De Novo Assembly and Annotation of The Acropora gemmifera Transcriptome

Abstract: Stony corals from the genus Acropora are widely distributed, important reef-builders and have become increasingly utilized for investigating links between genetics and spawning behaviour. We assembled and annotated a composite transcriptome from Acropora gemmifera using Illumina HiSeq2500 analysis of two libraries from different lunar and solar phases to identify genes that have potential functional roles in reproductive-related traits. A total of 31.6 million combined raw reads were assembled using Trinity and built into 104,000 contigs. Functional gene annotation was performed using dammit, Gene Ontology (GO), KOG (WebMGA) and KEGG pathway analyses (Kaas). This resource will be valuable for researchers studying gene expression patterns in coral reproductive cycles and evolution of the genus Acropora.

Author: Oldach, M. J., P.D. Vize
Year: 2018
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Marine Genomics. doi:10.1016/j.margen.2017.12.007

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Connecting Palau’s Marine Protected Areas: A Population Genetics Approach to Conservation

(INTERNAL RIGHTS ONLY) Aerial view of Kmekumer, Rock Islands, Republic of Palau, Palau, Asia Pacific. Photo credit: © Jez O'Hare

Aerial view of Kmekumer, Rock Islands, in Palau. Photo © Jez O’Hare

Listen to our interview with author Dr. Annick Cros, researcher at the Hawaiian Institute of Marine Biology, as she shares highlights from her recent publication on connecting Palua’s marine protected areas and discusses how findings from this study can guide conservation strategies for coral reef managers. 

Click the play button below to hear the interview.

Interview Transcript

Reef Resilience (RR): Hello everyone, Reef Resilience is interviewing Dr. Annick Cros, researcher at the Hawaiian Institute of Marine Biology and today she will share highlights from her recent publication on connecting Palau’s marine protected areas.

Annick Cros (AC): Hi everybody, thanks for having me today.

RR: Great, thanks for joining us. So how does this paper challenge how we are currently designing MPA networks?

AC: This paper challenges old assumptions about larval dispersal and connectivity. Connectivity is the exchange of individuals between populations. It is one factor that shapes the size and composition of a population. It plays a key role in genetics because connectivity acts against speciation and it may bring key genetic diversity that allows for adaptation. In the marine world, adults don’t move much or not at all and most of the connectivity happens with the dispersal during the pelagic larval stage of organisms.

RR: What did you assume about this topic before your paper and what were some of the take home messages from your research?

AC: Well larvae are so small, they are difficult to track. For example, we assumed that the longer a larvae could survive in the water column, the further it would travel, dispersed by currents due to its small size. Therefore, we assumed that most dispersal took place at large scales of hundreds of kilometers. We also assumed that at a small scale, genetically, a population would be very homogeneous because the exchange would happen at larger scales so that we would see genetic diversity at large scales. However, more recently an increasing amount of research has shown that dispersal is happening at a much smaller scale than expected and that most larvae recruit close to home.

AC: In our paper, we use population genetics to study the dispersal of Acropora hyacinthus around the barrier reef of Palau, Micronesia to test some of these assumptions. And the reason why we selected Palau was because in 1998 it suffered from heavy mortality from bleaching, in particular the coral Acropora hyacinthus. Since then it has recovered and the colonies we observe on Palau today are the result of recent patterns of dispersal making it easier to understand what is happening. What we found is that the patches of Acropora hyacinthus separated by a few kilometers around Palau’s reef do not mix very much, there is little connectivity. Instead we find surprisingly high numbers of colonies related to each other over a few hundred meters, indicating that dispersal happens at a very small scale. 

RR: So how can research on larval dispersal guide effective conservation strategies for coral reef managers?

AC: Well what we found is that instead of having a homogenous reef we had a mosaic of genetically different patches of corals which reflects the diversity that could play a role in the resilience and resistance of corals. So to manage it is a challenge because it requires protection of the entire reef, leading to the need for a more comprehensive approach than an MPA to manage Palau’s reef.

