scholarly journals The evolution of pathogenic trypanosomes

1999 ◽  
Vol 15 (4) ◽  
pp. 673-684 ◽  
Author(s):  
Jamie R. Stevens ◽  
Wendy C. Gibson
Keyword(s):  
Trypanosoma Brucei ◽  
Ribosomal Rna ◽  
Fossil Record ◽  
Phylogenetic Trees ◽  
Recent Progress ◽  
Molecular Data ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
History Of ◽  
Vertebrate Hosts

In the absence of a fossil record, the evolution of protozoa has until recently largely remained a matter for speculation. However, advances in molecular methods and phylogenetic analysis are now allowing interpretation of the "history written in the genes". This review focuses on recent progress in reconstruction of trypanosome phylogeny based on molecular data from ribosomal RNA, the miniexon and protein-coding genes. Sufficient data have now been gathered to demonstrate unequivocally that trypanosomes are monophyletic; the phylogenetic trees derived can serve as a framework to reinterpret the biology, taxonomy and present day distribution of trypanosome species, providing insights into the coevolution of trypanosomes with their vertebrate hosts and vectors. Different methods of dating the divergence of trypanosome lineages give rise to radically different evolutionary scenarios and these are reviewed. In particular, the use of one such biogeographically based approach provides new insights into the coevolution of the pathogens, Trypanosoma brucei and Trypanosoma cruzi, with their human hosts and the history of the diseases with which they are associated.

Halojulellaceae a new family of the order Pleosporales

Phytotaxa ◽  
2013 ◽  
Vol 130 (1) ◽  
pp. 14 ◽  
Author(s):  
HIRAN A. ARIYAWANSA ◽  
EVAN B.G. JONES ◽  
SATINEE SUETRONG ◽  
SITI A. ALIAS ◽  
JI-CHUAN KANG ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Marine Species ◽  
Morphological Characters ◽  
Molecular Data ◽  
Marine Habitat ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
New Family ◽  
Distinct Genus ◽  
Rna Genes

Halojulellaceae fam. nov. and Halojullela gen. nov. are introduced to accommodate Julella avicenniae, a marine species in the suborder Pleosporineae, order Pleosporales, Dothideomycetes. Justification for the new family is based on combined gene analysis of the large and small subunits of the nuclear ribosomal RNA genes (LSU, SSU) and two protein coding genes RPB2 and TEF1, as well as morphological characters.  Halojulellaceae and Halojulella are characterized by immersed to semi-immersed, clypeate ascomata, with short, papillate ostioles, cellular, hyphae-like, pseudoparaphyses, 8-spored, fissitunicate, clavate to cylindrical asci with a well-developed apical apparatus, a moderately long pedicel with a club-like base and hyaline or golden brown, ellipsoidal, muriform ascospores and is typified by Halojulella avicenniae. Halojullela differs from Julella, (type J. buxi) in its marine habitat and distinctly differing ascus with the apical apparatus being well-developed and moderately long club-like pedicel. Morphological characters and molecular data show that H. avicenniae belongs in the Pleosporales, outside any of the known families, and thus a new family is introduced to accommodate it. Julella is maintained as a distinct genus which is presently most likely polyphyletic with saprobic and lichenized elements and needs further study as no molecular data is presently available for any species.

Dissecting the major African snake radiation: a molecular phylogeny of the Lamprophiidae Fitzinger (Serpentes, Caenophidia)

Zootaxa ◽  
2008 ◽  
Vol 1945 (1) ◽  
pp. 51-66 ◽  
Author(s):  
NICOLAS VIDAL ◽  
WILLIAM R. BRANCH ◽  
OLIVIER S. G. PAUWELS ◽  
S. BLAIR HEDGES ◽  
DONALD G. BROADLEY ◽  
...  
Keyword(s):  
Mitochondrial Protein ◽  
Sister Group ◽  
Molecular Data ◽  
Rrna Genes ◽  
Phylogenetic Position ◽  
Data Set ◽  
Protein Coding ◽  
Mitochondrial Rrna ◽  
Protein Coding Genes ◽  
History Of

