scholarly journals Integrated Genomic Analyses From Low-Depth Sequencing Help Resolve Phylogenetic Incongruence in the Bamboos (Poaceae: Bambusoideae)

2021 ◽  
Vol 12 ◽  
Author(s):  
Domitille Chalopin ◽  
Lynn G. Clark ◽  
William P. Wysocki ◽  
Minkyu Park ◽  
Melvin R. Duvall ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Sequence Data ◽  
Nuclear Gene ◽  
Genomic Information ◽  
Genomic Tools ◽  
Herbaceous Bamboos ◽  
Genomic Analyses ◽  
Woody Bamboos ◽  
First Time ◽  
Ancient Hybridization

The bamboos (Bambusoideae, Poaceae) comprise a major grass lineage with a complex evolutionary history involving ancient hybridization and allopolyploidy. About 1700 described species are classified into three tribes, Olyreae (herbaceous bamboos), Bambuseae (tropical woody bamboos), and Arundinarieae (temperate woody bamboos). Nuclear analyses strongly support monophyly of the woody tribes, whereas plastome analyses strongly support paraphyly, with Bambuseae sister to Olyreae. Our objectives were to clarify the origin(s) of the woody bamboo tribes and resolve the nuclear vs. plastid conflict using genomic tools. For the first time, plastid and nuclear genomic information from the same bamboo species were combined in a single study. We sampled 51 species of bamboos representing the three tribes, estimated their genome sizes and generated low-depth sample sequence data, from which plastomes were assembled and nuclear repeats were analyzed. The distribution of repeat families was found to agree with nuclear gene phylogenies, but also provides novel insights into nuclear evolutionary history. We infer two early, independent hybridization events, one between an Olyreae ancestor and a woody ancestor giving rise to the two Bambuseae lineages, and another between two woody ancestors giving rise to the Arundinarieae. Retention of the Olyreae plastome associated with differential dominance of nuclear genomes and subsequent diploidization in some lineages explains the paraphyly observed in plastome phylogenetic estimations. We confirm ancient hybridization and allopolyploidy in the origins of the extant woody bamboo lineages and propose biased fractionation and diploidization as important factors in their evolution.

scholarly journals Phylogenomic resolution of scorpions reveals multilevel discordance with morphological phylogenetic signal

2015 ◽  
Vol 282 (1804) ◽  
pp. 20142953 ◽  
Author(s):  
Prashant P. Sharma ◽  
Rosa Fernández ◽  
Lauren A. Esposito ◽  
Edmundo González-Santillán ◽  
Lionel Monod
Keyword(s):  
Fossil Record ◽  
Evolutionary History ◽  
Digestive System ◽  
Sequence Data ◽  
Phylogenetic Signal ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Single Origin ◽  
As Species ◽  
First Time

Scorpions represent an iconic lineage of arthropods, historically renowned for their unique bauplan, ancient fossil record and venom potency. Yet, higher level relationships of scorpions, based exclusively on morphology, remain virtually untested, and no multilocus molecular phylogeny has been deployed heretofore towards assessing the basal tree topology. We applied a phylogenomic assessment to resolve scorpion phylogeny, for the first time, to our knowledge, sampling extensive molecular sequence data from all superfamilies and examining basal relationships with up to 5025 genes. Analyses of supermatrices as well as species tree approaches converged upon a robust basal topology of scorpions that is entirely at odds with traditional systematics and controverts previous understanding of scorpion evolutionary history. All analyses unanimously support a single origin of katoikogenic development, a form of parental investment wherein embryos are nurtured by direct connections to the parent's digestive system. Based on the phylogeny obtained herein, we propose the following systematic emendations: Caraboctonidae is transferred to Chactoidea new superfamilial assignment ; superfamily Bothriuroidea revalidated is resurrected and Bothriuridae transferred therein; and Chaerilida and Pseudochactida are synonymized with Buthida new parvordinal synonymies .

scholarly journals Host-switching by a vertically transmitted rhabdovirus in Drosophila

