What does the 5S rRNA multigene family tell us about the origin of the annual Triticeae (Poaceae)?

Genome ◽  
2013 ◽  
Vol 56 (5) ◽  
pp. 245-266 ◽  
Author(s):  
B.R. Baum ◽  
T. Edwards ◽  
D.A. Johnson
Keyword(s):  
Multigene Family ◽  
Phylogenetic Analyses ◽  
5S Rrna ◽  
Phylogenetic Networks ◽  
Local Alignment ◽  
Gene Trees ◽  
Next Of Kin ◽  
Close Link ◽  
Unit Classes ◽  
Complex Relationships

We have investigated the complex relationships among the annual genera within the tribe Triticeae through phylogenetic analyses of the 5S rRNA multigene family. Cloned sequences were assigned to groups of orthologous sequences, called unit classes, that were subjected to several analyses including BLAST (Basic Local Alignment Search Tool) searches to assess possible ancestral relationships with perennial genera; phylogenetic analyses using parsimony (Pars), maximum likelihood (ML), and Bayesian methods; and minimum reticulation networks from the Pars, ML, and Bayesian trees. In this study, we included genera with both annual and perennial species, such as Dasypyrum, Hordeum, and Secale. BLAST pointed to Pseudoroegneria (carrier of the St genome) and possibly Thinopyrum (carrier of the J genome) as the potential next of kin. However, Thinopyrum and Pseudoroegneria have never fallen together on the individual trees with the former generally associated with Crithopsis, Aegilops, Triticum, and Dasypyrum, while the latter is usually associated with the rest of the genera within Triticeae. The “long” unit classes placed Dasypyrum breviaristatum together with Dasypyrum villosum, whereas the “short” unit classes put them far apart on the trees. None of the gene trees alone was able to summarize the complex relationships among the genera, in line with previous results in the Triticeae. However, the application of tools designed to display phylogenetic networks was able to depict the complex links among the genera based on the short and the long gene trees, including the close link between Thinopyrum and Pseudoroegneria suggested by the phylogenetic analyses. In addition, our analyses provide support for the hypothesis that at least some annual Triticeae taxa are derived from their perennial relatives.

scholarly journals A Polynomial-Time Algorithm for Minimizing the Deep Coalescence Cost for Level-1 Species Networks

2020 ◽  
Author(s):  
Matthew LeMay ◽  
Ran Libeskind-Hadas ◽  
Yi-Chieh Wu
Keyword(s):  
Polynomial Time ◽  
Incomplete Lineage Sorting ◽  
Phylogenetic Analyses ◽  
Polynomial Time Algorithm ◽  
Time Algorithm ◽  
Phylogenetic Networks ◽  
Gene Trees ◽  
Lineage Sorting ◽  
Hybrid Species ◽  
Level 1

Phylogenetic analyses commonly assume that the species history can be represented as a tree. However, in the presence of hybridization, the species history is more accurately captured as a network. Despite several advances in modeling phylogenetic networks, there is no known polynomial-time algorithm for parsimoniously reconciling gene trees with species networks while accounting for incomplete lineage sorting. To address this issue, we present a polynomial-time algorithm for the case of level-1 networks, in which no hybrid species is the direct ancestor of another hybrid species. This work enables more efficient reconciliation of gene trees with species networks, which in turn, enables more efficient reconstruction of species networks.

Codependence of repetitive sequence classes in genomes: phylogenetic analysis of 5S rDNA families in Hordeum (Triticeae: Poaceae)

Genome ◽  
2010 ◽  
Vol 53 (3) ◽  
pp. 180-202 ◽  
Author(s):  
Bernard R. Baum ◽  
Tara Edwards ◽  
Douglas A. Johnson
Keyword(s):  
Phylogenetic Analyses ◽  
5S Rdna ◽  
Rrna Gene ◽  
Consensus Sequences ◽  
Rdna Sequences ◽  
Unit Classes ◽  
Unit Class ◽  
Comprehensive Picture ◽  
Host Parasite

To complete our study of the genus Hordeum and to elaborate a phylogeny of species based upon 5S rDNA sequences, we have cloned and sequenced PCR amplicons from seven American polyploid species to generate 164 new 5S rRNA gene sequences. These sequences were analysed along with the more than 2000 5S rDNA sequences previously generated from the majority of species in Hordeum to provide a comprehensive picture of the distribution (presence or absence) of 5S rDNA unit classes (orthologous groups) in this genus as well as insights into the phylogeny of Hordeum. Testing of substitution models for each unit class based upon the consensus sequences of all the taxa as well as for each unit class within the genus found that the general best fit was TPM3uf+G, from which a maximum-likelihood tree was calculated. A novel application of cophylogenetic analysis, where relationships among unit classes were treated as host–parasite interactions, depicted some significant pair links under tests of randomness indicative of nonrandom codivergence among several unit classes within the same taxon. The previous classification of four genomic groups is reflected in combinations of unit classes, and it is proposed that current taxa developed from ancient diploidized paleopolyploids and that some were subjected to gene loss, i.e., unit class loss. Finally, separate phylogenetic analyses performed for the tetraploid and hexaploid species were used to derive a working model describing the phylogeny of the polyploid taxa from their putative diploid ancestry.

