scholarly journals Novel Molecular Synapomorphies Demarcate Different Main Groups/Subgroups of Plasmodium and Piroplasmida Species Clarifying Their Evolutionary Relationships

Genes ◽  
2019 ◽  
Vol 10 (7) ◽  
pp. 490 ◽  
Author(s):  
Sharma ◽  
Gupta
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Trees ◽  
Plasmodium Species ◽  
Protein Sequences ◽  
Evolutionary Relationships ◽  
Major Life ◽  
Comparative Analyses ◽  
Large Numbers ◽  
Conserved Signature Indels ◽  
Relationship Of

The class Hematozoa encompasses several clinically important genera, including Plasmodium, whose members cause the major life-threating disease malaria. Hence, a good understanding of the interrelationships of organisms from this class and reliable means for distinguishing them are of much importance. This study reports comprehensive phylogenetic and comparative analyses on protein sequences on the genomes of 28 hematozoa species to understand their interrelationships. In addition to phylogenetic trees based on two large datasets of protein sequences, detailed comparative analyses were carried out on the genomes of hematozoa species to identify novel molecular synapomorphies consisting of conserved signature indels (CSIs) in protein sequences. These studies have identified 79 CSIs that are exclusively present in specific groups of Hematozoa/Plasmodium species, also supported by phylogenetic analysis, providing reliable means for the identification of these species groups and understanding their interrelationships. Of these CSIs, six CSIs are specifically shared by all hematozoa species, two CSIs serve to distinguish members of the order Piroplasmida, five CSIs are uniquely found in all Piroplasmida species except B. microti and two CSIs are specific for the genus Theileria. Additionally, we also describe 23 CSIs that are exclusively present in all genome-sequenced Plasmodium species and two, nine, ten and eight CSIs which are specific for members of the Plasmodium subgenera Haemamoeba, Laverania, Vinckeia and Plasmodium (excluding P. ovale and P. malariae), respectively. Additionally, our work has identified several CSIs that support species relationships which are not evident from phylogenetic analysis. Of these CSIs, one CSI supports the ancestral nature of the avian-Plasmodium species in comparison to the mammalian-infecting groups of Plasmodium species, four CSIs strongly support a specific relationship of species between the subgenera Plasmodium and Vinckeia and three CSIs each that reliably group P. malariae with members of the subgenus Plasmodium and P. ovale within the subgenus Vinckeia, respectively. These results provide a reliable framework for understanding the evolutionary relationships among the Plasmodium/Piroplasmida species. Further, in view of the exclusivity of the described molecular markers for the indicated groups of hematozoa species, particularly large numbers of unique characteristics that are specific for all Plasmodium species, they provide important molecular tools for biochemical/genetic studies and for developing novel diagnostics and therapeutics for these organisms.

A Phylogenetic Analysis for Gene ITPK1

2012 ◽  
Vol 466-467 ◽  
pp. 27-30
Author(s):  
Kun Luo ◽  
Dong Hui Luo
Keyword(s):  
Phylogenetic Analysis ◽  
Protein Sequence ◽  
Selection Pressure ◽  
Phylogenetic Trees ◽  
Essential Role ◽  
Protein Sequences

Inositol 1,3,4-trisphosphate 5/6 kinase (ITPK1) is a pivotal enzyme in producing IP6 , a moleculae that play an essential role in many biochemistry process in mammal cells. In this paper, two phylogenetic trees are constructed based on the mRNA sequences and the protein sequences, respectively. The results indicate that the protein sequences are more conserved than mRNA sequences in primates. Although both plant and animal have an abundant distribution of ITPK1 domain, there exists a great variation in protein sequence between plant and animal. The protein-based tree reflects an evolution orders that is consistent with that of organisms evolution. Z-test of selection indicates that evolution of protein ITPK1 is caused by selection pressure.

scholarly journals Phylogenetic and ecomorphologic diversifications of spiriferinid brachiopods after the end-Permian extinction

