The research being conducted and the media for sharing findings change through time. In the past decade, these changes have been particularly rapid, as the technology available for measuring the world and for publishing papers have each gone through multiple step changes. Thejournal is adapting to these changes in service of our research community. This Journal News section of the blog is intended to communicate these adaptations to maintain a leading quality outlet for your work.
All changes at the Journal of Biogeography will reflect our commitment to continually (1) keep pace with and lead advances in the discipline, (2) deliver a constructive, productive process for publishing your biogeographical studies, (3) enhance value to the community, such as replication and reuse of your work, and (4) add value to you by widely disseminating your research to a global audience.
The Journal of Biogeography aims to support early career researchers by highlighting their recently published journal articles and providing a space where the community can get to know the authors behind the works and learn from their publication experiences. In our featured posts, researchers dive into the motivations, challenges, and highlights behind their recent papers, and give us a sense of the broader scientific interests that drive their biogeographic research. This is where we also get a sneak peek into novel and interesting research that is yet to come!
Based on the information provided when manuscripts are submitted, the editorial team will routinely contact authors each month to invite a contribution from those who are both (1) early career researchers, i.e. up to and including postdocs, and (2) corresponding author on their upcoming publication in Journal of Biogeography. However, we also welcome contributions from other early career researchers who may be first or middle authors on these papers; if the study has multiple authors, we very much welcome a single submission from the cadre of early career co-authors involved.
To keep the process simple for all involved, we invite contributions to follow a standard format (see below). Responses need not be given to all prompts, but there should be a critical mass of responses to be informative; responses to prompts that are answered should be concise; thus the experience is streamlined, personalized, and easy.
We encourage a tone and standard suitable for social media and that conveys the excitement and intrigue of being a biogeographer. Previous submissions can provide a guide for your own individualized entries. The social media editors are happy to provide feedback and assistance in revising content before posting. The senior editorial team approves all posts.
If you have any questions or would like to submit your own contribution, please contact one of our social media editors: Dr. Leanne Phelps and Dr. Joshua Thia using the journal’s gmail address, firstname.lastname@example.org. To help you get started, the questionnaire is provided below. Check out recent contributions for examples and ideas!
Links to social media and/or personal website(s)
Current academic life stage (Honours, Masters, PhD, Postdoc?)
Major research themes and interests
Current study species/system? What makes it interesting (/cool!)? (100 words)
Recent paper in Journal of Biogeography (citation)
Describe the motivation behind this recent paper (100–150 words)
Describe the key methodologies in this recent paper, highlighting anything particularly novel or ingenious and how this provides new insights (100–150 words)
Describe any unexpected outcomes of this research, or any challenges you and your coauthors experienced and overcame along the way (100–150 words)
Describe the major result of this recent paper and its contribution toward the field (100–150 words)
What is the next step in this research? (100 words)
If you could study any organism on Earth, what would it be and why?
Is there anything else you would like to tell us about yourself or your featured research? (Any hidden gems the above questions might have missed?)
If available, please provide three or more visually appealing photos (with captions) that relate to your work, so we can feature you on our social media platforms.
Every month, each new issue of the Journal of Biogeography (JBI) includes at least two highlighted articles—the Editors’ Choice and the paper associated with the cover image—and periodically we highlight a topic with a series of papers as part of a special issue. Our intention on the blog is to communicate additional aspects of these, and other papers published in JBI, from slightly different perspectives.
Every published paper has a story behind it that complements and enriches our understanding of the published science. Very rarely, the parallel narrative might provide as radical a reframing of the entirety of our scientific work as did Thomas Kuhn’s “The Structure of Scientific Revolutions”, Bruno Latour’s study of “Laboratory Life”, and the feminist critique of science by Evelyn Fox Keller, Sandra Harding, Helen Longino, and others. On occasion it may cause us to rethink the history of the discipline and its modern consequences—as in recent works on decolonialization of biogeography—or likewise to consider current approaches and what they may mean for the future. Oftentimes the parallel narrative is simply a personal perspective on how we stumbled upon a particular question, co-opted a tool for a different job, ran into unexpected difficulties or found something easier than anticipated, visited wonderful places, worked with fascinating organisms and systems, became aware of related challenges, saw something on the side that sparked our curiosity for the next study, and so on.
Irrespective of what your story is, these pages are intended to provide a small window onto that complimentary narrative that details the human endeavor of biogeography. The idea is to try to demystify how the polished published biogeographical story emerges from at times complicated studies of a complex world. No matter what our career stage, each study comes with its challenges, the solutions merit acknowledgement (and can potentially help others), and each publication is an achievement to be celebrated. In recognizing these commonalities, we hope the diversity of routes and strategies for publishing become a little more transparent and a little more accessible to all.
The format for highlighting papers is flexible (within a limit of ~750 words [+/- 250]), but we provide a few optional prompts below to get you started and make sure some key information is available.