2011 ◽  
Vol 7 (5) ◽  
pp. 747-750 ◽  
Author(s):  
Ben Longdon ◽  
Lena Wilfert ◽  
Jewelna Osei-Poku ◽  
Heather Cagney ◽  
Darren J. Obbard ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Sequence Data ◽  
Horizontal Transmission ◽  
Virus Infections ◽  
Diverse Range ◽  
Host Fidelity ◽  
Bacterial Endosymbionts ◽  
Host Lineage ◽  
Sigma Virus ◽  
First Time

A diverse range of endosymbionts are found within the cells of animals. As these endosymbionts are normally vertically transmitted, we might expect their evolutionary history to be dominated by host-fidelity and cospeciation with the host. However, studies of bacterial endosymbionts have shown that while this is true for some mutualists, parasites often move horizontally between host lineages over evolutionary timescales. For the first time, to our knowledge, we have investigated whether this is also the case for vertically transmitted viruses. Here, we describe four new sigma viruses, a group of vertically transmitted rhabdoviruses previously known in Drosophila . Using sequence data from these new viruses, and the previously described sigma viruses, we show that they have switched between hosts during their evolutionary history. Our results suggest that sigma virus infections may be short-lived in a given host lineage, so that their long-term persistence relies on rare horizontal transmission events between hosts.

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.

scholarly journals Investigation of the molecular signatures of selection on ATP synthase genes in the marine bivalve Limecola balthica

2019 ◽  
Vol 32 ◽  
pp. 3 ◽  
Author(s):  
Eric Pante ◽  
Vanessa Becquet ◽  
Amélia Viricel ◽  
Pascale Garcia
Keyword(s):  
Atp Synthase ◽  
Sequence Data ◽  
Nuclear Gene ◽  
Cellular Respiration ◽  
Marine Bivalve ◽  
Gamma Subunit ◽  
Genetic Barriers ◽  
Different Populations ◽  
Peptide Interaction ◽  
Evolutionarily Stable

We used transcriptomic sequence data to describe patterns of divergence and selection across different populations of a marine bivalve (Limecola balthica). Our analyses focused on a nuclear gene (atp5c1) that was previously detected in an FST scan as highly structured among populations separated by the Finistère Peninsula in France. This gene encodes the gamma subunit of the FO/F1 ATP synthase, a multi-protein complex that is paramount to cellular respiration and energy production. Analysis of non-synonymous to synonymous mutation ratios revealed that 65% of the gene is highly conserved (dN/dS ≤ 0.1, min = 0), while 6% of the gene is likely under positive selection (dN/dS ≥ 1, max = 2.03). All replacement mutations are clustered on a 46 residues portion of the protein, within an inter-peptide interaction zone. Comparative genomics suggests that these mutations are evolutionarily stable, and we hypothesize that they are involved in inter-population genetic incompatibilities with other subunits of the ATP synthase complex. The protein stability of the gamma subunit conferred by southern variants was inferred to be higher under warmer temperatures, suggesting that environmental conditions may contribute to the strength of genetic barriers in L. balthica.

Molecular phylogeny of diploid Hordeum species and incongruence between chloroplast and nuclear datasets

Genome ◽  
2011 ◽  
Vol 54 (12) ◽  
pp. 986-992 ◽  
Author(s):  
Huan Wang ◽  
Dongfa Sun ◽  
Genlou Sun
Keyword(s):  
Evolutionary History ◽  
Nuclear Gene ◽  
Intergenic Spacer ◽  
Molecular Data ◽  
Genome Species ◽  
Different Types ◽  
History Of ◽  
Morphological And Molecular Data ◽  
Hordeum Species ◽  
Eurasian Species

