Revision and phylogenetic analysis of the Gyrocotylidea Poche, 1926 (Platyhelminthes: Cercomeria: Cercomeromorpha)

1987 ◽  
Vol 65 (10) ◽  
pp. 2369-2389 ◽  
Author(s):  
Susan M. Bandoni ◽  
Daniel R. Brooks
Keyword(s):  
Phylogenetic Analysis ◽  
Initial Phase ◽  
Phylogenetic Trees ◽  
Parallel Evolution ◽  
Tectonic Plate ◽  
Low Degree ◽  
Two Phases ◽  
Index Value ◽  
Dispersal Events ◽  
Later Phase

Phylogenetic analysis of 10 gyrocotylidean platyhelminth species, based on 24 character states comprising 13 homologous series, produced two similar phylogenetic trees of equal length. The consistency index value for each tree is 87.5%, indicating a low degree of parallel evolution in the morphology of gyrocotylidean platyhelminths. Slightly more than half of the observed associations between gyrocotylideans and holocephalan hosts can be attributed to coevolution. Remaining associations must be attributed to colonization, but these represent recolonizations of plesiomorphic hosts. The geographic distribution of gyrocotylideans remains enigmatic, as part of it seems to predate tectonic plate movements. Extensive dispersal has occurred; dispersal events are correlated with host transfers. It is hypothesized that the origin of gyrocotylideans predates separation of the continents, and that there were two phases in the evolution of the gyrocotylideans, an initial phase of coevolution and a later phase of colonization and dispersal.

Revision and phylogenetic analysis of the Amphilinidea Poche, 1922 (Platyhelminthes: Cercomeria: Cercomeromorpha)

1987 ◽  
Vol 65 (5) ◽  
pp. 1110-1128 ◽  
Author(s):  
Susan M. Bandoni ◽  
Daniel R. Brooks
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Tree ◽  
Geographic Distribution ◽  
Homologous Series ◽  
Consistency Index ◽  
Low Degree ◽  
Systematic Relationships ◽  
Index Value ◽  
High Degree

Systematic relationships of amphilinidean platyhelminth species were investigated. Eight species and three genera are considered valid. Analysis of 46 character states comprising 34 homologous series produced a single phylogenetic tree with a consistency index value of 87%, indicating a very low degree of parallelism in the evolution of amphilinidean morphology. Comparison of host and parasite phylogenies produced a fit of 70%, suggesting a high degree of coevolution between amphilinideans and their teleostean hosts. The geographic distribution of the amphilinideans was compared with four current hypotheses of area relationship for the southern land masses. Consistency index values obtained range from 87.5% to 100%, indicating that vicariance may be sufficient to explain the biogeographic distribution of amphilinidean platyhelminths.

Phylogenetic analysis of the Digenea (Platyhelminthes: Cercomeria) with comments on their adaptive radiation

1985 ◽  
Vol 63 (2) ◽  
pp. 411-443 ◽  
Author(s):  
Daniel R. Brooks ◽  
Richard T. O'Grady ◽  
David R. Glen
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Tree ◽  
Morphological Change ◽  
Adaptive Radiation ◽  
Parallel Evolution ◽  
Morphological Diversification ◽  
Ecological Diversification ◽  
Low Degree ◽  
Adaptive Radiations ◽  
Low Levels

Phylogenetic analysis of 63 digenean family groups, based on 113 adult characters and 90 larval characters, produced a phylogenetic tree comprising nine orders. Adult characters alone resolved 76% of the phylogenetic tree, whereas larval characters alone resolved 74%. There was no disagreement in phylogenetic inferences drawn from only larval or only adult characters, and yet the larval forms of digeneans do not seem to be recapitulations of ancestral adult forms. The consistency index for the tree is 74%, indicating a low degree of parallel evolution in digenean morphology. Diversification in six sets of ecological characteristics combined resolves 26% of the phylogenetic tree. The combination of (i) larval and adult congruence in the absence of recapitulation, (ii) low levels of parallel evolution in morphology, and (iii) ecological diversification lagging far behind morphological change discounts traditional notions of adaptive radiations. Digeneans have experienced great morphological diversification constrained by their developmental programs and history, and have maintained their functional intergrity with few changes caused by extrinsic, "adaptive," forces.