Format & some optional prompts:
Title for blog post
Author name, title, institutional details
Links to social media and/or personal website(s)
Citation including URL for recent paper in Journal of Biogeography
Describe the motivation behind this recent paper. — What’re the major research themes and interests it addresses? — What makes it interesting/cool/important? — What surprised you / the team while designing, conducting, completing the study? What knotty problem did you have to overcome? — Reflecting on the whole process, beyond the published research, what were other important outcomes from the project? — Where do you / the team go from here? — Is there anything else you would like to tell us (any hidden gems the prompts might have missed)? — Two to three visually appealing photos/images (with captions) that relate to the work and this narrative is possible.
Shahan is a postdoc at the Museum of Comparative Zoology, Harvard University. He is a systematic and evolutionary biologist with a keen interest in Opiliones, an order of arachnids. Shahan shares his recent work on the opilionoid family, Triaenonychidae, investigating the role of geological events and past climate on their geographical distribution.
Shahan Derkarabetian sifting leaf litter for triaenonychids in southern Australia. Photo courtesy Jennifer Trimble.
Institute. Museum of Comparative Zoology, Harvard University
Academic life stage. Postdoc
Major research interests. Opiliones, Systematics, Evolutionary Biology
Current study system. My current and ongoing study system is a group of arachnids called Opiliones (a.k.a. harvesters, harvestmen, daddy-long-legs). A plethora of reasons make Opiliones interesting, including their diverse morphology and behaviour. There are Opiliones that are covered in sharp spines, some that are as green as moss, some that aggregate in groups numbering in the1000s, some that build mud nests, and so much more. Another reason is because there is still much to discover about their basic biology and ecology, and there are still many new species that need to be described, even from places that are considered well studied, like North America.
Recent paper in JBI. Derkarabetian S, Baker CM, Giribet G. 2021. Complex patterns of Gondwanan biogeography revealed in a dispersal-limited arachnid. DOI: 10.1111/jbi.14080
Motivation behind this paper. This study focused on one family of Opiliones, called Triaenonychidae, that we have been working on for many years. This group is widely distributed throughout the temperate forests of the southern hemisphere in continents associated with Gondwana. Our motivation for this study was to determine their biogeographic history through geologic time, and how geologic events and climate shaped their present-day distribution and diversity. Previous research suggested very complex patterns of geographic distribution not found in other studies of Gondwanan taxa, which is especially interesting given their low dispersal ability. We wanted to explore this complexity in more detail using modern phylogenomic approaches.
A representative of a new and undescribed genus of Triaenonychidae from southern Australia. Photo by Shahan Derkarabetian.
Key methodologies. We relied on excellent taxon sampling for this study; we included ~80% of the 100+ genera in this family. These specimens were either acquired through fieldwork we conducted ourselves over the last 20 years, or through borrowing specimens held in natural history museum collections all over the world. Using modern sequencing approaches we not only included all the freshly collected specimens but were also able to sequence DNA from historical museum specimens collected up to 100 years ago. Our thorough sampling allowed us to infer both large scale inter-continental patterns as well as more regional geographic patterns within continents.
Unexpected challenges. The big challenge for this research was integrating all the sources of information to form a cohesive picture of the biogeographic history of this group. We inferred a phylogeny with dated taxonomic splits and had to correlate these relationships and dates with both the geologic and paleoclimatic history. In order to tie these disparate sources of information together I had to do some deep dives into the literature for geologic reconstructions, paleoclimate reconstructions through time, and learn a bit about how plant fossils are used as indicators for past regional climates. Much of this was new to me as a scientist, so the challenge was becoming familiar with it enough to put it all together and tell the story.
Shahan Derkarabetian searching for triaenonychids under woody debris, in typical southern temperate forest habitat of Tasmania, Australia. Photo courtesy Marshal Hedin.
Major results. In our study system, we found unexpectedly complex phylogenetic relationships and patterns in the geographic distribution of different lineages across continental landmasses. For example, the species that are endemic to New Zealand were found across 5–6 genetically distinct lineages, suggesting multiple transitions to New Zealand. Previous studies have tended to report fewer numbers of lineages within continents. Yet as evidenced from New Zealand taxa in our study, there can be incredible intra-continental diversity. We think these differences between our study and previous works have to do with the biology of these organisms. Triaenonychidae are low-dispersal organisms, so they are more directly affected by geologic events. However, they are not completely without dispersal, so they do have those very rare events where there is some chance of a long-distance dispersal event happening. This particular balance of dispersal ability led to geographic patterns and diversity shaped by both geology and rare long-distance dispersal across small and large geographic ranges.