Redescription and SSU rRNA gene-based phylogeny of an anaerobic ciliate, Plagiopyla ovata Kahl, 1931 (Ciliophora, Plagiopylea)

2021 ◽  
Vol 71 (8) ◽  
Author(s):  
Ran Li ◽  
Wenbao Zhuang ◽  
Congcong Wang ◽  
Hamed El-Serehy ◽  
Saleh A. Al-Farraj ◽  
...  
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Small Subunit ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Gene Trees ◽  
Ssu Rrna Gene ◽  
Anaerobic Ciliate ◽  
Pr China

The morphology and molecular phylogeny of Plagiopyla ovata Kahl, 1931, a poorly known anaerobic ciliate, were investigated based on a population isolated from sand samples collected from the Yellow Sea coast at Qingdao, PR China. Details of the oral ciliature are documented for the first time to our knowledge and an improved species diagnosis is given. The small subunit ribosomal RNA (SSU rRNA) gene was newly sequenced and phylogenetic analyses revealed that P. ovata clusters within the monophyletic family Plagiopylidae. However, evolutionary relationships within both the family Plagiopylidae and the genus Plagiopyla remain obscure owing to undersampling, the lack of sequence data from known species and low nodal support or unstable topologies in gene trees. A key to the identification of the species of the genus Plagiopyla with validly published names is also supplied.

scholarly journals Genomic Characterization and Curation of UCEs Improves Species Tree Reconstruction

2020 ◽  
Author(s):  
Matthew H Van Dam ◽  
James B Henderson ◽  
Lauren Esposito ◽  
Michelle Trautwein
Keyword(s):  
Marine Invertebrates ◽  
Phylogenetic Analyses ◽  
Single Gene ◽  
Gene Tree ◽  
Single Copy ◽  
Species Tree ◽  
Bootstrap Support ◽  
Gene Trees ◽  
Species Trees ◽  
Tree Reconstruction

Abstract Ultraconserved genomic elements (UCEs) are generally treated as independent loci in phylogenetic analyses. The identification pipeline for UCE probes does not require prior knowledge of genetic identity, only selecting loci that are highly conserved, single copy, without repeats, and of a particular length. Here, we characterized UCEs from 11 phylogenomic studies across the animal tree of life, from birds to marine invertebrates. We found that within vertebrate lineages, UCEs are mostly intronic and intergenic, while in invertebrates, the majority are in exons. We then curated four different sets of UCE markers by genomic category from five different studies including: birds, mammals, fish, Hymenoptera (ants, wasps, and bees), and Coleoptera (beetles). Of genes captured by UCEs, we find that many are represented by two or more UCEs, corresponding to nonoverlapping segments of a single gene. We considered these UCEs to be nonindependent, merged all UCEs that belonged to a particular gene, constructed gene and species trees, and then evaluated the subsequent effect of merging cogenic UCEs on gene and species tree reconstruction. Average bootstrap support for merged UCE gene trees was significantly improved across all data sets apparently driven by the increase in loci length. Additionally, we conducted simulations and found that gene trees generated from merged UCEs were more accurate than those generated by unmerged UCEs. As loci length improves gene tree accuracy, this modest degree of UCE characterization and curation impacts downstream analyses and demonstrates the advantages of incorporating basic genomic characterizations into phylogenomic analyses. [Anchored hybrid enrichment; ants; ASTRAL; bait capture; carangimorph; Coleoptera; conserved nonexonic elements; exon capture; gene tree; Hymenoptera; mammal; phylogenomic markers; songbird; species tree; ultraconserved elements; weevils.]

scholarly journals Novel Single Hematophagous Insect RNA Detection Method Supports Its Use as Sentinels to Survey Flaviviruses Circulation

2020 ◽  
Author(s):  
Juliana Sá Teles de Oliveira Molina ◽  
Andreia Moreira dos Santos Carmo ◽  
Gabriel Lopes Pereira ◽  
Leticia Abrantes de Andrade ◽  
Felipe Trovalim Jordão ◽  
...  
Keyword(s):  
Control Strategies ◽  
Phylogenetic Analyses ◽  
Rna Extraction ◽  
Local Alignment ◽  
Rna Detection ◽  
Public Park ◽  
Preventive Control ◽  
Culex Flavivirus ◽  
Search Tool ◽  
Pcr Targeting

