Interview with the authors: Anthropization level of Lascaux Cave microbiome shown by regional‐scale comparisons of pristine and anthropized caves

Estimated to be around 17,000 years old, the Paleolithic paintings in the Lascaux cave of southwestern France give us a rare insight into the history and culture of communities that existed long before modern society. The conservation of caves such as Lascaux is a high priority for historians, scientists, and the general public. The anthropization, or human use, of caves may have dramatic effects on cave-dwelling macro- and micro-organisms, though few studies have been conducted on this topic. By comparing ‘pristine’ caves with anthropized caves frequently visited by humans, Dr. Lise Alonso and colleagues demonstrate that the anthropization of caves is associated with reduced microbial diversity for bacteria and archaea living on cave walls, though microeukaryotes and arthropods were not as strongly affected. In this post, we go behind-the-scenes with Dr. Yvan Moënne-Loccoz on their recent publication in Molecular Ecology and talk about the importance and challenges of working in cave ecosystems.

Link to the study: https://onlinelibrary.wiley.com/doi/10.1111/mec.15144

Great Hall of the Bulls in Lascaux Cave. The cables connect to monitoring probes. Source: DRAC Nouvelle Aquitaine

What led to your interest in this topic / what was the motivation for this study? 
Cave conservation is an important issue, especially when dealing with caves displaying Paleolithic artwork, as engravings and particularly paintings can be very fragile. There are many of these caves in Dordogne (South-West of France), some of them listed on the UNESCO World Heritage List (https://whc.unesco.org/en/list/85). The most famous Paleolithic cave in Dordogne is the Lascaux Cave, which was closed to the public in the 1960s for conservation reasons. To guide conservation efforts, it is important to understand the ecology and functioning of these caves, especially at the levels of microorganisms and arthropods, which form the main communities present. Against this background, the project was carried out to understand better the biotic communities residing in Lascaux Cave.

Entrance of Lascaux Cave. Source: DRAC Nouvelle Aquitaine

What difficulties did you run into along the way? 
When dealing with microorganisms and arthropods populating soils, sediments or water, in a majority of cases it is rather straightforward to collect samples and there is no restriction on sample size. In caves, taking samples from walls for microbial analyses, using a scalpel, may leave long-lasting marks. This is an issue in all caves, and particularly so in Paleolithic caves. In the Lascaux Cave, the sample list was prepared after discussions with the cave staff and approved by the cave conservator, and the samples were collected (away from ornate surfaces) by qualified restorers, under the guidance of microbial ecologists, so as to avoid any marks on the wall. It also means that only minute samples were available. Restrictions also apply for the type and location of arthropods traps, as sediments at the bottom of caves might contain historical artefacts.

Sampling of rock wall surface in a pristine cave, using a sterile scalpel. Source: B. Bigaï

What is the biggest or most surprising finding from this study? 
Caves are oligotrophic environments, so it is always a surprise to find diversified, rather large microbial communities on cave walls. In this study, the Lascaux Cave was compared with eight other caves from the same region, and these caves were quite different from one another in terms of size, architecture, distance from the soil surface, presence/absence of stream underground, human frequentation patterns, etc. Yet, there were clear distinctions in terms of microbial and arthropod communities when comparing anthropized caves versus non-anthropized (almost pristine) caves, which suggests that anthropization was more influential than these cave-specific features. Finally, we were rather surprised to find that prokaryotes (bacteria and archaea) were comparatively more impacted than eukaryotic residents (fungi, other micro-eukaryotes, arthropods) by cave anthropization.

Pristine cave used for sampling. Source: Y. Moënne-Loccoz

Moving forward, what are the next steps for this research?
This work was carried out with the Lascaux Cave and eight other caves from Dordogne, which corresponds to a relatively small area. There were at the most 35 km between two caves in this study. Therefore, it remains to be seen whether the results of the current investigation are also relevant elsewhere. At a larger geographic scale, several differences in cave properties can be expected, for instance in geological features (e.g. limestone type) and climatic conditions, which have the potential to influence cave biotic communities. In addition, we evidenced parallel variations in the diversity of microbial and arthropod communities, and it will be important to explore and understand better the ecological interactions between both types of cave inhabitants.