The Elapoidea includes the Elapidae and a large (~60 genera, 280 sp.) and mostly African (including Madagascar) radiation termed Lamprophiidae by Vidal et al. (2007), that includes at least four major groups: the psammophiines, atractaspidines, lamprophiines and pseudoxyrhophiines. In this work, we reviewed the recent taxonomic history of the lamprophiids, and built a data set including two nuclear protein-coding genes (c-mos and RAG2), two mitochondrial rRNA genes (12S and 16S rRNA) and two mitochondrial protein-coding genes (cytochrome b and ND4) for 85 species belonging to 45 genera (thus representing about 75% of the generic diversity and 30% of the specific diversity of the radiation), in order to clarify the phylogenetic relationships of this large and neglected group at the subfamilial and generic levels. To this aim, 480 new sequences were produced. The vast majority of the investigated genera fall into four main monophyletic clusters, that correspond to the four subfamilies mentioned above, although the content of atractaspidines, lamprophiines and pseudoxyrhophiines is revised. We confirm the polyphyly of the genus Stenophis, and the relegation of the genus name Dromophis to the synonymy of the genus name Psammophis. Gonionotophis brussauxi is nested within Mehelya. The genus Lamprophis Fitzinger, 1843 is paraphyletic with respect to Lycodonomorphus Fitzinger, 1843. Lamprophis swazicus is the sister-group to Hormonotus modestus, and may warrant generic recognition. Molecular data do not support the traditional placement of Micrelaps within the Atractaspidinae, but its phylogenetic position, along with that of Oxyrhabdium (previously considered to belong to the Xenodermatidae), requires additional molecular data and they are both treated as Elapoidea incertae sedis. The interrelationships of Psammophiinae, Atractaspidinae, Lamprophiinae, Pseudoxyrhophiinae, Prosymna (13 sp.), Pseudaspis (1 sp.) and Pythonodipsas (1 sp.), Buhoma (2 species), and Psammodynastes (1 sp.) remain unresolved. Finally, the genus Lycognathophis, endemic to the Seychelles, does not belong to the African radiation, but to the Natricidae.

scholarly journals Phylogenetic relationships and taxonomic position of genus Hyperacrius (Rodentia: Arvicolinae) from Kashmir based on evidences from analysis of mitochondrial genome and study of skull morphology

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10364
Author(s):  
Natalia I. Abramson ◽  
Fedor N. Golenishchev ◽  
Semen Yu. Bodrov ◽  
Olga V. Bondareva ◽  
Evgeny A. Genelt-Yanovskiy ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
De Novo ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Morphological Characters ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
Skull Morphology ◽  
Protein Coding ◽  
Protein Coding Genes

In this article, we present the nearly complete mitochondrial genome of the Subalpine Kashmir vole Hyperacrius fertilis (Arvicolinae, Cricetidae, Rodentia), assembled using data from Illumina next-generation sequencing (NGS) of the DNA from a century-old museum specimen. De novo assembly consisted of 16,341 bp and included all mitogenome protein-coding genes as well as 12S and 16S RNAs, tRNAs and D-loop. Using the alignment of protein-coding genes of 14 previously published Arvicolini tribe mitogenomes, seven Clethrionomyini mitogenomes, and also Ondatra and Dicrostonyx outgroups, we conducted phylogenetic reconstructions based on a dataset of 13 protein-coding genes (PCGs) under maximum likelihood and Bayesian inference. Phylogenetic analyses robustly supported the phylogenetic position of this species within the tribe Arvicolini. Among the Arvicolini, Hyperacrius represents one of the early-diverged lineages. This result of phylogenetic analysis altered the conventional view on phylogenetic relatedness between Hyperacrius and Alticola and prompted the revision of morphological characters underlying the former assumption. Morphological analysis performed here confirmed molecular data and provided additional evidence for taxonomic replacement of the genus Hyperacrius from the tribe Clethrionomyini to the tribe Arvicolini.

scholarly journals Simultaneous Bayesian inference of phylogeny and molecular coevolution

