MS 397

Gabriella Juliane L. Maala

1. Molecular approaches have vastly improved the assessment of biological

diversity. Discuss two aspects and provide relevant examples. (25 pts)

Before the advent of molecular approaches, biologist heavily relied on morphological

characteristics to identify organisms to the species level. However, this method
proved to be insufficient in doing so. Aside from instances of having identical-looking
organisms of separate species, other taxa do not have definite morphological
parameters for accurate identification. As such, the corresponding inferences cannot
reflect the true biological diversity in the environment or habitat of interest.

Molecular markers are genetic barcodes that could be specific to a certain taxa or
species. The use of markers is universal to all organisms, and this makes it useful for
correct species identification and precise assessment of biological diversity. As in the
case of sponges which are difficult to identify based on their simple and rather plastic
morphology, DeBaisse and Hellberg (2015) used markers COI, 28S, and single-copy
nuclear protein-coding genes. They found out that the revealed lineages of
Callyspongia were not parallel to the present species assignment, and that spicule
configuration also cannot accurately identify the sponges. Thus, changes with regards
to sponge taxonomy must be made in accordance to the evolutionary lineages.

Through metabarcoding of environmental DNA, which, if sampled at the right way at

the right time (and with the right choice of eDNA type to sample), could also
accurately assess biodiversity. Stat et al. (2017) used eDNA from seawater to explore
Lethrinus biodiversity and encourages the use of eDNA in biomonitoring.

Taking biological diversity assessment to the next level, metabarcoding of eDNA

could also pave way for the discovery of cryptic species present in an environment.

2. Discuss the conceptual link between a unified species concept and an

integrative taxonomic approach to species identification. (15 pts)

De Quieroz (2007) cleared the overdue confusion with regards to species concept and
delimitation. In summary, the primary criteria in identifying a species concept is that
it must be of a separately evolving lineage; other differences between these species
concepts are only provisional such that they only confirm the separation of lineages.
In relation to species identification using a taxonomic approach, the first and
foremost consideration must be seeing how the species is related to others in an
evolutionary perspective. Then, a check list of the secondary species criteria can come
in handy when evidences of evolutionary separation are needed.

3. Molecular approaches have greatly advanced the study of gene flow in natural
populations.
a) Discuss two examples of insights derived from molecular approaches, on
historical or contemporary patterns of gene flow in the marine
environment. (25 pts)

There is a myriad of factors that affect gene flow patterns, including the
emergence of barriers after significant geological events, pelagic larval duration
of the organism, and stability of seascape features. Studying these factors and
their effects on the observed distribution of certain taxa shed light on the past and
present their gene flow patterns.

Phylogeography . Gaither et al.’s (2011) study on Cephalopholis argus depicts the

essence of phylogeography. Upon doing a genetic survey on C. argus found in the
Pacific, the Indian Ocean, and the coral triangle in between, the authors found out
that two separate mitochondrial lineages were present in each of the said oceans.
This implies the significant effect of the Pleistocene sea level fluctuations
inhibiting gene flow between the two subpopulations. Furthermore, the presence
of hybrids in the coral triangle connecting the two oceans means that sea levels
rose after the last glacial maximum, thereby restoring gene flow and population
connectivity.

From this study, it could be said that the phylogeography of C. argus in these
oceanic regions were indeed affected by the emergence of the barrier caused by
decreased sea levels. However, a caveat that the effectivity of the barrier (at least
at the time of study), only holds true for C. argus. In confirming if certain barriers
are significant enough, they must contribute to similar patterns of genetic
structure of other marine organisms in the same geographic area. This is where
seascape genetics comes in.

Seascape genetics deals with the influence of environmental patterns on the

observed genetic structure in marine species. Present seascape genetic factors
could be considered significant if they play a common denominator in the genetic
patterns found, an example of which is the Mona Passage region.