Paleobiology ◽  
2020 ◽  
Vol 46 (4) ◽  
pp. 495-510
Author(s):  
Zhen Guo ◽  
Zhong-Qiang Chen ◽  
David A. T. Harper
Keyword(s):  
Phylogenetic Analysis ◽  
Small Group ◽  
Phylogenetic Trees ◽  
Early Jurassic ◽  
Late Triassic ◽  
Evolutionary Relationships ◽  
Early Triassic ◽  
Permian Extinction ◽  
Recovery Dynamics

AbstractThe Order Spiriferinida spanning the latest Ordovician to Early Jurassic is a small group of brachiopods overshadowed by other taxon-rich clades during the Paleozoic. It diversified significantly after the end-Permian extinction and became one of the four major clades of Triassic brachiopods. However, the phylogeny and recovery dynamics of this clade during the Triassic still remain unknown. Here, we present a higher-level parsimony-based phylogenetic analysis of Mesozoic spiriferinids to reveal their evolutionary relationships. Ecologically related characters are analyzed to indicate the variances in ecomorphospace occupation and disparity of spiriferinids through the Permian–Triassic (P-Tr) transition. For comparison with potential competitors of the spiriferinids, the pre-extinction spiriferids are also included in the analysis. Phylogenetic trees demonstrate that about half of the Mesozoic families appeared during the Anisian, indicating the greatest phylogenetic diversification at that time. Triassic spiriferinids reoccupied a large part of the ecomorphospace released by its competitor spiriferids during the end-Permian extinction; they also fully exploited the cyrtiniform region and developed novel lifestyles. Ecomorphologic disparity of the spiriferinids dropped greatly in the Early Triassic, but it rebounded rapidly and reached the level attained by the pre-extinction spiriferids in the Late Triassic. The replacement in ecomorphospace occupation between spiriferids and spiriferinids during the P-Tr transition clearly indicates that the empty ecomorphospace released by the extinction of Permian spiriferids was one of the important drivers for the diversification of the Triassic spiriferinids. The Spiriferinida took over the empty ecomorphospace and had the opportunity to flourish.

Referral of Miacis jepseni Guthrie to Oödectes Wortman, and an assessment of phylogenetic relationships among early Eocene Miacidae (Mammalia: Carnivora)

1997 ◽  
Vol 71 (6) ◽  
pp. 1172-1178 ◽  
Author(s):  
Ronald E. Heinrich
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationship ◽  
Phylogenetic Relationships ◽  
Sister Taxon ◽  
Evolutionary Relationships ◽  
Early Eocene ◽  
Relationship Of ◽  
Early Cenozoic

A phylogenetic analysis was conducted to address evolutionary relationships among the earliest members of the Miacidae (one of two early Cenozoic carnivoran families) and to ascertain the position of an ambiguous taxon, “Miacis” jepseni, with respect to the genera Miacis, Uintacyon, Vulpavus, Vassacyon, and Oödectes. The results of this analysis indicate that “Miacis” jepseni should be referred to the genus Oödectes, and both genus and currently included species are rediagnosed. The phylogenetic relationship of Oödectes to other miacids, and relationships among early Eocene miacids more generally, however, are less well resolved. Support is found for sister taxon relationships between Miacis and Vulpavus and between Uintacyon and Vassacyon, and it is suggested that this latter clade is the sister taxon to all other members of Miacidae.

scholarly journals Exploring the relationship of Homalosilpha and Mimosilpha (Blattodea, Blattidae, Blattinae) from a morphological and molecular perspective, including a description of four new species

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10618
Author(s):  
Shuran Liao ◽  
Yishu Wang ◽  
Duting Jin ◽  
Rong Chen ◽  
Zongqing Wang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Phylogenetic Trees ◽  
Close Relationship ◽  
Relationship Of ◽  
The Relationship ◽  
Six Genes