The phylogeny of diploid Hordeum species has been studied using both chloroplast and nuclear gene sequences. However, the studies of different nuclear datasets of Hordeum species often arrived at similar conclusions, whereas the studies of different chloroplast DNA data generally resulted in inconsistent conclusions. Although the monophyly of the genus is well supported by both morphological and molecular data, the intrageneric phylogeny is still a matter of controversy. To better understand the evolutionary history of Hordeum species, two chloroplast gene loci (trnD-trnT intergenic spacer and rps16 gene) and one nuclear marker (thioreoxin-like gene (HTL)) were used to explore the phylogeny of Hordeum species. Two obviously different types of trnD-trnT sequences were observed, with an approximately 210 base pair difference between these two types: one for American species, another for Eurasian species. The trnD-trnT data generally separated the diploid Hordeum species into Eurasian and American clades, with the exception of Hordeum marinum subsp. gussoneanum. The rps16 data also grouped most American species together and suggested that Hordeum flexuosum has a different plastid type from the remaining American species. The nuclear gene HTL data clearly divided Hordeum species into two clades: the Xu + H genome clade and the Xa + I genome clade. Within clades, H genome species were well separated from the Xu species, and the I genome species were well separated from the Xa genome species. The incongruence between chloroplast and nuclear datasets was found and discussed.

scholarly journals Sequences of the second internal transcribed spacer of ribosomal DNA for three species of Trichostrongylus (Nematoda: Trichostrongylidae) from sheep in Russia

2007 ◽  
Vol 44 (2) ◽  
pp. 43-46 ◽  
Author(s):  
D. Kuznetsov ◽  
N. Kuznetsova
Keyword(s):  
Dna Sequence ◽  
Intraspecific Variation ◽  
Ribosomal Dna ◽  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Moscow Region ◽  
Dna Sequence Data ◽  
Interspecific Differences ◽  
Second Internal Transcribed Spacer ◽  
First Time

AbstractFor the first time, DNA sequence data were obtained for three species of Trichostrongylus from Russia. Internal transcribed spacer (ITS-2) of ribosomal DNA was sequenced for T. axei, T. colubriformis and T. probolurus from sheep from the Moscow region. ITS-2 rDNA length was estimated as 238 nucleotides for T. colubriformis and T. probolurus and 237 nucleotides for T. axei. The G+C content of the ITS-2 sequences of T. colubriformis, T. axei and T. probolurus were 31 %, 32 % and 34 % respectively. The level of interspecific differences in ITS-2 of rDNA of T. axei, T. probolurus and T. colubriformis ranged from 3 to 4 %. The ITS-2 sequences from the Russian specimens were compared with those of T. axei, T. probolurus and T. colubriformis from Australia and Germany. Intraspecific variation ranged from 0 % in T. colubriformis to 3.0 % in T. axei.

Clathrosporium retortum, a novel aeroaquatic fungus in the Sordariomycetidae (Ascomycota) from Brazil

Phytotaxa ◽  
2015 ◽  
Vol 239 (1) ◽  
pp. 17
Author(s):  
Larissa Bernardino Moro ◽  
Gregorio Delgado ◽  
Iracema Helena SCHOENLEIN-CRUSIUS
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Type Specimen ◽  
Molecular Data ◽  
Sao Paulo ◽  
São Paulo ◽  
Present Fungus ◽  
Broad Concept ◽  
Morphological And Molecular Data ◽  
First Time

Clathrosporium retortum sp. nov., collected on submerged mixed leaf litter samples at Ilha do Cardoso State Park, São Paulo state, Brazil, is described based on morphological and molecular data. The fungus is characterized by forming whitish, dense, subglobose to irregular propagules, hyaline to subhyaline when young, subhyaline to dark brown at maturity, that are formed by densely interwoven conidial filaments with each conidial cell repeatedly branching bilaterally or occasionally unilaterally. Phylogenetic analyses using partial LSU nrDNA sequence data suggest that C. retortum belongs in the Sordariomycetes (Ascomycota) where it forms a well-supported clade with Clohesia corticola in the Sordariomycetidae, but its ordinal or familial placement remains unresolved. Its phylogenetic placement confirms the polyphyletic nature of aeroaquatic fungi like Clathrosporium, as it was distantly related to one available sequence in GenBank named as C. intricatum, the type species, which is phylogenetically related to the Helotiales (Leotiomycetes). However, due to lack of authenticity of the identity of this sequence with the type specimen of C. intricatum, a broad concept of Clathrosporium is tentatively adopted here to accommodate the present fungus instead of introducing a new genus. Beverwykella clathrata, Helicoön septatissimum and Peyronelina glomerulata are recorded for the first time from Brazil. Cancellidium applanatum and Candelabrum brocchiatum are new records for the state of São Paulo.

scholarly journals Discordant evolution of organellar genomes in peas (Pisum L.)