Anthropogenic actions, including deforestation, disorganized urbanization, and globalization, contribute to emergence and reemergence of arboviruses worldwide, where Flavivirus is the most prevalent, and its continuous monitoring can help in preventive control strategies. Thus, the aim of this study was to detect flavivirus RNA in single hematophagous insects, which are used as sentinels. Total RNA was extracted from six Aedes aegypti stored since 2003 and from 100 Culicidae and collected through CDC trap in a public park of a Brazilian Northwest city of São Paulo State. Flavivirus was detected through RT/PCR targeting 230–250 bp of the RNA polymerase coding sequence (NS5). PCR amplicons were sequenced by Sanger method, used in comparative analysis over Basic Local Alignment Search Tool (BLAST) in GenBank, and subjected to Neighbor-Joining phylogenetic analyses. Efficiency of Flavivirus diagnosis was confirmed by detection of Dengue virus serotype 2 in Ae. aegypti. From the 100 collected insects, 19 were positive for Culex flavivirus (CxFV). NS5 partial sequence phylogenetic analysis clustered all CxFV in one branch separated from vertebrate flaviviruses, being applicable to the identification of Flavivirus species. The dipteran RNA extraction methodology described in this work supports detection of flaviviruses in single insects maintained in 80% ethanol, which can be used to constant arbovirus surveillance.

scholarly journals The impact of incongruence and exogenous gene fragments on estimates of the eukaryote root

2021 ◽  
Author(s):  
Caesar Al Jewari ◽  
Sandra L Baldauf
Keyword(s):  
Phylogenetic Analyses ◽  
Single Gene ◽  
Evolutionary Model ◽  
Bootstrap Support ◽  
Gene Trees ◽  
Full Data ◽  
Data Set ◽  
Gene Level ◽  
The Impact ◽  
Exogenous Gene

Phylogenomics uses multiple genetic loci to reconstruct evolutionary trees, under the stipulation that all combined loci share a common phylogenetic history, i.e., they are congruent. Congruence is primarily evaluated via single-gene trees, but these trees invariably lack sufficient signal to resolve deep nodes making it difficult to assess congruence at these levels. Two methods were developed to systematically assess congruence in multi-locus data. Protocol 1 uses gene jackknifing to measure deviation from a central mean to identify taxon-specific incongruencies in the form of persistent outliers. Protocol_2 assesses congruence at the sub-gene level using a sliding window. Both protocols were tested on a controversial data set of 76 mitochondrial proteins previously used in various combinations to assess the eukaryote root. Protocol_1 showed a concentration of outliers in under-sampled taxa, including the pivotal taxon Discoba. Further analysis of Discoba using Protocol_2 detected a surprising number of apparently exogenous gene fragments, some of which overlap with Protocol_1 outliers and others that do not. Phylogenetic analyses of the full data using the static LG-gamma evolutionary model support a neozoan-excavate root for eukaryotes (Discoba sister), which rises to 99-100% bootstrap support with data masked according to either Protocol_1 or Protocol_2. In contrast, site-heterogeneous (mixture) models perform inconsistently with these data, yielding all three possible roots depending on presence/absence/type of masking and/or extent of missing data. The neozoan-excavate root places Amorphea (including animals and fungi) and Diaphoretickes (including plants) as more closely related to each other than either is to Discoba (Jakobida, Heterolobosea, and Euglenozoa), regardless of the presence/absence of additional taxa.

scholarly journals Revising transcriptome assemblies with phylogenetic information in Agalma1.0

2017 ◽  
Author(s):  
August Guang ◽  
Mark Howison ◽  
Felipe Zapata ◽  
Charles Lawrence ◽  
Casey Dunn
Keyword(s):  
Phylogenetic Analysis ◽  
Transcriptome Assembly ◽  
Phylogenetic Analyses ◽  
Supplementary Information ◽  
Gene Trees ◽  
Phylogenetic Information ◽  
Short Branch ◽  
Multiple Genes ◽  
Branch Lengths ◽  
Supplementary Material

AbstractMotivationOne of the most common transcriptome assembly errors is to mistake different transcripts of the same gene as transcripts from multiple closely related genes. It is difficult to identify these errors during assembly, but in a phylogenetic analysis these errors can be diagnosed from gene trees containing clades of tips from the same species with improbably short branch lengths.Resultstreeinform is a module implemented in Agalma1.0 that uses phylogenetic analyses across species to refine transcriptome assemblies. It identifies transcripts of the same gene that were incorrectly assigned to multiple genes and reassign them as transcripts of the same gene.Availability and Implementationtreeinform is implemented in Agalma1.0, available at https://bitbucket.org/caseywdunn/[email protected] informationSupplementary information is available at bioRxiv.

