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Roha Khan
Jan Just
BI 212
May 30, 2021
Foraminifera: Relationships Among Genus and Species
Introduction
Phylum Foraminifera is classified under Rhizaria, a clade within the supergroup SAR. Rhizaria,
an incredibly diverse clade, is interestingly classified: largely using molecular genetics. (Burki et
al. 2019) The placing of Foraminifera within this clade is actually weakly supported because of
the controversy over which of its sister clades it is closer to due to evolving SSU rDNA
sequences. (Burki et al. 2010) Species withing the clade are classified based on the scheme
Loeblich and Tappan which is based on the microstructure of the test wall. Another defining
feature is their granular pseudopodia (streaming ectoplasm). It can be argued that this is more
overarching feature used to classify as there are species that lack a test, one of which we will also
be looking at, from the genus Reticulomyxa. We will also be looking at species from the genus
Globigerinoides, Ammonia, and Elphidium, all of which come under the Order, Rotaliida which
is classified by morphology, and confirmed by some limited molecular phylogenetics. The
purpose of this paper is to, through careful examination of the relationships between species and
genus and molecular phylogenetics, support that classification through molecular and
morphological data come hand in hand.
Identifying and understanding the relationships that these organisms have is important in
furthering our understanding of what mean in our lives and how they contribute to life on Earth.
They are incredibly important in the fields of Biostratigraphy -providing evidence of the relative
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ages of marine rocks, Paleoecology & Paleobiology -providing evidence of past environments,
tracking global ocean temperatures, etc. and oil exploration. A contributing factor to their
importance (other than their make-up) is that they have been around since the Cambrian.
(Wetmore)
We will be using a compare and contrast method to see if the results our supported, looking at
know taxonomic data.
Materials and Methods
The experiment began with curating sequences from GenBank with initial selection of the genus
Globigerinoides. After finding a partial sequence for a small subunit ribosomal RNA gene for a
species, I used this as the keywords for finding more species, along with the genus name. After
curating for three species within the Globigerinoides genus I looked for species from two other
closely related taxa. I selected an outlier to curate as well, based on its interesting evolutionary
history. After collecting all sequences, I aligned them using T-Coffee, a multiple sequence
alignment package, specifically M-Coffee (Wallace et al. 2006). When the alignment was
complete, I copied it (in phylip format) into a phylogeny creator (EMBL-EBI, 2019) to get a
Neighbor-Joining (based on minimum evolution criterion) and a UPGMA (based on average
linkage method) tree.
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Results
To help keep track of each species and for readability when comparing relationships, a table is
provided:
Table 1. Foraminifera Species and their Accession Numbers
Organism Name
Accession Number
Globigerinoides elongatus
MN38392.1
Globigerinoides ruber albus
MN38390.1
Globigerinoides tenellus
MN282733.1
Reticulomyxa sp.
MH235216.1
Elphidium sp.
GQ853562.1
Ammonia sp.
MT586771.1
Below are the resulting phylogenetic trees from the small ribosomal Subunit. Both are based off
the same species and genes and only differ in clustering method which will be explained later.
Figure 1. Neighbor-Joining Molecular Phylogeny on the Small Ribosomal Subunit of Genus and
Species from the Foraminifera Phylum
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Figure 2. UPGMA Molecular Phylogeny on the Small Ribosomal Subunit of Genus and Species
from the Foraminifera Phylum
To be able to discuss our figures, we must understand that Figure 1. is produced using the
neighbor-joining method which produces an unrooted tree and is based on the minimum
evolution criterion. On the other hand, Figure 2. is produced using UPGMA, Unweighted Pair
Group Method with Arithmetic Mean. It assumes a constant rate of evolution which is why it
looks symmetrical.
Looking at what’s going on with the trees: both seem to be resolved really beautifully. The
Globigerinoides species all look very consistent on both trees.
Discussion
To begin with, the expectation for this experiment is that that all species from the
Globigerinoides genus are the closest on either tree, and that the species Ammonia sp. and
Elphidium sp. are closer to the Globigerinoides species than the Reticulomyxa sp. which should
act as our outgroup.
Taking a closer look at Figure 1. we can see that species from Globigerinoides behave
consistently, grouped together with Globigerinoides elongatus and Globigerinoides tenellus
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being closer together. Then, interestingly, we see Reticulomyxa sp. and Elphidium sp. closer
together and Ammonia sp. acting like an outgroup.
An interesting to point to make here is that research seems to tell us “naked” (without tests)
species such as Reticulomyxa sp. is the result of convergent evolution and do not precede the
evolution of testate lineages. (Pawlowski et al. 2003) However, scientists still hypothesize (and
there may be some research to support this) that some ancestral foraminifera could have been
naked. (Nature, 1999)
Figure 2. has similar distribution.
This result does not support my hypothesis, nor does it necessarily imply that molecular and
morphological classification are not related. Rather, it emphasizes the complexity of their
relationships and how much we don’t know.
Moving forward, in repeating the experiment or setting up any similar one, I would strongly
recommend including more species of each genus and more genus to understand the
relationships better and have something more substantial to look at. I don’t think there is a need
when working with smaller amounts of data, but after going through several other papers, for the
sake of clarity I’d recommend trying to focus on each (genus vs. species) in different trees.
I used small ribosomal subunit but there are other options. One trouble I ran into was a limited
amount of data for what I was looking for (for example plugging in Elphidium small ribosomal
subunit, I would not get very many species).
Some thing I noticed during the research for this experiment:
1. There is a high interest in the foraminifera phylum as it is incredibly abundant, diverse,
and useful
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2. We are moving from morphology-based research to molecular, supporting or refuting
long standing hypotheses about the phylogeny of Foraminifera.
3. We’re overlooking a clade within foraminifera, loosely termed “Monothalamids” (of
which Reticulomyxa sp. is a part of)
The first two points are the obvious ones. The third is what I would be interested in doing
something about. The most diverse out of all the Foraminiferans are within this paraphyletic
clade. That sentence alone makes me excited to do some research about it and see some
research done. I believe that would be a huge leap in understanding all Foraminiferans and
their phylogeny better. I also think that, because of their huge diversity, the nest way to go
about this would through phylogenetics.
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