DIVERSITY OF FISH LARVAE AROUND THE ESTUARY OF THE BANYUASIN RIVER, SOUTH SUMATERA PROVINCE

2020 ◽  
Vol 6 (2) ◽  
Author(s):  
Moh. Rasyid Ridho ◽  
Enggar Patriono ◽  
Sarno Sarno ◽  
Sahira Wirda
Keyword(s):  
Initial Phase ◽  
Sampling Method ◽  
Environmental Changes ◽  
Negative Impact ◽  
Fish Larvae ◽  
River Estuary ◽  
Sampling Technique ◽  
Critical Phase ◽  
Morisita Index ◽  
Index Value

The initial phase of the fish life cycle is a critical phase associated with high mortality due to sensitivity to predators, food availability, and also environmental changes that occur in nature. Disruption of the initial stages of fish life has a negative impact on fish populations. Until now there has been no information about fish larvae around the Banyuasin River Estuary. Therefore, research is needed on the diversity of fish larvae around the Banyuasin River Estuary, South Sumatra Province. This research were used purposive sampling method, sampling technique in the form of Cruise Track Design with continuous parallel survey trajectory. Based on the results of the study found as many as 10 families consisting of 1483 individuals of fish larvae in March and 1013 individuals of fish larvae in May consisting of Engraulidae 1,601 individuals of fish larvae, Mungiloidei as many as 109 individuals, Leiognathidae 50 individuals, Chanidae 453 individuals, Scatophagidae 20 individuals , Belonidae 39 individuals, Gobioididae 5 individuals, Chandidae 183 individuals, Syngnatihidae 6 individuals, and Gobiidae 30 individuals fish larvae. The index value of fish larvae diversity is classified as medium category (March 1.02 and May 1.12), Morisita index shows the distribution pattern of fish larvae classified as a group (March 0-14.17 and May 2.43-10.40 ), and the evenness index value is in the medium category (March 0.437 and May 0.521).

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 Extensive Phylogenetic Analysis of Piscine Orthoreovirus Genomic Sequences Shows the Robustness of Subgenotype Classification

Pathogens ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 41
Author(s):  
Marcos Godoy ◽  
Daniel A. Medina ◽  
Rudy Suarez ◽  
Sandro Valenzuela ◽  
Jaime Romero ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Variation ◽  
Sequence Analysis ◽  
Molecular Phylogeny ◽  
Phylogenetic Trees ◽  
Genomic Segment ◽  
Double Stranded Rna ◽  
The Family ◽  
Original Classification

Piscine orthoreovirus (PRV) belongs to the family Reoviridae and has been described mainly in association with salmonid infections. The genome of PRV consists of about 23,600 bp, with 10 segments of double-stranded RNA, classified as small (S1 to S4), medium (M1, M2 and M3) and large (L1, L2 and L3); these range approximately from 1000 bp (segment S4) to 4000 bp (segment L1). How the genetic variation among PRV strains affects the virulence for salmonids is still poorly understood. The aim of this study was to describe the molecular phylogeny of PRV based on an extensive sequence analysis of the S1 and M2 segments of PRV available in the GenBank database to date (May 2020). The analysis was extended to include new PRV sequences for S1 and M2 segments. In addition, subgenotype classifications were assigned to previously published unclassified sequences. It was concluded that the phylogenetic trees are consistent with the original classification using the PRV genomic segment S1, which differentiates PRV into two major genotypes, I and II, and each of these into two subgenotypes, designated as Ia and Ib, and IIa and IIb, respectively. Moreover, some clusters of country- and host-specific PRV subgenotypes were observed in the subset of sequences used. This work strengthens the subgenotype classification of PRV based on the S1 segment and can be used to enhance research on the virulence of PRV.

scholarly journals Phylogenetic Analysis to Explore the Association Between Anti-NMDA Receptor Encephalitis and Tumors Based on microRNA Biomarkers