What would your message be for students about to start their first research projects in this topic?
First of all, the underground world and the interface between ecology and artwork conservation issues are fascinating, so welcome to the field! More importantly, each cave is different and represents a complex situation of its own, so one can be very busy focusing on a single cave only. This is reflected by the literature on cave microbial ecology, where often a single cave is considered at a time. However, we found that the comparison of different caves, following the path of various groups (e.g. Campbell et al. 2011 J Cave Karst Stud 73:75 ; Hathaway et al. 2014 Geomicrobiol J 31:205 ; De Mandal et al. 2017 BMC Microbiol 17:90 ; Pfendler et al. 2018 Sci Tot Environ 615:1207), brought very interesting insights, so comparative assessments are worth the effort.

What have you learned about science over the course of this project? 
The majority of participants to this project usually work on soil or aquatic ecosystems, and we found (once again) that concepts and methodology are applicable across different types of ecosystems. More specifically, we realized that underground systems represent interesting models to investigate ecological perturbations, because they are rather confined environments, where community fluctuations in response to mild environmental variations can be documented.

Describe the significance of this research for the general scientific community in one sentence.
This research shows that microbiome diversity can be used as a bioindicator of the level of cave anthropization.

Citation
Alonso L, Pommier T, Kaufmann B, Dubost A, Chapulliot D, Doré J, Douady CJ, Moënne‐Loccoz Y. Anthropization level of Lascaux Cave microbiome shown by regional‐scale comparisons of pristine and anthropized caves. Molecular Ecology, 28(14), 3383-3394. https://onlinelibrary.wiley.com/doi/10.1111/mec.15144

Summary from the authors: Selection at behavioural, developmental and metabolic genes is associated with the northward expansion of a successful tropical colonizer

Link to paper: https://onlinelibrary.wiley.com/doi/10.1111/mec.15162

Picture: Green Anole Lizard (Anolis carolinensis) on railing in Hilo, Hawaii. Author: Paul Hirst. CC-BY-SA-2.5

The green anole (Anolis carolinensis), also called the American chameleon due to its ability to change color, is a common species in South-East USA. It has been studied for decades to understand how reptiles adapt to their environment.  Unlike other species of its genus, its range encompasses territories outside tropical climate, reaching the winter-exposed flanks of the Appalachians. The green anole colonized these colder regions from Florida in the last 300,000 years. We used DNA variation covering the whole genome and contrasted populations having recently colonized colder territories with the ones from tropical Florida. We compared multiple approaches to detect which segments in DNA sequences harbored variation compatible with selection. Since these signatures can also be produced by past demography, we took the latter into account to limit the detection of false positives. We then identified the most likely function of genes overlapping with candidate regions for selection, and observed that many of those were involved in exploratory behavior, immunity and response to cold. This suggests that the success of green anoles may have been due to changes in both physiology and behavioral shifts, a hypothesis that could be further tested experimentally.

Yann Bourgeois and Stephane Boissinot

Bourgeois, Y., & Boissinot, S. (2019). Selection at behavioral, developmental and metabolic genes is associated with the northward expansion of a successful tropical colonizer. Molecular Ecology. 2019. 28-15. 3523-3543

Interview with the authors: High indirect fitness benefits for helpers across the nesting cycle in the tropical paper wasp Polistes canadensis

Understanding how complex social systems evolve is a long-standing and challenging goal of evolutionary biology. Many animal taxa are eusocial, where individuals forego reproduction in order to help raise young produced by another member their group. This behavior only makes sense if there are potential benefits – either direct or indirect – to the helpers. The genus of paper wasps Polistes is commonly used as a model system for studying sociality, however most of the research on this group has been conducted in temperate ecosystems, whereas relatively little is known about their behavior in tropical ecosystems where the genus likely originated. Does our understanding of how direct and indirect benefits contribute to the evolution of complex social systems depend on the environment where we conduct the research? Below, we go behind the scenes with Emily Bell and Robin Southon on their latest paper in Molecular Ecology to find out.