Next steps. We want to take more detailed looks at the biogeography of smaller more regional groups within the Triaenonychidae with better species level sampling. The biological characteristics of triaenonychids, specifically low dispersal ability and specific microhabitat preferences, make them great candidates for biogeography at large and small geographic scales. As such, we expect to find equally new and complex geographic patterns within continental regions. Another aspect we were unable to explore is rare long-distance dispersal. For example, there is a species endemic to the isolated Crozet Islands, for which we were unable to obtain samples for this study. With newly acquired samples, we can ask: how and when did that species get there, and where did it come from?
If you could study any organism on Earth, what would it be? I think I would still study Opiliones, but I would want to study the species that existed 200, 300, and even 400 million years ago. I do not mean as fossils, but as they existed in those times, which would mean I would need a time machine. There were many time periods that were critical to the formation of much of the modern-day diversity in Opiliones, and it would be very cool to see what they looked like, where they were distributed, and how diversity formed through geologic time.
The joys of fieldwork in a campervan. Photo by Shahan Derkarabetian.
Anything else you would like to share? Fieldwork! This was of course the best part of doing this type of research. For this project I did quite a bit of fieldwork in south-eastern Australia, including Tasmania. Collecting Opiliones gives us a good idea of their preferred habitat, which helps infer biogeographic history. It also provides hints at the true amount of diversity that exists, especially what still needs to be described. Fieldwork often leads to new species discoveries, and Opiliones are no exception. From a two-week trip through southern Australia, we collected about 30–35 species, only five of which are formally named and described. As a taxonomist, this means I still have a lot of work to do!
Jacob Suissa is a PhD candidate at Harvard University. His major research interest is in the evolution of plants, particularly ferns. Jacob shares his recent work that has utilised vast herbarium records to understand global diversity in montane fern assemblages.
Whether its collecting plants in the Peruvian Andes or the New England Berkshires, mountains have always fascinated me. Specifically, I am captivated by the way vegetation drastically changes as I ascend a mountain. Mountain ranges across Earth, however, are not all the same with respect to their diversity. Tropical mountains contain many more species than temperate mountains of similar or larger size. For instance, there are over 10,000 flowering plant species in the Talamanca Mountain range in tropical Central America, compared to only around 5,000 species in the temperate Rocky Mountains (the “Rockies”) of North America. This difference is even more striking when considering their size: the Rockies are 3,000 miles long with a maximum height of over 14,000ft, while the Talamanca’s are only 250 miles long with a maximum height of 12,500ft. Determining what drives this uneven distribution of species across tropical and temperate ecoregions is a major biogeographical question.
Visa of the Costa Rican continental divide along the Talamanca Mountain range.
I study ferns, the second most diverse group of vascular plants, and they are a great study system for understanding these patterns of biodiversity. Contrary to the common depictions of ferns as ancient shade and water loving plants, the majority of fern diversity is actually relatively young (<100 my), and they occur in a variety of different ecosystems ranging from lowland desert outcrops to the high elevation Páramo (tropical alpine meadows). For over 100 years it has been suggested that, relative to temperate mountains and the lowland tropics, tropical mountains may contribute disproportionately to shaping the patterns of global fern biodiversity. Massive amounts of digitized herbarium specimen data exist (from decades of botanical collections) that could be used to explore these biogeographic patterns. However, to date, no such study has been conducted.
Pleopeltis from the Peruvian Andes
In our paper, we stand on the shoulders of past botanists by leveraging over 800,000 global occurrence records for nearly 8,000 fern species from the database of digitized herbarium records hosted on the Global Biodiversity Information Facility (GBIF). We integrated these occurrence data with genetic and climatic information to uncover how historical, ecological, and evolutionary processes contribute to patterns of global fern biodiversity. We first divided the Earth into a series of 1×1˚ grid cells and quantified a series of metrics within each cell including species richness, environmental variability, and lineage diversification. We discovered that the majority of fern species (58%) occur in eight principally montane hotspots that only cover a total of 7% of Earth’s land area. These spots include the Greater Antilles, Mesoamerica, the tropical Andes, Guianas, Southeastern Brazil, Madagascar, Malesia and East Asia. Importantly, within these hotspots we found that fern diversity is highest above 3500ft in elevation and peaks around 8,000ft in the tropics, which corresponds to cloud forests, the home of fern epiphytes. This recovered pattern echoes the importance of tropical mountains and cloud forests in contributing to fern biodiversity.