2019 ◽  
Vol 116 (11) ◽  
pp. 5027-5036 ◽  
Author(s):  
Xavier Meyer ◽  
Linda Dib ◽  
Daniele Silvestro ◽  
Nicolas Salamin
Keyword(s):  
16S Rrna ◽  
Phylogenetic Trees ◽  
Organic Molecules ◽  
Evolutionary Process ◽  
Protein Coding ◽  
Rrna Molecule ◽  
Shared Ancestry ◽  
History Of ◽  
Dependent Site ◽  
Synthetic Datasets

Patterns of molecular coevolution can reveal structural and functional constraints within or among organic molecules. These patterns are better understood when considering the underlying evolutionary process, which enables us to disentangle the signal of the dependent evolution of sites (coevolution) from the effects of shared ancestry of genes. Conversely, disregarding the dependent evolution of sites when studying the history of genes negatively impacts the accuracy of the inferred phylogenetic trees. Although molecular coevolution and phylogenetic history are interdependent, analyses of the two processes are conducted separately, a choice dictated by computational convenience, but at the expense of accuracy. We present a Bayesian method and associated software to infer how many and which sites of an alignment evolve according to an independent or a pairwise dependent evolutionary process, and to simultaneously estimate the phylogenetic relationships among sequences. We validate our method on synthetic datasets and challenge our predictions of coevolution on the 16S rRNA molecule by comparing them with its known molecular structure. Finally, we assess the accuracy of phylogenetic trees inferred under the assumption of independence among sites using synthetic datasets, the 16S rRNA molecule and 10 additional alignments of protein-coding genes of eukaryotes. Our results demonstrate that inferring phylogenetic trees while accounting for dependent site evolution significantly impacts the estimates of the phylogeny and the evolutionary process.

scholarly journals Ancestral polymorphisms in Drosophila pseudoobscura and Drosophila miranda

2011 ◽  
Vol 93 (4) ◽  
pp. 255-263 ◽  
Author(s):  
REUBEN W. NOWELL ◽  
BRIAN CHARLESWORTH ◽  
PENELOPE R. HADDRILL
Keyword(s):  
Balancing Selection ◽  
Molecular Data ◽  
Sequence Polymorphism ◽  
Substantial Proportion ◽  
Drosophila Pseudoobscura ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Speciation Event ◽  
Ancestral Polymorphisms ◽  
Polymorphism Data

SummaryAncestral polymorphisms are defined as variants that arose by mutation prior to the speciation event that generated the species in which they segregate. Their presence may complicate the interpretation of molecular data and lead to incorrect phylogenetic inferences. They may also be used to identify regions of the genome that are under balancing selection. It is thus important to take into account the contribution of ancestral polymorphisms to variability within species and divergence between species. Here, we extend and improve a method for estimation of the proportion of ancestral polymorphisms within a species, and apply it to a dataset of 33 X-linked and 34 autosomal protein-coding genes for which sequence polymorphism data are available in both Drosophila pseudoobscura and Drosophila miranda, using Drosophila affinis as an outgroup. We show that a substantial proportion of both X-linked and autosomal synonymous variants in these two species are ancestral, and that a small number of additional genes with unusually high sequence diversity seem to have an excess of ancestral polymorphisms, suggestive of balancing selection.

scholarly journals Plastome Diversity and Phylogenomic Relationships in Asteraceae

Plants ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 2699
Author(s):  
Joan Pere Pascual-Díaz ◽  
Sònia Garcia ◽  
Daniel Vitales
Keyword(s):  
Ribosomal Rna ◽  
Evolutionary Rate ◽  
Plastid Dna ◽  
Single Copy ◽  
Phylogenomic Analysis ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Plastid Genomes ◽  
The Family ◽  
Rna Genes