Link to the study: https://onlinelibrary.wiley.com/doi/10.1111/mec.15137

Polistes canadensis nest. Photo by RJ Southon.

What led to your interest in this topic / what was the motivation for this study? 
Wasps provide a fascinating insight into the evolution of sociality; among them you can find various levels of social complexity ranging from solitary to highly eusocial. Many studies have focused on the emerging model organism Polistes dominula. An interesting aspect of this wasp’s behaviour is that female ‘foundresses’ often form new nests in the spring with unrelated individuals – they help even though reproductive skew is monopolised by a single female. However, this is unlikely to be true in tropical species. Tropical Polistes do not experience an overwinter break in the colony cycle, and highly related foundresses may form new nests together directly from their previous natal nest. We wanted to highlight that although Polistes species share many traits, such as high reproductive skew, fitness payoffs for nonreproductive foundresses in temperate and tropical species are unlikely to be equivalent. This is an important consideration in making conclusions about the evolution of group living within the genus – Robin Southon

https://onlinelibrary.wiley.com/doi/10.1111/mec.15137

What difficulties did you run into along the way? 
With most field work it comes down to logistical issues. Along the Panama Canal are many ‘wasp havens’ – abandoned buildings containing a high density of nests. Which is great, unless you happen to live on the other side of the canal to your field site. There is one bridge that crosses the canal near our site, which is only accessible when boats are not passing through the nearby lock. This takes many hours for giant container ships! We’d spot ships approaching from afar and try to beat them to the lock in time to cross. Although if we missed our chance, at least all our datasheets were processed and backed up in the downtime – Robin Southon

Beating a container ship to the lock. Photo by EF Bell.

What is the biggest or most surprising finding from this study? 
In large established nests a reproductive monopoly is held by one queen. Our SNP and microsatellite pedigree analyses of post-emergence nests revealed in nearly all nests brood belonged to a single queen. Control over reproduction in Polistes is maintained primarily through physical aggression, and in the case of small temperate nests there is relatively few nestmates to dominate. However, nests of the tropical Polistes canadensis can reach 200+ in membership. It seems unlikely the queen could physically aggress that many wasps in a network! It would be interesting to see what other mechanisms may be at play, such as vibrational or odour signalling – Robin Southon

Moving forward, what are the next steps for this research?
We have established that there are differences in founding group structure between Polistes from different environments, but it’s rather simplistic to look at such differences as tropical vs temperate. There will be exceptions in both environments, for example montane ecosystems. The next step should look at what exactly is it about these environments that influence founding behaviour. Studying wasps in subtropical climates is likely to be key, especially in looking at species that have distributions which transition through tropical, subtropical, and temperate regions – Robin Southon

What would your message be for students about to start their first research projects in this topic?
Do your background research before you start a new project – literature reviews are an invaluable learning experience. They act as a chance for you to explore your new field and come up with lots of ideas for where you may want to take your project over your studies. Wasps are an amazing organism to work with, fascinating life history and captivating to watch in the field. I would wholehearted recommend taking a chance to observe your species in their natural habitat, if that is possible. It will enable you to learn what techniques might work for your project and novel ways that you could implement techniques in the field – Emily Bell

What have you learned about science over the course of this project? 
Molecular work is never straight forwards, it takes time (lots of time) to perfect methodologies – problem solving is a key skill that will always help with this. Sharing troubleshooting ideas with your lab group and other experts in departments is a brilliant way to learn new ways to analyse data. Once you have got a technique that works it really is such a satisfying experience and so exciting to be able to explore your species in a totally new way
– Emily Bell