This study utilized six genes (12S, 16S, 18S, 28S, COII and H3) from a total of 40 samples to construct maximum likelihood (ML) and Bayesian inference (BI) phylogenetic trees in order to infer the relationships between the morphologically similar genera Homalosilpha Stål, 1874 and Mimosilpha Bey-Bienko, 1957. The phylogenetic analysis showed the two genera have a close relationship and were recovered as sister groups based on ML and BI analyses. Four new species are described among these samples, i.e., Homalosilpha obtusangula sp. nov., Homalosilpha recta sp. nov., Homalosilpha alba sp. nov. and Homalosilpha clavellata sp. nov. based on morphological and COI data. A key to the worldwide Homalosilpha is provided.

scholarly journals Chemical characterizations of Neurotransmission Receptors of human and plant to unfold the evolutionary relationships among them

2021 ◽  
Author(s):  
ANTARA SENGUPTA ◽  
SUBHADIP CHAKRABORTY ◽  
PABITRA PAL CHOUDHURY
Keyword(s):  
Amino Acids ◽  
Nervous System ◽  
Comparative Study ◽  
Phylogenetic Trees ◽  
Chemical Properties ◽  
Protein Sequences ◽  
Close Relation ◽  
Receptor Protein ◽  
Evolutionary Relationships ◽  
Numerical Representation

Abstract Vertebrates have very well defined nervous system. It is established that plant also has an alternative sort of sensitive nervous system. Researchers find a close relationship of the neurotransmission mechanism of animal with the plant and suspects close relation in amino acid transport mechanism among both the organisms. Along with the abilities of determining protein structure and various functions, the chemical properties of amino acids also have great contribution in molecular evolution. Hence, in this present work it is aimed at making comparative study on the distribution of amino acids in the neurotransmission receptors associated to animals and plants, based on the chemical properties the amino acids contain. It is possible to classify 20 amino acids into 8 chemical groups and are identified by specific numeric value. The common pattern finding procedure in numerical representation of protein sequences find some conserved regions in the receptor protein sequences of both the species. The comparative study has been made on distributions of chemical properties in protein sequences of ionotropic glutamate receptor protein sequences and GABA receptor protein sequences of two species namely human, a vertebrate and Arabidopsis thaliana, a plant. Experiments have been carried out to calculate proximity between protein sequences based on the distribution of each chemical group (in percentage) in them and phylogenetic trees have been constructed to find evolutionary relationships of neurotransmission receptors of both the spices.

Living Trees: High-Quality Reproducible and Reusable Construction of Bacterial Phylogenetic Trees

2019 ◽  
Vol 37 (2) ◽  
pp. 563-575 ◽  
Author(s):  
Dalong Hu ◽  
Bin Liu ◽  
Lei Wang ◽  
Peter R Reeves
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Trees ◽  
Bacterial Genome ◽  
Strain Level ◽  
Genome Sequences ◽  
Major Step ◽  
Living Tree ◽  
Large Numbers ◽  
Global Standardization ◽  
Tree Resolution

Abstract An ideal bacterial phylogenetic tree accurately retraces evolutionary history and accurately incorporates mutational, recombination and other events on the appropriate branches. Current strain-level bacterial phylogenetic analysis based on large numbers of genomes lacks reliability and resolution, and is hard to be replicated, confirmed and reused, because of the highly divergent nature of microbial genomes. We present SNPs and Recombination Events Tree (SaRTree), a pipeline using six “living trees” modules that addresses problems arising from the high numbers and variable quality of bacterial genome sequences. It provides for reuse of the tree and offers a major step toward global standardization of phylogenetic analysis by generating deposit files including all steps involved in phylogenetic inference. The tree itself is a “living tree” that can be extended by addition of more sequences, or the deposit can be used to vary the programs or parameters used, to assess the effect of such changes. This approach will allow phylogeny papers to meet the traditional responsibility of providing data and analysis that can be repeated and critically evaluated by others. We used the Acinetobacter baumannii global clone I to illustrate use of SaRTree to optimize tree resolution. An Escherichia coli tree was built from 351 sequences selected from 11,162 genome sequences, with the others added back onto well-defined branches, to show how this facility can greatly improve the outcomes from genome sequencing. SaRTree is designed for prokaryote strain-level analysis but could be adapted for other usage.