Once we had characterized general trends in species richness, we turned our attention to understanding the ecological and evolutionary processes that generated these patterns. We incorporated climate, soil, and topological data and found a strong positive relationship between increased climatic space with species richness and diversification within our montane hotspots. These patterns suggest that ferns might be undergoing greater lineage diversification across ecological gradients within tropical montane ecosystems, compared to adjacent lowlands and temperate mountains. Lowland tropical rainforests like the Amazon are touted for their plant biodiversity; while they are diverse for certain organisms like woody trees, herbaceous understory fern species are quite depauperate. We think that this is because of the relatively low diversity of different ecosystems in these lowland tropical zones. Furthermore, unlike temperate mountains, a unique set of dynamics occurs in tropical mountains. First, in the tropics small amounts of elevational change leads to a high degree of climatic change, which creates a series of stacked ecosystems within a small geographic space. Second, there is very low temperature seasonality within each of these stacked ecosystems, meaning each habitat band is climatically stable throughout the year. The relationship between these two processes creates a diversity of seemingly allopatric or isolated habitats in a relatively narrow geographic space, and we suspect that these processes facilitate greater diversification of ferns across elevational gradients in tropical mountains, relative to adjacent lowlands and temperate mountains.
Descending Cerro Bruster (Panama) with bags full of ferns.
Our findings are not only important for deepening our understanding of global patterns of fern biodiversity, but also for contextualizing biodiverse regions for conservation. With the discovery of fine-scale patterns of geographical and elevational diversity in a major group of land plants, we can pinpoint where on Earth the important centers of biodiversity are. Given that tropical montane plant communities are at a disproportionately higher risk of climate-induced extinction, knowing that these sites are biodiversity hotspots can help make decisions on conservation efforts in the face of anthropogenic and climate-mediated habitat destruction.
Thiago Laranjeiras is an an environmental analyst at Instituto Chico Mendes de Conservação da Biodiversidade. He is a biogeographer with a keen interest in the ecology and biodiversity of birds. Thiago shares his recent work on transitions in avifauna communities across floodplain habitats in the Amazon.
Institute. Instituto Chico Mendes de Conservação da Biodiversidade (Chico Mendes Institute for Biodiversity Conservation)
Current position. Environmental analyst.
Major research themes. Biogeography, ecology, natural history, ornithology, and conservation.
Current study system. I studied Amazonian birds during my PhD, especially those that inhabit floodplain forests. Amazonia is home to more than 10% of all known bird species, yet most of them are poorly studied and are data deficient. Many of the birds that inhabit the Amazonian floodplains are habitat specialists and have restricted distributions. They are conspicuous, with loud beautiful songs that can travel far distances over river water. Listening to a dawn-chorus while drifting down the river in a boat is an incredibly peaceful activity.
Klagesi’s antwren, Myrmotherula klagesi, one of the floodplain forest bird specialists that best represent the effects of the confluence of the Negro and Branco rivers for the floodplain avifauna
Recent paper in JBI. Laranjeiras TO, Naka LN, Leite GA, Cohn-Haft M. Effects of a major Amazonian river confluence on the distribution of floodplain forest avifauna. J Biogeogr. 2021;48:847–860. https://doi.org/10.1111/jbi.14042
Motivation behind this paper. One of Amazonia’s most striking features is the diversity of “colors” of its many rivers. Different drainages associated with distinct geological features (the Andes, the sandy-soil lowlands or the Brazilian and Guianan shields) create ‘white’, ‘black’, and ‘clearwater’ rivers. These different river types are also associated with varying biodiversity. Previously, comparing distinct rivers in the Rio Negro basin (in northwestern Brazilian Amazonia), the world’s largest blackwater river, it became clear that these nutrient-poor waters create floodplain forests that contain distinct avifauna from those found in sediment-rich whitewater rivers. However, not everything was “coffee au lait” or “weak black tea”. We found “intermediate” avifauna in some of the rivers. Also, rivers of distinct water types can meet and such river confluences, as critical hydrogeological phenomena, may have important implications for floodplain systems. Those who are familiar with the “meeting of the waters” of the Rio Solimões and the Rio Negro itself, in front of Manaus (the largest Amazonian city), can easily notice the magnitude of such confluences. The relevance of mixing distinct water types on floodplain terrestrial fauna has so far been largely overlooked. So, we went to the Rio Negro at the confluence with its largest tributary, the sediment-rich whitewater river, the Rio Branco, to characterise diversity variation between mixed and unmixed water types.
The meeting of two Amazonian rivers, showing the contrasts in the water and in the floodplain forests (the blackwater Rio Canumã and the whitewater Paranã do Urariá, in the Brazilian state of Amazonas)
Key methodologies. To investigate how the entrance of the Rio Branco affects the avifauna along the Rio Negro, we implemented a rapid and standardized avian sampling of floodplains of both riverbanks and nearby islands, above and below the confluence of the two rivers. Focusing on the commonest bird species that are easily identified by song, this rapid and standardized sampling allowed us to cover a huge area in a relatively small time period (stretching more than 400km of rivers). It took us a few field expeditions to sample 52 sites. More complete and traditional avian inventories would take decades. In a similar way, we retrieved estimates of sediment concentration in river water (a main parameter in Amazonian water type classification) using satellite imagery. Covering a 15-year time-series, these estimates avoided the limitations of direct measures of sediment concentration in the field in a single period and allowed us to better understand the variation throughout the confluence of these two rivers.