Plastid genomes are in general highly conserved given their slow evolutionary rate, and thus large changes in their structure are unusual. However, when specific rearrangements are present, they are often phylogenetically informative. Asteraceae is a highly diverse family whose evolution is long driven by polyploidy (up to 48x) and hybridization, both processes usually complicating systematic inferences. In this study, we generated one of the most comprehensive plastome-based phylogenies of family Asteraceae, providing information about the structure, genetic diversity and repeat composition of these sequences. By comparing the whole-plastome sequences obtained, we confirmed the double inversion located in the long single-copy region, for most of the species analyzed (with the exception of basal tribes), a well-known feature for Asteraceae plastomes. We also showed that genome size, gene order and gene content are highly conserved along the family. However, species representative of the basal subfamily Barnadesioideae—as well as in the sister family Calyceraceae—lack the pseudogene rps19 located in one inverted repeat. The phylogenomic analysis conducted here, based on 63 protein-coding genes, 30 transfer RNA genes and 21 ribosomal RNA genes from 36 species of Asteraceae, were overall consistent with the general consensus for the family’s phylogeny while resolving the position of tribe Senecioneae and revealing some incongruences at tribe level between reconstructions based on nuclear and plastid DNA data.

scholarly journals LongGeneDB: a data hub for long genes

2020 ◽  
Author(s):  
Yura Kim ◽  
Mariam Naghavi ◽  
Ying-Tao Zhao
Keyword(s):  
Mouse Genome ◽  
Research Community ◽  
Easy Access ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
History Of ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome ◽  
User Friendly ◽  
Long Genes

ABSTRACTThe human genome contains more than 4000 genes that are longer than 100 kb. These long genes require more time and resources to make a transcript than shorter genes do. Long genes have also been linked to various human diseases. Specific mechanisms are utilized by long genes to facilitate their transcription and co-transcriptional processes. This results in unique features in their multi-omics profiles. Although these unique profiles are important to understand long genes, a database that provides an integrated view and easy access to the multi-omics profiles of long genes does not exist. We leveraged the publicly accessible multi-omics data and systematically analyzed the genomic conservation, histone modifications, chromatin organization, tissue-specific transcriptome, and single cell transcriptome of 992 protein-coding genes that are longer than 200 kb in the mouse genome. We also examined the evolution history of their gene lengths in 15 species that belong to six Classes and 11 Orders. To share the multi-omics profiles of long genes, we developed a user-friendly and easy-to-use database, LongGeneDB (https://longgenedb.com), for users to search, browse, and download these profiles. LongGeneDB will be a useful data hub for the biomedical research community to understand long genes.

scholarly journals Complete mitochondrial genomes of five raptors and implications for the phylogenetic relationships between owls and nightjars

2019 ◽  
Author(s):  
Gang Liu ◽  
Lizhi Zhou ◽  
Guanghong Zhao
Keyword(s):  
Control Region ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Stop Codon ◽  
Mitochondrial Genomes ◽  
Closely Related Species ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Independent Families ◽  
Complete Mitochondrial Genomes

The phylogenetic relationships between owls and nightjars are rather complex and controversial. To clarify these relationships, we determined the complete mitochondrial genomes of Glaucidium cuculoides, Otus scops, Glaucidium brodiei, Caprimulgus indicus, and Strix leptogrammica, and estimated phylogenetic trees based on the complete mitochondrial genomes and aligned sequences from closely related species that were obtained in GenBank. The complete mitochondrial genomes were 17392, 17317, 17549, 17536, and 16307 bp in length. All mitochondrial genomes contained 13 protein-coding genes, two rRNAs, 22 tRNAs, and a putative control region. All mitochondrial genomes except for that of Strix leptogrammica contained a pseudo-control region. ATG, GTG, and ATA are generally start codons, whereas TAA is the most frequent stop codon. All tRNAs in the new mtDNAs could be folded into canonical cloverleaf secondary structures except for tRNASer (AGY) and tRNALeu (CUN) , which missing the “DHU” arm. The phylogenetic relationships demonstrated that Strigiformes and Caprimulgiformes are independent orders, and Aegothelidae is a family within Caprimulgiformes. The results also revealed that Accipitriformes is an independent order, and Pandionidae and Sagittariidae are independent families. The results also supported that Apodiformes is polyphyletic, and hummingbirds (family Trochilidae) belong to Apodiformes. Piciformes was most distantly related to all other analyzed orders.

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