliable genetic resources and results for the phylogeny, introgression, hybridization and adaptive evolution, and could be used as a guide for the formulation of the protection and proliferation release policies.

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 ◽  
...  
Keyword(s):  
Sister Group ◽  
Sister Group Relationship ◽  
The Matrix ◽  
Biological Interpretation ◽  
Animal Phylogeny ◽  
Inference Methods ◽  
Matrix Construction ◽  
Genome Scale ◽  
Future Work ◽  
Metazoan Phylogeny

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.

scholarly journals Taxonomic sampling and rare genomic changes overcome long-branch attraction in the phylogenetic placement of pseudoscorpions

2020 ◽  
Author(s):  
Andrew Z. Ontano ◽  
Guilherme Gainett ◽  
Shlomi Aharon ◽  
Jesús A. Ballesteros ◽  
Ligia R. Benavides ◽  
...  
Keyword(s):  
Sister Group ◽  
Sister Group Relationship ◽  
Long Branch Attraction ◽  
Genomic Changes ◽  
Phylogenetic Placement ◽  
Taxonomic Sampling ◽  
Rare Genomic Changes ◽  
Litmus Test ◽  
Relationship Of ◽  
Genome Scale

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.

scholarly journals Taxonomic sampling and rare genomic changes overcome long-branch attraction in the phylogenetic placement of pseudoscorpions

2021 ◽  
Author(s):  
Andrew Z Ontano ◽  
Guilherme Gainett ◽  
Shlomi Aharon ◽  
Jesús A Ballesteros ◽  
Ligia R Benavides ◽  
...  
Keyword(s):  
Sister Group ◽  
Sister Group Relationship ◽  
Long Branch Attraction ◽  
Genomic Changes ◽  
Phylogenetic Placement ◽  
Taxonomic Sampling ◽  
Rare Genomic Changes ◽  
Litmus Test ◽  
Relationship Of ◽  
Genome Scale

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.

Diversification of the North American Doellingeria-Eucephalus Clade (Astereae: Asteraceae) Inferred from Molecular and Morphological Evidence

2019 ◽  
Vol 44 (4) ◽  
pp. 930-942
Author(s):  
Geraldine A. Allen ◽  
Luc Brouillet ◽  
John C. Semple ◽  
Heidi J. Guest ◽  
Robert Underhill
Keyword(s):  
North American ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Morphological Evidence ◽  
South American ◽  
New Combinations ◽  
The North ◽  
Hybridization Event ◽  
Ancient Hybridization

Abstract—Doellingeria and Eucephalus form the earliest-diverging clade of the North American Astereae lineage. Phylogenetic analyses of both nuclear and plastid sequence data show that the Doellingeria-Eucephalus clade consists of two main subclades that differ from current circumscriptions of the two genera. Doellingeria is the sister group to E. elegans, and the Doellingeria + E. elegans subclade in turn is sister to the subclade containing all remaining species of Eucephalus. In the plastid phylogeny, the two subclades are deeply divergent, a pattern that is consistent with an ancient hybridization event involving ancestral species of the Doellingeria-Eucephalus clade and an ancestral taxon of a related North American or South American group. Divergence of the two Doellingeria-Eucephalus subclades may have occurred in association with northward migration from South American ancestors. We combine these two genera under the older of the two names, Doellingeria, and propose 12 new combinations (10 species and two varieties) for all species of Eucephalus.

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