Major results. We found a mixed and richer avifauna along the Rio Negro below its confluence with the Rio Branco. Bird species that are typical of whitewater floodplains occurred predominantly on the left riverbank or nearby islands of the lower Rio Negro, on the same side into which the Rio Branco sediment-rich waters seem to be channelled. Rather than just representing a potential blackwater barrier between whitewater systems, the lower Rio Negro comprises a unique biogeographical transitional zone. These results indicated the importance of the dynamics and distribution of nutrient-rich sediments and that confluences of large Amazonian rivers not only affect aquatic species, but also the distribution of floodplain terrestrial fauna. Several other confluences of contrasting large rivers occur throughout the Amazon and these phenomena emerge as a key factor explaining boundaries of species’ distributions and geographic patterns of Amazonian floodplain biodiversity.
Wire-tailed Manakin, Pipra filicauda, a typical floodplain forest bird species of the Rio Negro basin
Challenges you overcame. Despite our rapid approach, sampling all the 52 sites along the confluence still had its challenges. To optimize the time in the field, we had to navigate at night from one site to another, including along stretches away from the main channel of the river. Given water level of the river was descending, some sandbars were still submerged, but close to the water surface. Navigating in this situation requires a lot of experience from the boat driver and the use of the sonar to avoid hitting the sandbars. However, one time we miscalculated, and our boat literally jumped out of the water! Fortunately, it was a small sandbar, so we narrowly missed a stranding that would have been disastrous for continuing our field work!
Thiago boating between sampling sites.
Next steps. To look at other dimensions of the diversity than taxonomic (phylogenetic and functional) is a natural next step for understanding heterogeneity of the Amazonian floodplains and the importance of major river confluences. Investigating other confluences will also shed light on the generality of the patterns we found. Overall, synthesis of avian geographical patterns in Amazonian floodplains would offer a new background for future studies on the evolution of these ecosystems, providing new guidelines for conservation of Amazonian avian diversity. I hope such work is conducted in the near future.
If you could study any organism on Earth, what would it be? Birds are organisms hard to let aside. Their diversity and geographic patterns are captivating. Rather than other organisms, I feel that I would study birds from other regions. Amazonia is deeply fixed in my dreams. There are other huge and interesting rivers confluences and even poorly explored rivers, filled with poorly known birds and communities. I have been talking to myself for years about a long-term expedition, navigating through several Amazonian rivers from the mouth to their headwaters. Also, on my radar are the remote, almost untouched Amazonian mountains, the tepuis. Recently, I also had the opportunity to explore some of them, but this is another subject. Altogether, I feel that Amazonia is where we arrived with one question to leave with ten or to never more leave.
Sun rise provides an incredible background for listening to the dawn-chorus of birds in the floodplain forest of Anavilhanas in the lower Rio Negro.
Anything else you’d like to add? I would like to say that this research, as well as my journey as a biologist, would not be possible without support from many important people and institutions. To study birds in the remote Amazonian floodplains is a privilege. I feel that I am worth of such privilege by making Amazon my home for more than 15 years. As an environmental analyst, I also have the opportunity to apply and put in practice the ecological and biogeographical concepts into biodiversity conservation, especially regarding the protected areas in the Brazilian state of Roraima. To put these concepts into conservation practice is a duty that I am happy to deal with. Finally, I think we still need to improve our ability to communicate our results from biodiversity research with the general public, using all available media. I hope here we make greater progress in this area.
Andrea Paz recent started her postdoc at ETH Zürich in Switzerland. She is an evolutionary biologist interested in unveiling the processes generating the patterns of species distributions. Here, Andrea shares her recent work investigating the environmental correlates of diversity for multiple clades and diversity measures in the Atlantic Forest.
Andrea visiting the Atlantic Forest during a trip she had with part of the US and Brazil team. The photo is in Boracéia Biological Station – a field station from the Universidade de São Paulo.
Institute. Research conducted as a PhD student at the Graduate Center, City University of New York | Currently a postdoc at ETH Zürich.
Academic life stage. Starting a postdoc.
Major research themes. Biogeography, species distributions, amphibians, environmental drivers of species and community distributions.
Current study system. I just finished my PhD studying several taxa in the Atlantic Forest of Brazil. The Atlantic Forest is considered a biodiversity hotspot because of its high diversity and endemism levels and its high level of threat (less than 10% of the original forest persists). This forest is a super interesting system that includes broad latitudinal and altitudinal gradients (not a very usual combination) and thus has huge environmental variation and heterogeneity. All this variation makes this system perfect for testing many ecological and evolutionary questions related to the effect of environmental differences in biodiversity.
Boracéia Biological Station – field station from the Universidade de São Paulo.
