Phylogenomic Analysis of Echinoderm †Free Samples to Students

Question: Discuss about the Phylogenomic Analysis of Echinoderm. Answer: Introduction: The echinoderms share similar benthic habitats, comprising of the five phylum classes. Over there are variations based on their classes. This is consistent with mitochondrial genomics analysis which show that there is conservation of 37 mt genes on Echinoderms; however this is not same for all the phyla classes, with differences being observed among the two species or families. At the same time similarities have been observed among four classes, however there were difference on two families of the Ophiuridae and Ophiactidae, which show differences as can be exhaled by the inversion differences, (Michonneau Paulay, 2015). The notable usage of mitochondrial genomes in analysing the Echnodermata on the phylogenetic relationship shave been controversial due to the conservation of the different genes order in the different families of echinoderms. Further compounding this biological question is the position which revolves around the ophiouroids. Several hypothesis have been put forwards to explain this by none has been explicit in elaborating sufficient evidences to support this, (Khor Ettensohn, 2017). Further analysis of genomes have shown that strong similarities among four classes which its gene orders can be interconvert through evolutionary means, while other gene orders for three species of two families of Ophiuridae, Ophiactidaeshows one inversion having nine mitochondrial genes with TRNA rearrangements, (Gittenberger, Rikoh de Voogd, 2016). Thus this observed similarities and differences have made it to biologically relate the relationship of the phylum echnodemerta and the observable differences in its states management. Hypothesis on evolution of echinoderms According to the study by Reich et al, (2015), there is occurrence of rapid radiation of echinodermata which occurred 10-15 million years ago with most recent ancestor in 500 million years ago referred to as Asterozoan hypothesis, which states that there is sister relationship between Ophiuroidea and Asteroidea, which is further supported by molecular sequences, (OHara Byrne, 2017). In the study conducted by Perseke et al, (2010), the phylogenitc analysis of protein coding genes shows that phylogentic analysis of all the 13genes of the ophinorderm species had loner chain branches. The genes CytB and Coxl exhibit evolution in clock like formation, while shorter chains dont have phylogenomic analysis. Further in the study by Perseke et al, (2013), chordata lineages phylogeny have suggested it to be related to Craniota due to the possession of notochord and other characters. Referred to as Notochordata hypothesis, while others are assessed on phylogenomic data which favours close relationship of Tunicata and Craniot offered to as Olfactores hypothesis. Close relationship of Enteropneusta to Chordata has led to Cyrtotreta hypothesis or Echinodermata yielding Ambulacraria hypothesis. According toTelfold et al, (2014), Asteroza hypothesis suggest that ophiuroids are sister groups of asteroids while the Cryptosyringida hypothesis links the ophiuroids instead to the Echinozoa. This relationship has evolutionary significance in that both classes have pluteus-type larva. In the study done by Rech et al, (2015), on phylogenomic analysis of echnodermata on supporting sister groups of Asterozoa and Echnozoa, find out that there were major transitions which were observed occurring in echinoids after the splitting of Asterozoa and Echinozoa. This findings were similar to those of Telford et al, (2010), which found out that under the Asteroza hypothesis, there is existence of differing molecular mechanism which suggest parallel evolution of the echinoids and ophiuroids, (Zmora et al, 2017). Power of study findings depend on the methodology and analysis of the results. Perseke et al, (2010), analysed the protein sequences using a comprehensive analytical tool based on the three different taxon sets for the amino acids. The specimens were collected in Roscoff France and tired using ht eRNAaleter. The preparation of the DNA was done using tissue phenol chloroform. This study entailed isolation of the mictochodirion and DNA extraction process, (Cleary et al, 2016). The phylogenetic analyses revealed the mitcohrodrial genomes within the Echinodermata which showed many difficulties as to pertaining the nucleotide compositions and the different evolutionary rates between the echinoderm classes. The analysis showed that the echinoderm genomes are conserved in echinodermata having gene differences, characterised by low unassigned sequences and high similarity sequences. This analysis, the phylogenetic analysis of the discrimanitated lineages within the Echinodermata, he Crinoidea, the Ophiuroidea, and a group containing Echinoidea, Holothuroidea and Asteroidia having similar amino acids sequence with gene