Describe the significance of this research for the general scientific community in one sentence.
Environment influences the membership composition of new groups, resulting in varied group genetic structure and fitness payoffs for nonreproductive helpers in Polistes paper wasps – Robin Southon

Citation
Robin J. Southon, Emily F. Bell, Peter Graystock, Christopher D. R. Wyatt, Andrew N. Radford, & Seirian Sumner (2019). High indirect fitness benefits for helpers across the nesting cycle in the tropical paper wasp Polistes canadensis. Molecular Ecology, 28(13), 3271-3284. https://onlinelibrary.wiley.com/doi/10.1111/mec.15137

Interview with the author: A hierarchical Bayesian Beta regression approach to study the effects of geographical genetic structure and spatial autocorrelation on species distribution range shifts

Forecasting the effects of global climate change on species distributions is a major challenge with direct relevance for conservation, management, and policy. Incorporating genetic information into these models may help improve these predictions by accounting for within-species variation in demographic history and adaptation to local environments. In a recent issue of Molecular Ecology Resources, Dr. Joaquín Martínez-Minaya and colleagues present a new approach to forecasting species distributions accounting for within-species genetic variation and spatial autocorrelation using the model species Arabidopsis thaliana. Here, co-author Dr. F. Xavier Picó gives us a behind-the-scenes look at the study.

Link to study: https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13024

Arabidopsis thaliana in the wild. Photo provided by Xavier Picó

What led to your interest in this topic / what was the motivation for this study? 
Climate change models ought to incorporate more realistic species’ attributes to better understand their response in predicted and probably inevitable warming scenarios for the near future. In other words, we need to model the demographic, ecological, genetic and evolutionary processes that account for changes in distribution range mediated by warming. However, these data are hard to obtain at large spatial scales even for a single species, which seriously limits our understanding of the impact of global climate change on biodiversity. Our motivation was to develop a model to overcome such limitations using long-term existing data for an annual plant that, interestingly, may be the result of the suite of processes mentioned above, such as genetic structure and spatial autocorrelation of data.

What difficulties did you run into along the way? 
This work is the result of a collaborative effort among scientists from different disciplines, including genetics, ecology and mathematics, that in some cases worked together for the very first time. We had to find the way to speak the same language to achieve a common objective from planning to execution. In a way, we taught each other as learned from each other throughout the development of this work. Although this can be regarded as a difficulty, it was also an extremely rewarding process to see how we all pulled off the project.

What is the biggest or most surprising innovation highlighted in this study? 
From a conceptual viewpoint, the heterogeneity that any species has – due to historical, demographic, ecological and genetic factors – can no longer be overlooked whatever the research question and goal. Molecular markers allow us to tackle such inherent heterogeneity beyond our full comprehension of the underlying forces accounting for it. From a technical viewpoint, spatial Bayesian models take spatial autocorrelation of data into account. Ignoring spatial autocorrelation is a huge problem when it comes to the correct interpretation of spatial models. Handling these two key elements at once represents the most remarkable innovation of this study.

Moving forward, what are the next steps for this research?
With no doubt, the most important next step is to include demographic and evolutionary processes explicitly into global climate change models. We need to expand our current Bayesian framework to include dispersal, establishment of new populations, and local adaptation in a context of rapid environmental and land-use changes fuelled by global climate change. These fundamental processes, which can be modelled and/or parameterized with empirical data, will confer realism and power to model predictions. Only realistic models will generate an array of likely global climate change scenarios upon which we will be able to pose working hypotheses and appropriate actions to mitigate the impacts of global climate change on biodiversity.

Photo provided by Xavier Picó

What would your message be for students about to start their first research projects in this topic? 
Learning in science is a tough process, but extremely rewarding. Try to learn from the best to acquire solid foundations. Nevertheless, do not forget that your particular view on a given problem may open up new paths to keep making progress on the discipline. Recall what all renowned artists normally do: they first copy the old masters to learn the techniques to end up innovating and developing their own artistic style. Innovation can only be done when one understands the potential and limitations that any technique has.