Recent JBIpaper. Paz, A., Brown, J.L., Cordeiro, C.L.O., Aguirre-Santoro, J., Assis, C., Amaro, R.C., Raposo do Amaral, F., Bochorny, T., Bacci, L.F., Caddah, M.K., d’Horta, F., Kaehler, M., Lyra, M., Grohmann, C.H., Reginato, M., Silva-Brandão, K.L., Freitas, A.V.L., Goldenberg, R., Lohmann, L.G., Michelangeli, F.A., Miyaki, C., Rodrigues, M.T., Silva, T.S. and Carnaval, A.C. (2021). Environmental correlates of taxonomic and phylogenetic diversity in the Atlantic Forest. Journal of Biogeography, 48(6), 1377-1391 https://doi.org/10.1111/jbi.14083
Motivation behind this paper. This study results from a huge collaborative effort between scientists in several countries, including the USA and Brazil. The Atlantic Forest is a big and diverse place in terms of its biology but also by the heterogeneity of landscapes it presents. For these reasons, it is hard to monitor and study this hotspot of diversity everywhere, because many factors may play a role in explaining its diversity patterns. We wanted to have a better understanding of what are the environmental correlates of different diversity dimensions in the Atlantic Forest and test whether those could apply to several taxonomic groups, including both plants and animals.
Key methodologies. Here, we used a machine learning approach where an ensemble of models (including random forest, neural networks among others) was created to better predict observed patterns of biodiversity based on abiotic variables. This allowed us to understand the correlates of diversity in the forest for several taxonomic groups. The literature shows incongruent results between different taxa, but using multiple taxa in a single biome helped us find some more general conclusions about the organisms in the forest, including how precipitation is a main predictor of diversity. In contrast, topography had a very small contribution.
A lot of the work for this publication was computer based and I did much of it working with Dr. Thiago Silva at UNESP Rio Claro in Brazil (left) and at University of Stirling in Scotland (right).
Unexpected challenges. It was very interesting getting data together from different research groups, universities and taxonomic groups. Standardizing it was definitely a challenge. For example, everyone has a different way of identifying their specimens, some use numbers from fieldwork, others use numbers from laboratory work and others from the museums. Also, the precision in naming taxa is different, with some specialties using just binomials (genus & species) and others an extra layer of clustering, such as tribes, subfamilies, etc. For the molecular portion, scientists in different disciplines also use different genes to understand the evolutionary history of their groups of interest and even different techniques to reconstruct those histories. On the other hand, bringing diverse perspectives together helped us better understand the potential processes driving diversity in this forest.
Major results. The major result is that even though the Atlantic Forest is huge and heterogeneous, we can indeed use environments to predict diversity patterns (at least for phylogenetic and taxonomic diversity) irrespective of the taxonomic group. Even more surprising is that a single driver – precipitation – was of particular importance to all groups and different measures of diversity. The model applied in our study shows a lot of promise to predict changes in diversity with a changing climate.
Next steps for this research. We are building a model that allows for predicting trends in biodiversity change in near real-time for the forest. This tool will allow us to flag areas that are either gaining or losing diversity for different groups of plants and animals because of environmental change. We hope this will become a tool easily applied in conservation actions in the near future.
Presenting the results of this work in São Paulo (Brazil), at the FAPESP International Symposium: Dimensions US and Biota São Paulo in 2019.
If you could study any organism on Earth, what would it be? I started my career studying amphibians and hope to keep going back to them :). They are amazing models to study environmental impacts at the population, species, and community levels. Also, they are beautiful!!
Anything else to add? This was the first chapter of my PhD and the first time I led a paper with so many collaborators. It was a really amazing experience getting to work with so many cool scientists!
Joint species distribution models may not yet be able to detect the signal of biotic interactions from empirical community data … due to the lack of sufficiently dense ecological datasets and fast-and-accurate algorithms.
Above: Eurasian nuthatch (Sitta europaea) at its nesting site in a former woodpecker cavity. (Photo by Josefine S. / CC BY-NC-ND 2.0 / flickr.com)
Every passionate naturalist knows how ecological communities are shaped by biotic interactions. Predators control the abundance of prey populations. Species at the same trophic level compete fiercely for resources. Other seemingly unrelated species form tight relationships of mutual benefit. Yet, when we describe ecological systems at scales above the very local, we usually neglect the effects of these interactions and assume that the environment is the prime determinant of ecological variation. But how much of an oversimplification is this? Theoretical consideration and simulation studies indeed suggest that the signal of biotic interactions should vanish at coarser spatial resolutions, but few studies have tested this proposition empirically. Thus, the aim of our paper “Scale dependency of joint species distribution models challenges interpretation of biotic interactions” was to fill this gap.