The Mona Passage region is a strait between islands of Hispaniola and Puerto Rico.
As summarized by Hellberg (2005) in his review, similar genetic breaks found in
two congeneric gobies assessed in 2003 were also reported in a coral species two
years after. This suggests the Mona Passage strait as a significant seascape genetic
factor that prevents the gene flow between organisms of Hispaniola and Puerto
Rico.

b) Discuss the practical significance of studying dispersal and connectivity in

the marine environment? (15 pts)
Knowing the dispersal pattern and connectivity of subpopulations in a marine
environment is a must when establishing marine protected areas and managing
fisheries. In identifying the “sinks” and “sources” of larvae and the patterns by
which they are transported among different potentially connected regions, people
 would be able to strategize MPA networks effectively, which would be
advantageous to both marine conservation and fisheries.

4. How has RNA sequencing revolutionized biological study? Discuss two aspects.
Provide examples to support your discussion. (25 pts)

Unlike older methods of gene expression analysis, RNA sequencing has allowed us to
study gene expression and determine differentially expressed genes (DEGs)
especially for organisms without established genomes.

For instance, in studying new oyster hybrids, RNA sequencing led to the creation of
the transciptome profile and corresponding differential gene expression analysis. Yan
et al. (2017) was then able to identify upregulated and downregulated DEGs in
hybrids, the functional group of these DEGs, and the comparison between gene
expression of hybrids with their purebred counterparts. RNA sequencing also led to
the assembled hybrid genome, which could then be used for marker development of
hybrids.

In relation to studying differential gene expression, studying genetic mechanisms that

allow resilient organisms to withstand an ever-changing environment could also be
done.

In Barshis et al.’s (2013) study, they were able to give a molecular basis for comparing
the performances of corals exposed to two different environments through a
transcriptome-wide gene expression using RNA sequencing. Corals from the highly-
variable (HV) and moderately-variable (MV) pools were collected and subjected to
bleaching stress in the lab. HV corals were observed to exhibit high expression of
thermally-related genes even in ambient conditions, and consequently, the
expression need not increase significantly under thermal stress. Termed as
“frontloaded” transcripts, this could be an indication of greater tolerance and
resilience in HV corals which could be vital to coral survival in the face of aggravating
environmental stressors.
Citations:

Barshis, D. J., Ladner, J. T., Oliver, T. A., Seneca, F. O., Traylor-Knowles, N., & Palumbi, S. R.
(2013). Genomic basis for coral resilience to climate change. Proceedings of the National
Academy of Sciences, 110(4), 1387–1392. doi:10.1073/pnas.1210224110

DeBiasse, M. B., & Hellberg, M. E. (2015). Discordance between morphological and molecular
species boundaries among Caribbean species of the reef spongeCallyspongia. Ecology and
Evolution, 5(3), 663–675. doi:10.1002/ece3.1381

De Queiroz, K. (2007). Species Concepts and Species Delimitation. Systematic Biology, 56(6),
879–886. doi:10.1080/10635150701701083

Gaither, M. R., Bowen, B. W., Bordenave, T.-R., Rocha, L. A., Newman, S. J., Gomez, J. A., …
Craig, M. T. (2011). Phylogeography of the reef fish Cephalopholis argus(Epinephelidae)
indicates Pleistocene isolation across the indo-pacific barrier with contemporary overlap in
the coral triangle. BMC Evolutionary Biology, 11(1). doi:10.1186/1471-2148-11-189

Hellberg, M. E. (2007). Footprints on water: the genetic wake of dispersal among reefs. Coral
Reefs, 26(3), 463–473. doi:10.1007/s00338-007-0205-2

Stat, M., Huggett, M. J., Bernasconi, R., DiBattista, J. D., Berry, T. E., Newman, S. J., … Bunce, M.
(2017). Ecosystem biomonitoring with eDNA: metabarcoding across the tree of life in a
tropical marine environment. Scientific Reports, 7(1). doi:10.1038/s41598-017-12501-5

Yan, L., Su, J., Wang, Z., Yan, X., Yu, R., Ma, P., … Du, J. (2017). Transcriptomic analysis of
Crassostrea sikamea × Crassostrea angulata hybrids in response to low salinity stress. PLOS
ONE, 12(2), e0171483. doi:10.1371/journal.pone.0171483