Phylogenomic analysis of evolutionary relationships in Ranitomeya poison frogs (Family Dendrobatidae) using ultraconserved elements

The genus Hosta, which has a native distribution in temperate East Asia and a number of species ranging from 23 to 40, represents a taxonomically important and ornamentally popular plant. Despite its taxonomic and horticultural importance, the genus Hosta has remained taxonomically challenging owing to insufficient diagnostic features, continuous morphological variation, and the process of hybridization and introgression, making species circumscription and phylogenetic inference difficult. In this study, we sequenced 11 accessions of Hosta plastomes, including members of three geographically defined subgenera, Hosta, Bryocles, and Giboshi, determined the characteristics of plastomes, and inferred their phylogenetic relationships. We found highly conserved plastomes among the three subgenera, identified several mutation hotspots that can be used as barcodes, and revealed the patterns of codon usage bias and RNA editing sites. Five positively selected plastome genes (rbcL, rpoB, rpoC2, rpl16, and rpl20) were identified. Phylogenetic analysis suggested (1) the earliest divergence of subg. Hosta, (2) non-monophyly of subg. Bryocles and its two sections (Lamellatae and Stoloniferae), (3) a sister relationship between H. sieboldiana (subg. Giboshi) and H. ventricosa (subg. Bryocles), and (4) reciprocally monophyletic and divergent lineages of H. capitata in Korea and Japan, requiring further studies of their taxonomic distinction.

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Bacterial Origin and Reductive Evolution of the CPR Group

Genome Biology and Evolution ◽

10.1093/gbe/evaa024 ◽

2020 ◽

Vol 12 (3) ◽

pp. 103-121 ◽

Cited By ~ 3

Author(s):

Rijja Hussain Bokhari ◽

Nooreen Amirjan ◽

Hyeonsoo Jeong ◽

Kyung Mo Kim ◽

Gustavo Caetano-Anollés ◽

...

Keyword(s):

Cell Interaction ◽

Protein Domain ◽

Evolutionary Relationships ◽

Current Debate ◽

Phylogenomic Analysis ◽

Origin And Evolution ◽

Protein Superfamilies ◽

Metabolic Functions ◽

Structure Databases ◽

Bacterial Proteomes

Abstract The candidate phyla radiation (CPR) is a proposed subdivision within the bacterial domain comprising several candidate phyla. CPR organisms are united by small genome and physical sizes, lack several metabolic enzymes, and populate deep branches within the bacterial subtree of life. These features raise intriguing questions regarding their origin and mode of evolution. In this study, we performed a comparative and phylogenomic analysis to investigate CPR origin and evolution. Unlike previous gene/protein sequence-based reports of CPR evolution, we used protein domain superfamilies classified by protein structure databases to resolve the evolutionary relationships of CPR with non-CPR bacteria, Archaea, Eukarya, and viruses. Across all supergroups, CPR shared maximum superfamilies with non-CPR bacteria and were placed as deep branching bacteria in most phylogenomic trees. CPR contributed 1.22% of new superfamilies to bacteria including the ribosomal protein L19e and encoded four core superfamilies that are likely involved in cell-to-cell interaction and establishing episymbiotic lifestyles. Although CPR and non-CPR bacterial proteomes gained common superfamilies over the course of evolution, CPR and Archaea had more common losses. These losses mostly involved metabolic superfamilies. In fact, phylogenies built from only metabolic protein superfamilies separated CPR and non-CPR bacteria. These findings indicate that CPR are bacterial organisms that have probably evolved in an Archaea-like manner via the early loss of metabolic functions. We also discovered that phylogenies built from metabolic and informational superfamilies gave contrasting views of the groupings among Archaea, Bacteria, and Eukarya, which add to the current debate on the evolutionary relationships among superkingdoms.

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Phylogenomic analysis of a rapid radiation of misfit fishes (Syngnathiformes) using ultraconserved elements

Molecular Phylogenetics and Evolution ◽

10.1016/j.ympev.2017.05.002 ◽

2017 ◽

Vol 113 ◽

pp. 33-48 ◽

Cited By ~ 17

Author(s):

S.J. Longo ◽

B.C. Faircloth ◽

A. Meyer ◽

M.W. Westneat ◽

M.E. Alfaro ◽

...