evolution order, (Falkner et al, 2015). Thus this convincing pathway is entailed in the genetic makeup which characteristics the DNA of any material conforming the relationship in between the different phylum classes available in Echinodermata. Telford et al, (2014) showed most compelling data with the analysis soft h data sets of 219 genes from the echinoderm classes, which utilised analysis of probalistic Bayesen phylogenies methods which strongly supported the Asterozoa . This data signified the most reliable and evolving quartile of genes which gave the highest support to the Asteroza. Further this support in the study decline in second and third quartile with the fastest changing quartiles being placed on the ophiourides which is close to the root. Utilizing the phylogentic digital dissection, the study showed heterozygous sites which have unlikely grouping of Ophiuroidea with Holothuria, while the homogenous sites heavily supported Asterozoa family. Thus this data analysis supported the cryptosyringid hypothesis which supports heavily the Asterozoa. The phylogeny analysis performed in this study using the phylobayes analysis with computer intensive heterogeneous mixture having CAT+GTR+G with duration of one month analysis was performed. The reliability of the trees was done suing the 50 boot strap analysis replication. Cross validation sets were performed using the CAT+GTR+G, the WAG+G and GTR+G models using cross validation tests, (Semmens Elphick, 2017). Parsimony analysis entails the principle of offering simplest explanation to illustrate data. In phylogeny analysis it refers the relationships of hypothesis which requires the smallest number of changes in characters which is most likely to be correct. In molecular analysis, this offers DNA mutations. The article review, Telford et al, (2010), used parsimony to analyse the maximum phylogenitc signal dissection. Baysian phylogenetic analyses uses the likelihood of phylogeny in creating the quantity also referred to as posterior probability of trees, it is crucial in production of phylogentic tree for any given data. In the study by, Bayesian phylogenetic analyses was conducted with the phyloBayes having 1.3 b-mpi on the location of the dense supermatrix using the CAT-GTR model. Further in the study by Perseke, et al, (2010), performed Baysian analysis using MrBayes v.3.1.2 with MtRev as a mutation model with the variant size having varied substitution rates. Maximum likelihood estimation estimates the parameters for statistical models with observations. The maximum likelihood attempts to give a parameter values which maximizes the likelihood function. In the study, MLE was utilised in the study by Rech et al, (2015), maximum likelihood phylogentic analysis was utilised with RAxML (GAMMAWAG model) having 1000 boot strap iteration suited on the dense supermatrix sing the same model. Further in the study by Perseke et al, (2010), maximum likelihood tree for amino acid was constructed having all the sequence coding genes utilizing the taxon Hemichodata. Maximum likelihood estimates beneficial in using wide range analysis. It accomplishes the mean and variances which are estimated by the MLE, with reference with Bayesian inference, maximum likelihood estimate offers uniform distribution of parameters,(Silverman, 2018). Bayesian inference on the other hand is useful in estimating the probability of trees in any certain model. It gives appropriate phylogenetic tree for any provided data. Baysian phylogenetic analyses is a common molecular phylogenitics due to its user friendly model of evolution, (Gelman, 2014). Parsimony analysis phylogenetics is an optimal criterion which minimizes the total character in state changes. The optimal free minimizes the homoplasy, the results of this method is highly reliable with the shortest possible length is considered to have the best traits. It is a simple and intuitive criterion, which is easy to score management, (Zhou et al, 2015). Maximum likelihood estimate and Bayesian inference uses probability methodology thus estimates the values of any a given study sets. Parsimony analysis uses optimal criterion which minimizes the total number of character states. It is the preferred method due to its preference of homoplasy, indicating the shortest possible route. Thus in this task, Parsimony analysis will be beneficial in ensuring that all data is represented with genetic similarities having shorter tree diagram thus signifying linkage. It is a direct approach in assessing the phylogenies. Thus in tackling such a biological dilemma with regard to Echinoderma phylum species, all the families can form a tree diagram thus signifying genetic similarity. References Cleary, D.F.R., Polnia, A.R.M., Renema, W., Hoeksema, B.W., Rachello-Dolmen, P.G., Moolenbeek, R.G., Budiyanto, A., Tuti, Y., Draisma, S.G.A., Prud'homme van Reine, W.F. and Hariyanto, R., 2016. 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