Authors: Cros, A., R.J. Toonen, M.J. Donahue, and S.A. Karl
Year: 2017
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Coral Reefs: 1-14. doi: 10.1007/s00338-017-1565-x

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Population Genetic Structure Between Yap and Palau for the Coral Acropora Hyacinthus

(ALL INTERNAL, LIMITED EXTERNAL USAGE RIGHTS) Vibrant coral reef in Palau. While looking healthy, the white corals are the early signs of a struggling habitat as they begin to bleach from warm waters often attributed to climate change. Unfortunately there is not a reef in Palau that has not been affected in some way by coral bleaching. The coral reefs of Palau are part of a massive interconnected system that ties together Micronesia and the Western Pacific. To protect these reefs the Conservancy joined with other experts to develop Transforming Coral Reef Conservation. The Conservancy has worked with Palau’s community leaders and government agencies since 1992. In that time we have helped bridge the gap between traditional and modern approaches to conservation. The Conservancy helped establish the Palau Conservation Society, a local environmental organization dedicated to protecting Palau’s natural heritage. PHOTO CREDIT: © Ian Shive

Vibrant coral reef in Palau. Photo © Ian Shive

Listen to our interview with Dr. Annick Cros, coral reef scientist at the Hawaiian Institute of Marine Biology to hear about highlights from her recent publication on population genetic structure between Yap and Palau and how genetics can be used in coral reef management.

Click the play button below to listen to the interview.


Interview Transcript 

Reef Resilience (RR): Hello everyone, Reef Resilience is interviewing Dr. Annick Cros, coral reef scientist at the Hawaiian Institute of Marine Biology where she will share highlights from her recent publication on population genetic structure between Yap and Palau and how genetics can be used to tackle conservation issues.

Annick Cros (AC): Hi everyone! Thanks for having me here.

RR: Can you start with introducing what population genetics is?

AC: In very simple terms, it is the study of genetic variations in populations to understand their structure, boundaries and connectivity with other populations. When you study population genetics, you typically ask questions such as: “How much gene flow is there between these two populations?” As a manager, you surprisingly ask very similar questions! “How much spillover will I get from this MPA and where will larvae recruit?” Or “are these two groups of turtles related and should I manage them as one?”

RR: How can population genetics be used as a tool in management?

AC: So you are right in thinking that using population genetics to solve a conservation issue can be time consuming, expensive and requires resources and skills you may not have. However, in the case of connectivity of marine organisms, and the design of MPA networks, population genetics seems to be the best tool that we have at the moment. This is due to the fact most marine organisms reproduce via minute pelagic larvae that are very difficult to track. Since we often rely on oceanographic models to predict where larvae will go and settle we do not always get the right answer. Population genetics will not track larvae directly but will give information on where larvae have settled over time. The paper that we wrote actually is an example of how to use population genetics to answer one of these questions. 

We used Palau as our case study because in 1998 Palau suffered heavy bleaching mortality. Yet by 2004-2005, studies showed that the reef had almost recovered. Managers and scientists wanted to know how it had recovered so quickly and where the coral larvae came from. One hypothesis that we had was supported by an oceanographic model was that Palau recovered from a pulse recruitment event from Yap, a neighboring island approximately 500 km away. We wanted to test if this was true. Using the coral Acropora hyacinthus, we tested for a founder effect between Yap and Palau. The founder effect states that if larvae originating from Yap had traveled to Palau and recolonized the reef, the same genetic signatures should be found on Yap and Palau but with less genetic diversity in Palau. And that’s because only a small fraction of Yap’s genetic diversity would have traveled to Palau. We found that this was not the case and we rejected the hypothesis that Yap was the sole source of larvae for Palau’s recovery. Other signs indicated that it was more than likely that Palau recovered from its own surviving colonies.

RR: How do the results from your paper translate into management actions that can be implemented on the ground?

AC: Knowing that Palau had not recovered from Yap but from it’s own surviving colonies, this gave us the tools to tell managers that the best strategy to increase Palau’s reef resilience was to not to invest in Yap’s coral reefs but to instead invest in protecting their reefs at home. We are currently looking at further information to see how to protect these coral reefs at home based on population genetics. 

Author: Cros, A., R.J. Toonen, S.W. Davies, and S.A. Karl
Year: 2016
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PeerJ4e2330. doi:10.7717/peerj.2330

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