Tracing The Evolutionary Traits of the Order Verongida Through Utilization of

Software
Emilio V. Sebastian
Department of Biological Sciences, College of Science, University of Santo Tomas
España Boulevard, 1015 Manila, Philippines.

Abstract

The structure of poriferan body is plain, consisting of a set of channels and chambers by
which water is circulating.The taxonomy of marine sponges is mainly focused on
morphological characters that may demonstrate a high degree of phenotypic plasticity,
although existing classifications do not necessarily represent evolutionary relationships.
Data modules were developed in order to better evaluate the recorded organisms using
the Mesquite phylogenetic analysis program and the RASP software to examine the
biogeographic distribution of the sponges. The results suggest that there is a significant
difference between the configurations of the phylogenetic tree and the molecular tree
embedded in the phenotypic evidence. In addition, the biogeographic study offered
indication of the potential disappearance, distribution and vicariate of Verongid sponges.
Eventually, it was discovered that the Verongid sponges had experienced a range of
settings during evolution.

Keywords: taxonomy, vicariate, phylogenetic, morphological

Introduction

Taxonomy and classification of organisms are the basic foundations for both theoretical
and practical biological science. Modern taxonomy has been focused on comparative
morphology for decades, and still today most plant definitions are mostly centered on
morphology. Nevertheless, this conventional method can be arbitrary when defining the
protagonists, making it difficult to classify the animal. Verongida is the highest group of
the Myxospongiae. Verongid sponges are characterized by the presence of spongin fibres
(Bergquist, 1970). Phylum Porifera is a very complex and widespread species within the
aquatic benthic environment. Sponges are currently attracting growing interest due to
their evolutionary, ecological and economic importance in terms of pharmaceutical and
biotechnological fields.

Multiple alignment of protein sequences has relevance in certain aspects including

phylogenetic tree estimation, secondary structural prediction and critical residue
identification (Edgar, 2004). A number of options are provided to give the maximum
precision, distance, or other a balance between the two of them. Start by nature
parameters are those that have the highest composite precision. Mesquite is an
evolutionary biology program developed to support scientists handle and interpret
quantitative data on species. It focuses on phylogenetic analysis, but certain guidelines
concern population genetics, while others focus on non-phylogenetic multivariate
analysis. Since it is modular, the research and control capabilities available depend on
the modules installed (Maddison, 2018).

Biogeography is a systematic review of the geographical species diversity and, by

extension, the economic and environmental (distribution and functioning of ecological
systems), the high academic standards (richness and composition of wildlife collections)
and the biological (distribution and correlation between populations) measurements of
species diversity (Southern Ocean, 2015). The objective of this experiment is to trace the
possible origin of the order Verongida through the use of software.

Materials and Methods

In this experiment, two (2) software were utilized such as Mesquite and MUSCLE
(Multiple Sequence Comparison by Log-Expectation) to trace the evolutionary traits of the
order Verongida. This will allow to clearly see the differences of traits and to determine
the ancestral and derived traits from each of the given taxa.

Part 1. Using MESQUITE

Figure 1: Mesquite Window Log

Mesquite has several choices based on which modules are mounted and loaded. Its
modularity and flexibility make it possible to perform many analyses, but it also creates
challenges for the user There are so many potential analyzes for us to provide detailed
guidelines written for each of them. In the data provided, input the corresponding terms
in the character matrix. There were 13 taxa and 10 characters given. In order to create a
consensus tree, complete the character matrix first. First, input the data for taxa and
characters; a question mark will appear in the boxes as you input the data. Second,go
back to the Character Matrix tab and click the “blue i" icon. This opens the information tab
where you can edit the states and provide codes

Figure 2: Complete Character Matrix

After coding, you can now input states in the appropriate boxes using only the number
codes: type either 0, 1 or 2, etc. Complete states will automatically be placed once you
press enter. Repeat for all characters and taxa until you obtain the characters using the
data provided. After completing the matrix, it is now ready for tree construction. Take note
that the resulting tree is unrooted. It still needs to be aligned. From the tabs click 1.
ANALYSIS; 2.Tree Inference; 3. Tree Search; 4.Mesquite Heuristic Search (add and
arrange). This will result to “criteria for tree search” Select tree length and calculate the
parsimony length of the tree.
 Figure 3: Generated Tree based from the character matrix

The multiple trees created by the analysis can be reduced to a single tree with the best
representation of relationships. The software will generate certain number of trees but it
will only display the most parsimonious. Click, 1. “TAXA&TREES”; 2. highlight “Make
New Trees Block from”;3. Consensus Tree. Then choose “Source of Trees for
Consensus” . Reroot the tree if neccessary. Save the tree and the project file. Examine
the tree and observe the relationships.

Part 2. Molecular Data

 Figure 4 DNA Sequences acquired from GenBank

Molecular research is rendered possible by analyzing identified gene regions of the target
organism. You can obtain the gene regions given the accession number In this exercise,
the genetic material you are focusing on has been decided and is described on the
Supplementary Materials tab. Save this file as .fasta then open it at the Mequite window
for further analysis. Aligned sequences represented related data and reveals the
informative characters of the taxa in study. To align the sequences, click matrix and
proceed to MUSCLE. The given sequences will be aligned. The last part to construct the
molecular tree is to follow the first instructions once more.

Figure 5: RASP Software

The analysis used S-DIVA as its methodological solution. Numerous sets of data were
designed which also included a split comma (.csv) file and a tree (.trees) data set. The
Operating Taxonomic Units (OTUs) were established on the basis of a scholarly review
of re-analysis in which the position of the sample was documented in the.csv file using
Microsoft Excel.