scholarly journals Systematics of Vriesea (Bromeliaceae): phylogenetic relationships based on nuclear gene and partial plastome sequences

2019 ◽  
Vol 192 (4) ◽  
pp. 656-674 ◽  
Author(s):  
Talita Mota Machado ◽  
Oriane Loiseau ◽  
Margot Paris ◽  
Anna Weigand ◽  
Leonardo M Versieux ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Phylogenetic Trees ◽  
Nuclear Gene ◽  
Evolutionary Relationships ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
A Genome ◽  
Genome Skimming

Abstract Vriesea is the second largest genus in Tillandsioideae, the most diverse subfamily of Bromeliaceae. Although recent studies focusing on Tillandsioideae have improved the systematics of Vriesea, no consensus has been reached regarding the circumscription of the genus. Here, we present a phylogenetic analysis of core Tillandsioideae using the nuclear gene phyC and plastid data obtained from genome skimming. We investigate evolutionary relationships at the intergeneric level in Vrieseeae and at the intrageneric level in Vriesea s.s. We sampled a comprehensive dataset, including 11 genera of Tillandsioideae and nearly 50% of all known Vriesea spp. Using a genome skimming approach, we obtained a 78 483-bp plastome alignment containing 35 complete and 55 partial protein-coding genes. Phylogenetic trees were reconstructed using maximum-likelihood based on three datasets: (1) the 78 483 bp plastome alignment; (2) the nuclear gene phyC and (3) a concatenated alignment of 18 subselected plastid genes + phyC. Additionally, a Bayesian inference was performed on the second and third datasets. These analyses revealed that Vriesea s.s. forms a well-supported clade encompassing most of the species of the genus. However, our results also identified several remaining issues in the systematics of Vriesea, including a few species nested in Tillandsia and Stigmatodon. Finally, we recognize some putative groups within Vriesea s.s., which we discuss in the light of their morphological and ecological characteristics.

scholarly journals Open Reading Frame Phylogenetic Analysis on the Cloud

2013 ◽  
Vol 2013 ◽  
pp. 1-9 ◽  
Author(s):  
Che-Lun Hung ◽  
Chun-Yuan Lin
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Trees ◽  
Large Scale ◽  
Sequence Similarity ◽  
Open Reading Frames ◽  
Open Reading Frame ◽  
Evolutionary Relationships ◽  
Reading Frame ◽  
Complete Sequences

Phylogenetic analysis has become essential in researching the evolutionary relationships between viruses. These relationships are depicted on phylogenetic trees, in which viruses are grouped based on sequence similarity. Viral evolutionary relationships are identified from open reading frames rather than from complete sequences. Recently, cloud computing has become popular for developing internet-based bioinformatics tools. Biocloud is an efficient, scalable, and robust bioinformatics computing service. In this paper, we propose a cloud-based open reading frame phylogenetic analysis service. The proposed service integrates the Hadoop framework, virtualization technology, and phylogenetic analysis methods to provide a high-availability, large-scale bioservice. In a case study, we analyze the phylogenetic relationships amongNorovirus. Evolutionary relationships are elucidated by aligning different open reading frame sequences. The proposed platform correctly identifies the evolutionary relationships between members ofNorovirus.

scholarly journals Two Complete Mitochondrial Genomes of Mileewinae (Hemiptera: Cicadellidae) and a Phylogenetic Analysis

Insects ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 668
Author(s):  
Tinghao Yu ◽  
Yalin Zhang
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Strong Support ◽  
Intergenic Spacer ◽  
Taxonomic Status ◽  
Start Codon ◽  
Gene Arrangement ◽  
Mitochondrial Genomes ◽  
Protein Coding