Keyword(s):

Phylogenomic Analysis ◽

Rapid Radiation ◽

Ultraconserved Elements

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A Transcriptomic-Phylogenomic Analysis of the Evolutionary Relationships of Flatworms

Current Biology ◽

10.1016/j.cub.2015.03.034 ◽

2015 ◽

Vol 25 (10) ◽

pp. 1347-1353 ◽

Cited By ~ 98

Author(s):

Bernhard Egger ◽

François Lapraz ◽

Bartłomiej Tomiczek ◽

Steven Müller ◽

Christophe Dessimoz ◽

...

Keyword(s):

Evolutionary Relationships ◽

Phylogenomic Analysis

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Phylogenomic analysis of integral diiron membrane histidine motif-containing enzymes in ciliates provides insights into their function and evolutionary relationships

Molecular Phylogenetics and Evolution ◽

10.1016/j.ympev.2017.05.023 ◽

2017 ◽

Vol 114 ◽

pp. 1-13 ◽

Cited By ~ 4

Author(s):

Nicolas G. Cid ◽

María L. Sanchez Granel ◽

María G. Montes ◽

María E. Elguero ◽

Clara B. Nudel ◽

...

Keyword(s):

Evolutionary Relationships ◽

Phylogenomic Analysis

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Phylogenomic analysis of trichomycterid catfishes (Teleostei: Siluriformes) inferred from ultraconserved elements

Scientific Reports ◽

10.1038/s41598-020-59519-w ◽

2020 ◽

Vol 10 (1) ◽

Cited By ~ 9

Author(s):

Luz E. Ochoa ◽

Aléssio Datovo ◽

Carlos DoNascimiento ◽

Fabio F. Roxo ◽

Mark H. Sabaj ◽

...

Keyword(s):

Phylogenomic Analysis ◽

Ultraconserved Elements

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Phylogenomic Analysis of Concatenated Ultraconserved Elements Reveals the Recent Evolutionary Radiation of the Fairy Wrasses (Teleostei: Labridae: Cirrhilabrus)

Systematic Biology ◽

10.1093/sysbio/syab012 ◽

2021 ◽

Author(s):

Yi-Kai Tea ◽

Xin Xu ◽

Joseph D DiBattista ◽

Nathan Lo ◽

Peter F Cowman ◽

...

Keyword(s):

Phylogenetic Signal ◽

Estimation Error ◽

Gene Tree ◽

Molecular Dating ◽

Morphological Data ◽

Phylogenomic Analysis ◽

Gene Trees ◽

Data Set ◽

Ultraconserved Elements ◽

Species Complexes

Abstract The fairy wrasses (genus Cirrhilabrus) are among the most successful of the extant wrasse lineages (Teleostei: Labridae), with their 61 species accounting for nearly 10$\%$ of the family. Although species complexes within the genus have been diagnosed on the basis of coloration patterns and synapomorphies, attempts to resolve evolutionary relationships among these groups using molecular and morphological data have largely been unsuccessful. Here, we use a phylogenomic approach with a data set comprising 991 ultraconserved elements (UCEs) and mitochondrial COI to uncover the evolutionary history and patterns of temporal and spatial diversification of the fairy wrasses. Our analyses of phylogenetic signal suggest that most gene-tree incongruence is caused by estimation error, leading to poor resolution in a summary-coalescent analysis of the data. In contrast, analyses of concatenated sequences are able to resolve the major relationships of Cirrhilabrus. We determine the placements of species that were previously regarded as incertae sedis and find evidence for the nesting of Conniella, an unusual, monotypic genus, within Cirrhilabrus. Our relaxed-clock dating analysis indicates that the major divergences within the genus occurred around the Miocene–Pliocene boundary, followed by extensive cladogenesis of species complexes in the Pliocene–Pleistocene. Biogeographic reconstruction suggests that the fairy wrasses emerged within the Coral Triangle, with episodic fluctuations of sea levels during glacial cycles coinciding with shallow divergence events but providing few opportunities for more widespread dispersal. Our study demonstrates both the resolving power and limitations of UCEs across shallow timescales where there is substantial estimation error in individual gene trees.[Biogeography; concatenation; gene genealogy interrogation; gene trees; molecular dating; summary coalescent; UCEs.]

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