What have you learned about methods and resources development over the course of this project? 
Complex problems require imaginative solutions that, for common people, can only be addressed by gathering together professionals from different disciplines sharing similar interests. In addition, it is important to bear in mind that the biological knowledge of the study species is of paramount importance to assess the value and impact of new methodologies. Inevitably, we believe quite often that any new method developed by us might become a panacea to solve multiple problems. Although this enthusiasm is necessary to move forward, it is very important to clearly detect the caveats and limitations of the methods and resources developed. In our particular case, the knowledge of the study species across the region allowed us to identify when the model outcomes were interpretable and when they could be biased.

Describe the significance of this research for the general scientific community in one sentence.
Promising progress is being made to improve models that will allow us to figure out realistically the future of biodiversity in a context of warming, which seems to be inevitable.

Describe the significance of this research for your scientific community in one sentence.
Genetic heterogeneity and spatial autocorrelation, the result of multiple forces acting in concert, can be handled and interpreted to better understand the response of any species to global climate change.

Citation
Joaquín Martínez‐Minaya, David Conesa, Marie‐Josée Fortin, Carlos Alonso‐Blanco, F. Xavier Picó, & Arnald Marcer. (2019). A hierarchical Bayesian Beta regression approach to study the effects of geographical genetic structure and spatial autocorrelation on species distribution range shifts. Molecular Ecology Resources, 19(4), 929-943. https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13024

Interview with the author: Seed and pollen dispersal distances in two African legume timber trees and their reproductive potential under selective logging

Seed and pollen dispersal, which are critical processes that influence the regeneration of trees, are likely affected by human activities like logging. However, determining how far pollen and seed move is notoriously difficult in the field. Thankfully, modern genetic techniques have provided us new approaches to estimating pollen and seed dispersal, which alleviates some of this issue. Using genetic markers, Dr. Olivier Hardy and colleagues assessed how the movement of pollen and seed in two African timber species is affected by selective logging, where one or two trees per hectare is removed on a 25-30 year cycle. Read below for a behind the scenes interview with Olivier.

Link to the study: https://onlinelibrary.wiley.com/doi/10.1111/mec.15138

Inflorescence of Distemonanthus benthamianus. Photograph by Xander van der Burgt

What led to your interest in this topic / what was the motivation for this study? 
Tropical forests are fascinating but threatened ecosystems. Logging is usually perceived as one of their major threat by the public but selective logging might also be a solution when adequate management plans allows the regeneration of logged tree species, while the revenue generated prevents land conversion. However, forest regeneration is complex because many biotic and abiotic factors can be involved in the process. The extent of seed and pollen dispersal is one of the factors for which few data exist, and it can vary among species or locations. Fundamental research has developed methodologies based on genetic markers to quantify seed and pollen dispersal, so it is a great satisfaction to apply these methods for generating data that should help improving the management of tropical forests.

What difficulties did you run into along the way? 
The study required sampling exhaustively all adult trees of our focal species over several square kilometres in very remote sites of Central African forests, where visibility can be limited to a few tens of meters. This is the kind of field work that would have been very difficult to achieve for a small team of researchers. The collaboration with logging companies, FSC-certified, was a great advantage because we could rely on their field technicians who are trained to conduct similar inventories for planning logging activities.

What is the biggest or most surprising finding from this study? 
First that pollen dispersal distances were so different between two insect-pollinated tree species from the same family but bearing different flower types. It suggests that different flower types could attract different guilds of pollinators with contrasted flight abilities, but for now we ignore who are the pollinators. Second that about 25% of the seeds of the wind-dispersed species were transported over >500 m while their pods do not seem to be efficient gliders and, indeed, the majority falls within <100 m. It suggests that storm winds could play a crucial role in the dissemination of wind-dispersed canopy trees.