Results
 Figure 6: Consensus Tree showing the relationship of each Species

Performing the Mesquite software generated a consensus tree. This tree depicts the
relationship between each species. From its ancestral traits to derived traits and how it
evolved through out time. It showed that Aiolochroia crassa and Aplysinella rhax were
both ancestors as they possessed unique traits. The growth form and surface texture of
Aplysinella rhax were concluse and massive which makes it differ from the other sponge
species whereas the Aiolochroia crassa has a ridged growth form and a mound surface
texture. This two taxa are both monophyletic group as they include the ancestors and all
of its descendants. The taxon Aplysina aerophoba is a paraphyletic group because it
does not contain all the descendants. As seen in the tree, it is separated from the two first
taxa. Only monophyletic group are recognized in cladistic classification. The taxa
Pseidoceratina arabica, Verongula gigantea, Aplysina fulva, Ianthella basta,
Smenospongia aurea are polypyletic group as there were several clades converged to
each other but not their common ancestor. The fiber specialization of taxon
Smenospongia aurea is both primary and secondary which makes it not included in the
ancestral clade. The other groups possessed specialized characters that’s why they were
not also included in the ancestral clade such as surface texture and oscular arrangement.
Lastly the taxa Aplysina fistularis, Verongula reiswigi, Chondrilla nucula, and Aplysina
cauliformis are polypyletic group.
 Figure 7: Consensus tree based on the molecular data

The tree indicated that A. fistularis and A. fulva are closely related to each other based
on the molecular data and DNA sequences obtained from GENbank. Study of the two
tree analyzes shows that the analysis of both evaluations resulted in specific tests. Study
of the phylogenetic tree utilizing each morphology and molecular evidence resulted in
more detailed and reliable details.

Figure 8: Analysis of Verongid sponges using S-Diva

Analyses of occurrences have been integrated into the creation of a biogeographic
background tree. Result in extinction event indicated that node 24, a possible ancestor,
C. Nucula has undergone extinction because it can be interpreted that no other species
of Verongida have been observed.

Discussions

The species Aplysina (Order Verongida) are typical residents of freshwater, tropical and
subtropical marine waters. The group is distinguished by possessing a single-category
pituitary fiber shell, containing a standard polygonal mesh reticulum with no unique
ectosomal arrangement. Aplysina skeletons are mostly made not of spongin, but of alpha-
chitin (Borchiellini, et. al, 2004). The taxonomy of Aplysina was initially based on exterior
anatomy and skeleton, which was later augmented by sexual, histological which
biochemical characteristics. The lack of a mineral skeleton has hindered species
identification and study of the group's phylogenetic relationship, especially in the face of
possible cryptic species and intense phenotypic plasticity, which remain largely
unrecognized in these sponges (Ehrlich, et. al, 2007). Aplysin species is often known for
the presence of brominated alkaloid compounds with the occurrence of cytotoxic activity
and microbial symbionts that generate antibiotic activity compounds.

The Verongida species (Under the taxonomic sequence Order) is a cohesive community
of marine sponges whose systematics have historically been focused on morphology and,
more recently, on biochemical and genetic evidence. While morphological characters
have not been helpful in resolving their phylogeny molecular details, they have assisted
the community monophyll in many gene trees and have been shown to be useful in
addressing relationships (Padial & Vences, 2010). The lack of a mineral structure in
Aplysina spp. The problem was the recognition of the species and the calculation of the
phylogenetic relationship within the population. The chemical review revealed that alpha-
chitin is found in all organisms tested, which is highly important and supports the theory
that all organisms of Aplysina share with other members of the Verongida group (Bell,
2008). The difficulties in the morphological taxonomy of Aplysina is mainly due to the
absence of diagnostic features and the high phenotypic plasticity of individuals, rendering
it difficult to define distinctions between organisms. It is also very important to integrate
certain characters and to check that they are compatible with morphology in species
discrimination.

Some sponge taxa display a morphological complexity which offers little clinical
manifestations for comprehensive research and phylogenetic review. While the value of
morphological systematics should not be overlooked. The relative weight of different
morphological traits used to classify taxa can be arbitrary and problematic, given the
availability of quantitative methods for weighting traits (Nichols 2005). Although its
findings generally favor the existing classification of Verongida, they also illustrate two
concerns relevant to the morphology-based category of sponges: the location of variable-
character taxa and the identification of polarity of character. Molecular data have been
used more recently to resolve the relationships among sponge taxa and can have several
advantages over morphological data.

Conclusion

The full analysis of the phylogeny of the Verongid sponges, it could still be reached the
conclusion that the use of one type of data would not produce reliable results and that
supplemental analyzes should therefore be accepted. In response, genomic information
gives a more in-depth analysis of species and may provide understanding into adaptive
or dispersive occurrences. The recreated phylogenetic trees culminated in a distinct
configuration for the use of phylogenetic relationships relative to molecular markers using
phenotypic evidence. Consequently, a species diversity analysis of the Verongid sponges
indicates that various changes affect during the evolutionary time of the sponges.

References
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Websites

Edgar, R.C. (2004). MUSCLE: a multiple sequence alignment method with reduced
time and space complexity. BMC Bioinformatics 5, 113. https://doi.org/10.1186/1471-
2105-5-113

Maddison, D.R. (2018). What does Mesquite Does: Introduction to Mesquite. Retrieved
from https://www.mesquiteproject.org/What%20Mesquite%20does.html

The Southern Ocean. (2015). Biogeography and its Definition. Retrieved from
https://www.sciencedirect.com/science/article/pii/B9781785480478500047

Appendices (optional)

Figure 9: DNA sequences

Figure 10: Character Matrix