Editors’ Choice article: (Free to read online for a year.) König, C., Wüest, R.O., Graham, C.H., Karger, D.N., Sattler, T., Zimmermann, N.E. and Zurell, D. (2021), Scale dependency of joint species distribution models challenges interpretation of biotic interactions. J Biogeogr. 48:1541–1551. https://doi.org/10.1111/jbi.14106
The main idea originated at least six years ago, when the question of how to account for biotic interactions in species range predictions took up more and more pace. Joint species distribution models (JSDMs) had just come up as a new tool in spatial ecology and the prospect of disentangling the environmental and biotic drivers of species’ ranges was quite exciting. In contrast to classical single-species distribution models, JSDMs simultaneously model the environmental response of multiple species in a community. This joint approach allows us to look not only at species-environment relationships, but also at the residual structure in their (co-)occurrences that is not accounted for by the environment. The general idea underlying JSDMs is to statistically describe this residual structure and derive coefficients for pairwise species associations from it. These species associations (sometimes also called residual correlations) should then tell us whether a given pair of species co-occurs more or less often than expected by their environmental responses, and thus might be indicative of a positive or negative biotic relationship between those species.
High elevation forest habitat in the Swiss Alps.
However, already in very early discussions with collaborators from the fields of macroecology, statistics and ornithology, we were wondering about potential mismatches between the local scale at which interactions take place and the (often coarser) scale at which species occurrence data are available. If JSDMs were indeed able to separate biotic from abiotic signals in occurrence data, we hypothesized, scale mismatches should lead to a systematic change in JSDM estimates across different spatial resolutions. For example, two species might compete for nesting sites at the local scale while still preferring the same habitat overall, which should lead to a negative association at fine resolutions and a positive one at coarse resolutions. Initial simulation studies supported this intuition.
We used a very rich, long-term dataset of Swiss breeding birds from our collaborators at the Swiss Ornithological Institute Sempach. In this dataset, every breeding territory across a grid of more than 250 survey sites is marked during three visits per year, allowing us to define bird communities at varying spatial resolutions within a survey site. We benchmarked a few different JSDM implementations on the dataset and eventually settled for the one with the best balance between statistical flexibility and runtime efficiency. Nonetheless, the combination of multivariate, multi-level Bayesian models and large, long-term data turned out to be computationally quite challenging. The models at the finest spatial resolutions had a runtime of almost two weeks on a high-performance cluster, and every change in the methodology or model specification would require another two weeks of data wrangling.
However, once we had set up the models correctly and the MCMC algorithm did its magic, we were excited to analyse the results. To our surprise, they were not exactly as expected. Although we did find a moderate shift towards higher estimates of pairwise associations at coarser spatial resolutions, the majority of values were well above zero, indicating a positive spatial relationship among most species at most observational scales. Moreover, the estimates for a given species pair changed rather erratically from one resolution to another, so how exactly would you pinpoint the scale, at which estimates of species association accurately reflect a biotic interaction? We tried to do that by comparing the JSDM estimates to an independently derived matrix of pairwise functional similarity, assuming that functionally similar species should compete more strongly for resources and, thus, tend to have more negative values of species associations. Once again, our results surprised us by showing the exact opposite pattern: species with similar traits tended to have more positive species associations, especially at finer grain sizes. Overall, these results strongly suggested that JSDMs were not able to detect pairwise interactions among Swiss breeding birds in the analysed dataset, but rather that estimated species associations reflected common responses to unmeasured environmental gradients.
Although our findings challenge the notion that JSDMs can detect the signal of biotic interactions from empirical community data, we still think the underlying statistical reasoning is solid and, in principle, would be up for the task. The challenges seem to lie more in the collection of sufficiently dense ecological datasets and the implementation of sufficiently fast and accurate algorithms to deal with them. The ecological community is working hard to make progress on these fronts and we are thus hopeful that the JSDM approach will eventually help solving the elusiveness of biotic interactions in spatial data.
Written by: Christian König & Damaris Zurell Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
Antarctic lichens with different population history show grossly diverging genetic patterns.
Above: Antarctic lichens (Usnea) near Carlini station on King George Island, January 2016 (Elisa Lagostina).
The Antarctic is arguably the most remote place on Earth and difficult to reach for scientists and other organisms. In many people’s imagination it may just be a vast ice dome with scattered penguins along its margins. But in fact, it harbours isolated pockets of seasonally ice-free terrain with an amazing diversity of life. For lichenologists like us, Antarctica is a special place, because for once our favourites are not marginalized by vascular plants. They absolutely dominate the terrestrial landscape, as the photo above illustrates. This is of course due to the extreme environmental conditions, most of all low temperatures and a short vegetation period, which affect lichens to a much lesser degree than flowering plants. Lichens are symbioses between fungi and photosynthetic organisms. Most species can photosynthesize without liquid water when air humidity is high enough, some even at sub-zero temperatures. And when conditions get really tough, they can dry out completely and persist in a state of latent life.
