Studies at Hannibal Bank, Panama: A Study of Evolutionary History of Mollusks and Developing a Program to Review Dive Track Data

This study focuses on the phylum Mollusca from Hannibal Bank in Panama. Through DNA sequencing and phylogenetic analyses, the biodiversity and evolutionary history of mollusks were evaluated. The results of this study were found to support molluscan relationships reported in previous studies. Seventeen distinct species were collected. Bayesian and Maximum Likelihood analyses revealed that the class Polyplacophora was basal to the sister clades Bivalvia and Gastropoda. Gastropoda was also found to have two distinct clades in both analyses: Vetigastropoda and Caenogastropoda. In addition to the phylogenetic analysis, a user-friendly program was written in R to help review dive track data and to better visualize where samples were found. This streamlines removing errors from dive track data received from research cruises and allows the points to be mapped and visualized. Introduction The phylum Mollusca is a very diverse group. Of the benthic marine invertebrates, it is one of the largest phyla with an estimated 100,000 species. Mollusks are defined by certain characteristics. They are bilaterally symmetrical, triploblastic, protostomes, and have a complete gut with an anus and circulatory, digestive, and nervous system. Mollusks also have cephalization and a radula (except for bivalves), a shell, muscular foot, mantle tissue, and mantle cavity. There are seven different classes in the Mollusca phylum: Polyplacophora, Gastropoda, Bivalvia, Aplacophora, Monoplacophora, Scaphopoda, and Cephalopoda (Levinton, 2014). This study focuses on three of the classes: Polyplacophora, Gastropoda, and Bivalvia. Polyplacophora are generally known as chitons and have a radula, flattened foot, and eight dorsal plates. They are herbivorous grazers. Gastropoda are generally snails and have a radula, flattened foot, shell, and an operculum. They are distinguished by torsion, which is when the body of the gastropod twists during development, and the anus and mouth both connect to the shell’s one opening. Bivalvia are generally clams and have a mantle that secretes a shell and gills that help the bivalve breathe and collect phytoplankton. They are typically distinguished by two symmetrical valves that open on a hinge region (Levinton, 2014). Mollusca samples were collected at Hannibal Bank. Hannibal Bank is located off the Pacific coast of Panama and is an area of high productivity and biodiversity. It is a top sports fishing area and supports local fishing communities but is a marine protected area where commercial fishing is prohibited (Cunningham, M Guzman, & Bates, 2013). Hannibal Bank is part of Panama’s Coiba National Park and is a UNESCO World Heritage site (UNESCO.org, 2016). Hannibal Bank itself is technically considered to be a sea hill by some due to its size as it is less than 500m tall. However, Hannibal Bank has certain features that share characteristics with seamounts and is often referred to as a seamount (Yesson, Clark, Taylor, & Rogers, 2011). Seamounts are an important habitat for benthic organisms because they provide substrate for organisms to live on and may increase the water column’s productivity by affecting currents (Cho & Shank, 2010). In this study, two genes were used to study the evolutionary history of mollusks at Hannibal Bank: COI and 18S. COI is a mitochondrial gene that is often used in barcoding for identifying species. Mitochondrial genes are maternally inherited, have many copies, no introns, high substitution rates, and no recombination (Raupach et al., 2015). COI is therefore good at resolving shallow nodes of a phylogenetic tree. The non-protein coding nuclear rRNA 18S gene is slow-evolving. This conservative gene is good at resolving deep nodes of a phylogenetic tree and providing discrimination above the taxa of family (Wilke et al., 2001). Two different phylogenetic analyses were also used in this study: Bayesian and Maximum Likelihood. Bayesian analyses are based on the idea of posterior probabilities. These are probabilities that are based on a model after learning something from the data. It searches for the best set of trees representing relationships between the samples. After many generations, the analysis narrows down to a set of a few trees where the likelihoods are very similar and accepting or rejecting a change becomes a random choice; this is called a stable likelihood value (Hall, 2001). Maximum Likelihood analyses infer a tree by finding a tree that maximizes the probability of seeing the data. They look for a tree with the largest log likelihood. It’s often impossible to look at all possible trees, so a search method is used to find the most likely tree (Hall, 2001). Due to the high diversity of the molluscan phylum, there is no consensus for the evolutionary relationships of mollusks. Rather, there are three competing hypotheses of molluscan relationships that are generally discussed. The first is Aculifera that has Polyplacophora sister to Aplacophora and basal to all remaining Mollusca. The second is Testaria that has Aplacophora basal to Polyplacophora and all remaining Mollusca. The third is Serialia that has a clade of Polyplacophora and Monoplacophora separate from all remaining Mollusca (Sigwart & Lindberg, 2015). The results of this study will be compared with the results of a review by Sigwart & Lindberg (2015) that evaluated the molecular and morphological phylogenies of Mollusca. They identified eight different supertrees that served as hypotheses for different current molluscan evolutionary relationships. We will use our samples to test these hypotheses. The purpose of this study was to review the diversity and the evolutionary history of mollusks found at Hannibal Bank, Panama. This data will provide information for the biodiversity and number of species found at Hannibal Bank. This information can be useful to legislators trying to preserve and protect the bank. This data will also contribute to the general knowledge of the phylum Mollusca and will hopefully provide some support to clarify the phylum’s relationships. Along with reviewing the evolutionary history of mollusks, the purpose of this study was to develop a program to review dive track data. This program will help researchers to visualize and remove outliers and errors in the dive track data. Dive track data is collected on research cruises from the ship and submersibles and is typically a log of the date, time, latitude, and longitude of the vehicle, as well as additional metadata (depth, altitude, heading, etc.). The program was created using the R language (R. C. Team, 2018) through RStudio (R. Team, 2015) and uploaded to R Shiny so that the program could be accessed from any computer at any time. This will streamline the process of “cleaning up” dive track data. Materials and Methods