More studies are using mitochondrial genomes of insects to explore the sequence variability, evolutionary traits, monophyly of groups and phylogenetic relationships. Controversies remain on the classification of the Mileewinae and the phylogenetic relationships between Mileewinae and other subfamilies remain ambiguous. In this study, we present two newly completed mitogenomes of Mileewinae (Mileewa rufivena Cai and Kuoh 1997 and Ujna puerana Yang and Meng 2010) and conduct comparative mitogenomic analyses based on several different factors. These species have quite similar features, including their nucleotide content, codon usage of protein genes and the secondary structure of tRNA. Gene arrangement is identical and conserved, the same as the putative ancestral pattern of insects. All protein-coding genes of U. puerana began with the start codon ATN, while 5 Mileewa species had the abnormal initiation codon TTG in ND5 and ATP8. Moreover, M. rufivena had an intergenic spacer of 17 bp that could not be found in other mileewine species. Phylogenetic analysis based on three datasets (PCG123, PCG12 and AA) with two methods (maximum likelihood and Bayesian inference) recovered the Mileewinae as a monophyletic group with strong support values. All results in our study indicate that Mileewinae has a closer phylogenetic relationship to Typhlocybinae compared to Cicadellinae. Additionally, six species within Mileewini revealed the relationship (U. puerana + (M. ponta + (M. rufivena + M. alara) + (M. albovittata + M. margheritae))) in most of our phylogenetic trees. These results contribute to the study of the taxonomic status and phylogenetic relationships of Mileewinae.

scholarly journals An Investigation of the Relationship between Cyniclomyces guttulatus and Rabbit Diarrhoea

Pathogens ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 880
Author(s):  
Tuanyuan Shi ◽  
Xinlei Yan ◽  
Hongchao Sun ◽  
Yuan Fu ◽  
Lili Hao ◽  
...  
Keyword(s):  
New Zealand ◽  
Body Weight Gain ◽  
Animal Experiments ◽  
Zealand White Rabbit ◽  
Opportunistic Pathogen ◽  
Large Numbers ◽  
New Zealand White Rabbits ◽  
Positive Rate ◽  
Relationship Of ◽  
The Relationship

Cyniclomyces guttulatus is usually recognised as an inhabitant of the gastrointestinal (GI) tract in rabbits. However, large numbers of C. guttulatus are often detected in the faeces of diarrhoeic rabbits. The relationship of C. guttulatus with rabbit diarrhoea needs to be clearly identified. In this study, a C. guttulatus Zhejiang strain was isolated from a New Zealand White rabbit with severe diarrhoea and then inoculated into SPF New Zealand white rabbits alone or co-inoculated with Eimeriaintestinalis, another kind of pathogen in rabbits. Our results showed that the optimal culture medium pH and temperature for this yeast were pH 4.5 and 40–42 °C, respectively. The sequence lengths of the 18S and 26S ribosomal DNA fragments were 1559 bp and 632 bp, respectively, and showed 99.8% homology with the 18S ribosomal sequence of the NRRL Y-17561 isolate from dogs and 100% homology with the 26S ribosomal sequence of DPA-CGR1 and CGDPA-GP1 isolates from rabbits and guinea pigs, respectively. In animal experiments, the C. guttulatus Zhejiang strain was not pathogenic to healthy rabbits, even when 1 × 108 vegetative cells were used per rabbit. Surprisingly, rabbits inoculated with yeast showed a slightly better body weight gain and higher food intake. However, SPF rabbits co-inoculated with C. guttulatus and E. intestinalis developed more severe coccidiosis than rabbits inoculated with C. guttulatus or E. intestinalis alone. In addition, we surveyed the prevalence of C. guttulatus in rabbits and found that the positive rate was 83% in Zhejiang Province. In summary, the results indicated that C. guttulatus alone is not pathogenic to healthy rabbits, although might be an opportunistic pathogen when the digestive tract is damaged by other pathogens, such as coccidia.

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