Moving forward, what are the next steps for this research?
First, we need to identify the pollinators and seed dispersers. This is challenging, in particular for pollinators because flowers open in the canopy, 20 to 40 meters above the ground and we must invent devices to observe or capture pollinators. Sporty, adventurous and creative PhD or MSc students are welcome! Second, we need to replicate these studies on numerous tree species with different contrasted reproductive characters to be able to derive some generalizations about seed and pollen dispersal according to species traits and environmental conditions. Third, we need to translate these results into recommendations for the sustainable management of tropical forests in collaboration with the forestry sector, and disseminate the messages to policy makers. Fourth, beyond seed and pollen dispersal, many other key processes affect the regeneration cycle and must be considered as well.

What would your message be for students about to start their first research projects in this topic? 
Tropical biology is fascinating for those attracted by fundamental research on biotic interactions, and it is full of opportunities for those inclined towards applied research of societal importance. Some students might be afraid by the remote and little equipped field conditions, and this is obviously constraining. But most students who discovered tropical Africa for the first time returned enthusiastic by their experiences, and some decided to pursue scientific research there.

Describe the significance of this research for the general scientific community in one sentence.
Seed and pollen dispersal investigations are relevant to assess the sustainability of selective logging in tropical forests.

Describe the significance of this research for your scientific community in one sentence.
Seed and pollen dispersal appears to be non-limiting for the natural regeneration of two African tree species under selective logging, while the minimal cutting diameter should be defined by accounting of the relationship between reproductive success and tree size

Citation
Olivier J. Hardy, Boris Delaide, Hélène Hainaut, Jean‐François Gillet, Pauline Gillet, Esra Kaymak, Nina Vankerckhove, Jérôme Duminil, & Jean‐Louis Doucet (2019). Seed and pollen dispersal distances in two African legume timber trees and their reproductive potential under selective logging. Molecular Ecology, 28(12), 3119-3134. https://onlinelibrary.wiley.com/doi/10.1111/mec.15138

Interview with the author: Landscape genomic signatures indicate reduced gene flow and forest‐associated adaptive divergence in an endangered neotropical turtle

The Dahl’s Toad-headed turtle (Mesoclemmys dahli) is one of the 25 most endangered turtle species on Earth and one of the unlucky few that is constantly being compared to a toad. A previous study has shown that extensive habitat conversion and fragmentation in its native range in Colombia has led to genetic differentiation among populations. However, critical questions remain for the conservation and management of this species: how does habitat type and quality in this rapidly changing region influence gene flow? How can genomic data inform the management of this endangered species?

Dr. Natalia Gallego García (@NataGalle) and colleagues set out to answer these questions. Read below for an interview with Natalia about the challenges of working with such a rare species and how this study provides the foundation for a genetic rescue program for the Dahl’s Toad-headed turtle.

The critically endangered Dahl’s Toad‐headed turtle (Mesoclemmys dahli). Photo by N. Gallego García

What led to your interest in this topic / what was the motivation for this study? 
We conducted a previous population genetics study using microsatellite loci on this highly endangered species, in which we found significant genetic evidence of population fragmentation. In this follow-up study, we wanted to know how the current landscape, now composed of open grasslands for cattle instead of tropical dry forest, might be restricting gene flow and thus causing the observed fragmentation. We also wanted to know how this new anthropogenic environment was potentially driving local adaptation.

What difficulties did you run into along the way? 
The main difficulty was finding this rare species across its range to get the samples. Another difficulty was standardizing the RADseq protocol, as our research was the first genomic-level study on any side-necked (pleurodiran) turtle. Also, there is no reference genome for this species or for any closely related one, making the analysis of our data difficult. We had to assembly a de novo genome, which prevented us from running other analyses that could have allowed us to learn more about adaptive mechanisms to new environments.