Biomolecules ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 572 ◽  
Author(s):  
Wang
Keyword(s):  
Phylogenetic Analysis ◽  
Nmda Receptor ◽  
Phylogenetic Trees ◽  
Tumor Resection ◽  
Autoimmune Disorder ◽  
Control Of Gene Expression ◽  
Nmda Receptor Encephalitis ◽  
Nmdar Encephalitis ◽  
Non Coding Rna ◽  
The Relationship

MicroRNA (miRNA) is a small non-coding RNA that functions in the epigenetics control of gene expression, which can be used as a useful biomarker for diseases. Anti-NMDA receptor (anti-NMDAR) encephalitis is an acute autoimmune disorder. Some patients have been found to have tumors, specifically teratomas. This disease occurs more often in females than in males. Most of them have a significant recovery after tumor resection, which shows that the tumor may induce anti-NMDAR encephalitis. In this study, I review microRNA (miRNA) biomarkers that are associated with anti-NMDAR encephalitis and related tumors, respectively. To the best of my knowledge, there has not been any research in the literature investigating the relationship between anti-NMDAR encephalitis and tumors through their miRNA biomarkers. I adopt a phylogenetic analysis to plot the phylogenetic trees of their miRNA biomarkers. From the analyzed results, it may be concluded that (i) there is a relationship between these tumors and anti-NMDAR encephalitis, and (ii) this disease occurs more often in females than in males. This sheds light on this issue through miRNA intervention.

scholarly journals SHOOT: phylogenetic gene search and ortholog inference

2021 ◽  
Author(s):  
David Emms ◽  
Steven Kelly
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
Phylogenetic Trees ◽  
Query Sequence ◽  
Gene Tree ◽  
Biological Research ◽  
Gene Sequences ◽  
Multiple Sequence ◽  
Gene Search

Determining the evolutionary relationships between gene sequences is fundamental to comparative biological research. However, conducting such analyses requires a high degree of technical proficiency in several computational tools including gene family construction, multiple sequence alignment, and phylogenetic inference. Here we present SHOOT, an easy to use phylogenetic search engine for fast and accurate phylogenetic analysis of biological sequences. SHOOT searches a user-provided query sequence against a database of phylogenetic trees of gene sequences (gene trees) and returns a gene tree with the given query sequence correctly grafted within it. We show that SHOOT can perform this search and placement with comparable speed to a conventional BLAST search. We demonstrate that SHOOT phylogenetic placements are as accurate as conventional multiple sequence alignment and maximum likelihood tree inference approaches. We further show that SHOOT can be used to identify orthologs with equivalent accuracy to conventional orthology inference methods. In summary, SHOOT is an accurate and fast tool for complete phylogenetic analysis of novel query sequences. An easy to use webserver is available online at www.shoot.bio.

scholarly journals Whole Chloroplast Genomes reveals the uniqueness of Bolivian native cacao (Theobroma cacao) from the northern part of Bolivia

2021 ◽  
Author(s):  
Marcia Gumiel ◽  
Oscar M Rollano-Penaloza ◽  
Carmelo Peralta-Rivero ◽  
Leslie Tejeda ◽  
Valeria D. Palma Encinas ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Next Generation Sequencing ◽  
Theobroma Cacao ◽  
Phylogenetic Trees ◽  
Plastid Genome ◽  
Next Generation ◽  
Center Of Origin ◽  
Chloroplast Genomes ◽  
Geographical Locations ◽  
Generation Sequencing

We report the complete chloroplast sequences of two varieties of Theobroma cacao collected in the Bolivian Amazonia using Next-Generation Sequencing. Comparisons made between these two chloroplast genomes and the Belizean reference plastid genome identified 19 and 22 nucleotide variants. The phylogenetic analysis reported three main T. cacao clades belonging to the Forastero, Criollo and Trinitario groups. The Bolivian Native Cacao varieties were located inside the Trinitario group forming their unique branch. The Bolivian Native Cacao branch reveals a possible new subpopulation different from the well-characterized T. cacao subpopulations. The phylogenetic trees showed that the relationships among the T. cacao varieties were consistent with their geographical locations placing the Cacao Center of Origin in Western Amazon. The data presented here will contribute to the usage of ultrabarcoding to distinguish different T. cacao varieties and to identify native cacaos from introduced cacaos. Thus helping in the conservation of local native varieties of T. cacao.