2020 ◽  
Author(s):  
Vera S. Bogdanova ◽  
Natalia V. Shatskaya ◽  
Anatoliy V. Mglinets ◽  
Oleg E. Kosterin ◽  
Gennadiy V. Vasiliev
Keyword(s):  
Phylogenetic Trees ◽  
Nuclear Genome ◽  
Nuclear Gene ◽  
Plant Evolution ◽  
Hybrid Origin ◽  
Mitochondrial Genomes ◽  
North East ◽  
Plastid Genomes ◽  
First Time ◽  
Evolutionary Fate

AbstractPlastids and mitochondria have their own small genomes which do not undergo meiotic recombination and may have evolutionary fate different from each other and nuclear genome, thus highlighting interesting phenomena in plant evolution. We for the first time sequenced mitochondrial genomes of pea (Pisum L.), in 38 accessions mostly representing diverse wild germplasm from all over pea geographical range. Six structural types of pea mitochondrial genome were revealed. From the same accessions, plastid genomes were sequenced. Bayesian phylogenetic trees based on the plastid and mitochondrial genomes were compared. The topologies of these trees were highly discordant implying not less than six events of hybridisation of diverged wild peas in the past, with plastids and mitochondria differently inherited by the descendants. Such discordant inheritance of organelles is supposed to have been driven by plastid-nuclear incompatibility, known to be widespread in pea wide crosses and apparently shaping the organellar phylogenies. The topology of a phylogenetic tree based on the nucleotide sequence of a nuclear gene His5 coding for a histone H1 subtype corresponds to the current taxonomy and resembles that based on the plastid genome. Wild peas (Pisum sativum subsp. elatius s.l.) inhabiting Southern Europe were shown to be of hybrid origin resulting from crosses of peas similar to those presently inhabiting south-east and north-east Mediterranean in broad sense.

scholarly journals Making Genomic Surveillance Deliver: A Lineage Classification and Nomenclature System to Inform Rabies Virus Elimination

2021 ◽  
Author(s):  
Kathryn Campbell ◽  
Robert J Gifford ◽  
Joshua Singer ◽  
Verity Hill ◽  
Aine O'Toole ◽  
...  
Keyword(s):  
Rabies Virus ◽  
Sequence Data ◽  
Classification Systems ◽  
Virus Elimination ◽  
Data Resource ◽  
Genomic Tools ◽  
Control Programmes ◽  
History Of ◽  
Virus Sequence ◽  
Globally Distributed

The availability of pathogen sequence data and use of genomic surveillance is rapidly increasing. Genomic tools and classification systems need updating to reflect this. Here, rabies virus is used as an example to showcase the potential value of updated genomic tools to enhance surveillance to better understand epidemiological dynamics and improve disease control. Previous studies have described the evolutionary history of rabies virus, however the resulting taxonomy lacks the definition necessary to identify incursions, lineage turnover and transmission routes at high resolution. Here we propose a lineage classification system based on the dynamic nomenclature used for SARS-CoV-2, defining a lineage by phylogenetic methods for tracking virus spread and comparing sequences across geographic areas. We demonstrate this system through application to the globally distributed Cosmopolitan clade of rabies virus, defining 73 total lineages within the clade, beyond the 22 previously reported. We further show how integration of this tool with a new rabies virus sequence data resource (RABV-GLUE) enables rapid application, for example, highlighting lineage dynamics relevant to control and elimination programmes, such as identifying importations and their sources, and areas of persistence and transmission, including transboundary incursions. This system and the tools developed should be useful for coordinating and targeting control programmes and monitoring progress as we work towards eliminating dog-mediated rabies, as well as having potential for broad application to the surveillance of other viruses.

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