What is the biggest or most surprising finding from this study? 
First of all, we were able to show that population fragmentation was related to habitat loss. However, we were expecting movement through grasslands to be costly, given that this is a forest species, but we found that from a scale of 1 (easy) to 1000 (hard) the cost of traversing grassland was only 13. We believe that this low cost is associated with the presence of water ponds built in the pastures for the cattle to drink, which are increasingly being used by this species. These ponds might be serving as a sort of stepping stone array of lower quality but still usable aquatic habitat, enabling movement over an otherwise hostile matrix. Our second surprising finding was observing possible adaptive divergence between populations occupying areas with more forest than populations in areas with almost no forest. This result suggests that the populations might be adapting to this new transformed environment. However, adaptation alone is not rescuing this species from the negative effects of fragmentation, and currently the species is facing a high risk of extinction.

Moving forward, what are the next steps for this research?
The next steps can be divided in terms of management and research. In terms of management, we are currently designing a genetic rescue program to reduce inbreeding and increase population genetic diversity, without disrupting the potential ongoing adaptation that we observed. In terms of research, we are currently assembling the genome of a closely related species, which will allow us to map the putatively adaptive loci found, and better understand how this species is adapting to its new transformed environment. This will also allow us to design a field and/or laboratory experiment to further explore the possibility of adaptation to altered, and degraded habitat.

What would your message be for students about to start their first research projects in this topic? 
Working with non-model, rare, and threatened organisms, although challenging, can lead to valuable information that is vital in their conservation. So, accept the challenge and stand up for those forgotten species. Any new information on a data deficient species will increase its chance of survival, which in itself already makes the research worthwhile.

What have you learned about science over the course of this project? 
Science always comes with exciting surprises that do not always comply with our expectations, and it usually leaves more questions than answers. But it is gratifying to contribute, even in a small way, to the understanding of complex processes that can eventually be applied to solve difficult problems, such as the conservation of an endangered species.

Describe the significance of this research for the general scientific community in one sentence.
Adaptation to habitat change can happen, but perhaps not quickly or completely enough to overcome the negative effects of population reduction and fragmentation.

Describe the significance of this research for your scientific community in one sentence.
Landscape genomics analyses provide evidence of reduced gene flow in a fragmented habitat, leading to harmful effects on a critically endangered neotropical turtle, despite its possible adaptation to the new anthropogenically created environment.

Citation
Natalia Gallego‐García, Germán Forero‐Medina, Mario Vargas‐Ramírez, Susana Caballero, & Howard Bradley Shaffer. (2019). Landscape genomic signatures indicate reduced gene flow and forest‐associated adaptive divergence in an endangered neotropical turtle. Molecular Ecology, 28(11), 2757-2771. https://onlinelibrary.wiley.com/doi/10.1111/mec.15112

Interview with the author: Broadening the taxonomic scope of coral reef palaeoecological studies using ancient DNA

Imagine being able to take a small handful of sediment from the bottom of the ocean, and from that seemingly lifeless material, be able to reconstruct the dynamic history of life in that area over the past decades and millenia. No, that’s not quite science fiction– advances in DNA sequencing technology have now made this possible. Hidden inside that sediment is what’s known as palaeoenvironmental DNA (aeDNA), or ancient fragments of DNA that come from the organisms that used to occupy the area, which when sequenced and combined with fossil records, allows us this amazing insight into the past.

In this blog post, we go behind the scenes with Dr. Maria del Carmen (K-le) Gomez Cabrera to talk about their recent publication in Molecular Ecology using aeDNA in a coral reef off the coast of Australia to paint a picture of the historic and complex communities that have inhabited these diverse ecosystems over the past hundreds of years.