Characterization of Atrazine Accumulation by Excised Velvetleaf (Abutilon theophrasti) Roots

Weed Science ◽  
1983 ◽  
Vol 31 (1) ◽  
pp. 14-19 ◽  
Author(s):  
Thomas P. Price ◽  
Nelson E. Balke
Keyword(s):  
Initial Phase ◽  
External Solution ◽  
Abutilon Theophrasti ◽  
Linear Phase ◽  
Rapid Absorption ◽  
Two Temperatures ◽  
Two Phases ◽  
Excised Tissue

Long-term absorption of14C-atrazine [2-chloro-4 - (ethylamino) - 6 - (isopropylamino) -s- triazine] by excised velvetleaf (Abutilon theophrastiMedic.) roots was investigated. A rapid, initial phase of absorption was followed by a long-term, linear phase of absorption, which resulted in atrazine accumulation in the tissue to concentrations above the external solution. This accumulation did not result from metabolism of the atrazine. Aging of the excised tissue appeared to be responsible for the accumulation. Dinitrophenol, but not cyanide, inhibited accumulation. Atrazine accumulation decreased as the temperature during absorption was decreased. The Q10the absorption rate was ca. 2.5 between 15 and 25 C. Efflux of atrazine from the tissue occurred in two phases. At 25 C, loss of 80% of the atrazine occurred in 20 min. At 4C, the rate of this efflux was slower and the phase lasted longer. At both 4 and 25 C a second, slower phase of efflux occurred through at least 6 h and resulted in loss of equal amounts of atrazine at the two temperatures. These experiments show that, in addition to rapid absorption of atrazine to a passive equilibrium, excised velvetleaf roots accumulate atrazine by a metabolically dependent process over long periods of time.

scholarly journals A51 Genetic variability of small ruminant lentiviruses in sheep and goats from single-species flocks from Poland

2019 ◽  
Vol 5 (Supplement_1) ◽  
Author(s):  
Monika Olech ◽  
Jacek Kuźmak
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Variability ◽  
Phylogenetic Trees ◽  
Small Ruminant ◽  
Phylogenetic Analyses ◽  
Single Species ◽  
Genetic Distances ◽  
Sheep And Goats ◽  
Viral Recombination ◽  
Species Flocks

Abstract Previous phylogenetic analyses of small ruminant lentivirus (SRLV) sequences found in Poland revealed the circulation of subtype A1 in both sheep and goats, subtypes B1 in goats, and subtypes B2, A12, and A13 in sheep only. This study aimed to analyze the genetic nature of SRLV circulating in sheep and goats from single-species flocks. In order to analyze the degree of genetic variability, the fragments of gag and env genes of 24 SRLV strains were amplified by PCR, cloned into plasmid vectors, sequenced, and consensus sequences were aligned to each other and to reference sequences available from GenBank. Phylogenetic analysis was performed using the Geneious tree-builder tool, and phylogenetic trees were constructed using Mr Bayes (using the general time reversible substitution model) within Geneious Pro 5.3. Pairwise genetic distances were calculated in MEGA 6. Phylogenetic analysis revealed that the strains were highly heterogeneous and represented ovine strains belonging to subtypes A12 and B2 and caprine strains grouped in subtypes B1, B2, A1, and A12. In addition, two novel subtypes, A16 and A17, were found in goats. The mean pairwise genetic distances of gag and env sequences of both clusters were above 15 per cent nucleotide divergence when compared to all other subtypes within group A, which is a criterion required to distinguish a new subtype. Additionally, the existence of two separated clusters was confirmed by high bootstrap values. Co-infections with strains belonging to different subtypes within A and B groups were detected in one sheep and four goats originating from four flocks. Since the co-infection with more than one lentivirus genotype offers an opportunity for viral recombination, the possible recombination events were tested based on RDP analysis. For all co-infected animals, no evidence of recombination was found within the gag gene; however, env sequences showed some recombination patterns in three samples. In conclusion, we have demonstrated extended genetic variability of SRLV in sheep and goats from Poland with the existence of co-infection and recombination events.

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