scholarly journals Genomic characterization and curation of UCEs improves species tree reconstruction

2019 ◽  
Author(s):  
Matthew H. Van Dam ◽  
James B. Henderson ◽  
Lauren Esposito ◽  
Michelle Trautwein
Keyword(s):  
Marine Invertebrates ◽  
Phylogenetic Analyses ◽  
Single Gene ◽  
Single Copy ◽  
Species Tree ◽  
Bootstrap Support ◽  
Gene Trees ◽  
Species Trees ◽  
Tree Reconstruction ◽  
Phylogenomic Analyses

ABSTRACTUltraconserved genomic elements (UCEs), are generally treated as independent loci in phylogenetic analyses. The identification pipeline for UCE probes is agnostic to genetic identity, only selecting loci that are highly conserved, single copy, without repeats, and of a particular length. Here we characterized UCEs from 12 phylogenomic studies across the animal tree of life, from birds to marine invertebrates. We found that within vertebrate lineages, UCEs are mostly intronic and intergenic, while in invertebrates, the majority are in exons. We then curated 4 different sets of UCE markers by genomic category from 5 different studies including; birds, mammals, fish, Hymenoptera (ants, wasps and bees) and Coleoptera (beetles). Of genes captured by UCEs, we find that many are represented by 2 or more UCEs, corresponding to non-overlapping segments of a single gene. We considered these UCEs to be non-independent, merged all UCEs that belonged to a particular gene, constructed gene and species trees, and then evaluated the subsequent effect of merging co-genic UCEs on gene and species tree reconstruction. Average bootstrap support for merged UCE gene trees were significantly improved across all datasets. Increased loci length appears to drive this increase in bootstrap support. Additionally, we found that gene trees generated from merged UCEs were more accurate than those generated by unmerged and randomly merged UCEs, based on our simulation study. This modest degree of UCE characterization and curation impacts downstream analyses and demonstrates the advantages of incorporating basic genomic characterizations into phylogenomic analyses.

scholarly journals Genome-wide admixture is common across the Heliconius radiation

2018 ◽  
Author(s):  
Krzysztof M. Kozak ◽  
W. Owen McMillan ◽  
Mathieu Joron ◽  
Christopher D. Jiggins
Keyword(s):  
Gene Flow ◽  
Phylogenetic Networks ◽  
Z Chromosome ◽  
Putative Hybrid ◽  
Gene Trees ◽  
Tree Model ◽  
Interspecific Gene Flow ◽  
Individual Gene ◽  
Multispecies Coalescent ◽  
Genome Wide

ABSTRACTHow frequent is gene flow between species? The pattern of evolution is typically portrayed as a phylogenetic tree, implying that speciation is a series of splits between lineages. Yet gene flow between good species is increasingly recognized as an important mechanism in the diversification of radiations, often spreading adaptive traits and leading to a complex pattern of phylogenetic incongruence. This process has thus far been studied in cases involving few species, or geographically restricted to spaces like islands, but not on the scale of a continental radiation. Previous studies have documented gene flow, adaptive introgression and hybrid speciation in a small subsection of the charismatic Neotropical butterflies Heliconius. Using genome-wide resequencing of 40 out of 45 species in the genus we demonstrate for the first time that admixture has played a role throughout the evolution of Heliconius and the sister genus Eueides. Modelling of phylogenetic networks based on 6848 orthologous autosomal genes (Maximum Pseudo-Likelihood Networks) or 5,483,419 high quality SNPs (Ancestral Recombination Graph) uncovers nine new cases of interspecific gene flow at up to half of the genome. However, f4 statistics of admixture show that the extent of the process has varied between subgenera. Evidence for introgression is found at all five loci controlling the colour and shape of the mimetic wing patterns, including in the putative hybrid species H. hecalesia, characterised by an unusual hindwing. Due to hybridization and incomplete coalescence during rapid speciation, individual gene trees show rampant discordance. Although reduced gene flow and faster coalescence are expected at the Z chromosome, we discover high levels of conflict between the 416 sex-linked loci. Despite this discordant pattern, both concatenation and multispecies coalescent approaches yield surprisingly consistent and fully supported genome-wide phylogenies. We conclude that the imposition of the bifurcating tree model without testing for interspecific gene flow may distort our perception of adaptive radiations and thus the ability to study trait evolution in a comparative framework.

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