Coring marine sediments using an aluminium pipe. Acknowledgement Dr. Brian Beck

What led to your interest in this topic / what was the motivation for this study? 
I have previously study the coral-zooxanthellae symbiosis and for this I have used molecular techniques, since it is impossible to identify the symbiont otherwise, I spent endless hours in the lab extracting tiny amounts of DNA. Then I changed fields and started working with Prof. Pandolfi and the Marine Palaeoecology Lab at The University of Queensland. The tools of the trade are rock hammers and chisels. I ended up surrounded by an inordinate amount of large rocks. But been dependant on only fossils to reconstruct the past leaves a lot of the story out since soft bodied organisms are very unlikely to leave a fossil record, this was very frustrating for me. When I attended a talk by Prof. Alan Cooper (a co-authors of this study) on ancient DNA from plaque in ancient human teeth, and considering my background, I decided we needed to try this on coral reefs. Ancient environmental DNA opened a new world for us to study ancient marine ecosystems of which we only know the story that fossilised organisms tell.

What difficulties did you run into along the way? 
Been the first study of its kind that we have undertaken, we ran into many difficulties. Extracting DNA from our samples was the first hurdle. Although we had a well-resourced molecular lab, we could not use it for this study since any trace of modern DNA was a potential contaminant. We had to repurpose a room in a remote campus where no molecular work was carried out, to use it as a clean space for subsampling the sediment cores, we then sent these samples to the Australian Centre for Ancient DNA to be processed. Making sense of the data was also difficult; there is little genetic information about most marine organisms. Although a steep learning curve, now we are better prepared and it is incredible the amount of DNA sequences been generated around the world on marine organisms at present that will greatly benefit this type of studies in the future.

CT scan of a core with coral fragments marked in colour. Each colour represents a different coral genera. Acknowledgement Dr. George Roff

What is the biggest or most surprising finding from this study? 
That we managed to actually extract workable ancient environmental DNA from reef sediment cores that were not even collected with this purpose in mind. This really blew our minds and opened so many new possibilities to answer important ecological questions that otherwise would have remained unanswered. Moreover considering that these sediment cores were collected from tropical environments, we were really pushing the limits of this technique.

Moving forward, what are the next steps for this research?
This study was a proof of concept, it allowed us understand the capabilities of this technique in the context of coral reefs. We are now establishing a new line of research, incorporating a team of amazing PhD students to explore ecological interactions in the past between key marine organisms such as coral and seaweed, we are also working on a more accurate picture of ecological baselines of natural resources such as fish before European colonization of the Australian continent. These studies will give managers better tools to assist with the management of the Great Barrier Reefs and its resources.

Dr. K-le Gomez Cabrera in the field. Acknowledgement Dr. George Roff

What would your message be for students about to start their first research projects in this topic? 
Read profusely and cover many subjects, do not stick just to your particular area of research because your eureka moment may come from something you read on a different field (think about the connection between ancient DNA in plaque from human teeth and coral reefs’ biodiversity). Take the time to understand the capabilities of the techniques you are planning to use. Researching ancient DNA is very expensive, so you need to really know what you want to achieve and how before you start extracting DNA, preparing DNA libraries or even collecting samples.

What have you learned about science over the course of this project? 
I’ve learn that lateral thinking is very important for the scientific endeavour. That it is crucial not to be boxed in your small bubble in your field of research but to keep thinking big, reading broadly, and scouting for opportunities to apply new approaches from other fields.

Describe the significance of this research for the general scientific community in one sentence.
This study opened new avenues of research that can be used to help us understand meaningful ecological interactions between tropical marine organisms hundreds of years in the past that would not have been possible with traditional methods.

Describe the significance of this research for your scientific community in one sentence.
By incorporating ancient environmental DNA into palaeoecological studies of coral reefs, we can better understand ecological interactions involving soft bodied organisms, a feat not possible with traditional palaeoecological tools.

Citation
Maria del Carmen Gomez Cabrera, Jennifer M. Young, George Roff, Timothy Staples, Juan Carlos Ortiz, John M. Pandolfi, & Alan Cooper. (2019). Broadening the taxonomic scope of coral reef palaeoecological studies using ancient DNA. Molecular Ecology, 28(10), 2636-2652. https://onlinelibrary.wiley.com/doi/10.1111/mec.15038