Cover image article: (Free to read online for a year.) Lagostina, E., Andreev, M., Dal Grande, F., Grewe, F., Lorenz, A., Lumbsch, H.T., Rozzi, R., Ruprecht, U., Sancho, L.G., Søchting, U., Scur, M., Wirtz, N. and Printzen, C. (2021). Effects of dispersal strategy and migration history on genetic diversity and population structure of Antarctic lichens. J Biogeogr. 48:1635–1653. https://doi.org/10.1111/jbi.14101
Although Antarctica is the continent least affected by humans, it is no longer a pristine environment. Antarctic ecosystems are particularly threatened by global warming and ever increasing numbers of human visitors, both of which interact to increase the risk of invasive species being introduced. It is here that our project started. Most lichens have particularly wide distributional ranges. For example, the most common lichens of the Maritime Antarctic, Usnea antarctica and U. aurantiacoatra, had both been reported from southern South America as well. What seems to be good news at first view – the species are obviously able to cope with milder climatic conditions – could actually turn into a severe conservational threat, if warm-adapted genotypes from South America got a chance to outcompete their cold-adapted Antarctic neighbors. After all, the convention on biological diversity explicitly mentions genetic diversity as one of the fundamental elements of biodiversity.
Usnea antarctica on a stone on King George Island, the asexual species spread with soredia visible on the thallus. (Photograph by Elisa Lagostina.)
When we started this project, nothing was known about the genetic structure of Antarctic lichen populations or the extent of genetic exchange between isolated Antarctic regions and southern South America. In order to change this, we had to overcome two major obstacles. Sampling for population genetic projects in the terrestrial Antarctic is a nightmare, particularly within the framework of short-term projects. If you are lucky to get space on one of the few Antarctic research stations, you are basically stuck within a radius of at most 10-20 km and no chance to get access to any other station before the next season. The only workaround is to involve as many other lichenologists as possible into your project. We were extremely lucky that Austrian, Brazilian, Danish, Russian, and Spanish colleagues were more than willing to contribute to the sampling and managed to get their own projects funded.
The second obstacle was of a technical nature. Lichens are known to evolve slowly. DNA sequences usually show few differences and very rarely clear geographic patterns. We therefore decided to use SSR markers, which first had to be developed from newly assembled draft genomes. Designing the primers along genomic sequences of two closely related species offered the first nice surprise in this project: our more than 20 markers amplified extremely reliably and across species boundaries. In the end we had a data set almost without any gaps (“null alleles”). And because we were able to amplify the exact same loci in the two Usnea species, we could show once and for all that they were not conspecific as some (including the older one of us) had once assumed in the past.
Usnea aurantiacoatra on the ground in King George Island, the sexual species has big black Apothecia visible on the thallus. (Photograph by Elisa Lagostina.)
The third difficulty is typical for lichen studies but nevertheless caught us entirely unprepared. We had planned to study the two Usnea species along with two crustose lichens from the genus Placopsis to account for possible differences in growth form and reproductive mode. Usnea aurantiacoatra and Placopsis contortuplicata (lichenologists have a deeply rooted desire to create unpronounceable scientific names) reproduce sexually by ascospores, while Usnea antarctica and Placopsis antarctica use vegetative propagules, so-called soredia, to disperse both symbionts together. These four species are big and showy (for lichen standards) and had been reported from both sides of the Drake Passage. To our bewilderment, none of the U. antarctica look-alikes sampled in South America actually belonged to this species. Genetically, they all proved to be stunted forms of U. aurantiacoatra or its near relative U. trachycarpa. Apparently, the species had been wrongly reported from South America and is in fact an Antarctic endemic. Worse, we could not find the Placopsis species either. We decided to make a virtue out of necessity and adjusted our original sampling strategy to include Cetraria aculeata as an example of an asexually reproducing species. We had previously studied this species in various parts of the world including South America and the Antarctic and knew that it was disjunct between both continents. Moreover, we knew that it had colonized the Southern Hemisphere from the north in contrast to U. aurantiacoatra, which is not known further north than southern Chile and Argentina. This not only allowed us to assess the impact of phylogeographic history on regional patterns of genetic diversity but ultimately resulted in the detection of a crystal clear geographic pattern of genetic diversification and a more precise dating of a colonization event. The latter, by the way was also due to a reviewer nudging us to apply Approximate Bayesian Computation to compare different phylogeographic scenarios for our species.
We found evidence for glacial in situ survival of Usnea aurantiacoatra in South America and in the Antarctic, where also Usnea antarctica displays its highest diversity. Cetraria aculeata, on the other hand, colonized the Antarctic only after the Last Glacial Maximum from South America in at least three independent events. The good result for the Antarctic conservation is that we found no convincing evidence for ongoing gene flow from southern South America into the Maritime Antarctic. Nevertheless, maintaining the strong genetic differentiation of Antarctic populations of Cetraria aculeata requires strict conservation measures, whereas populations of Usnea aurantiacoatra are exposed to a much lower risk due to their higher diversity and connectivity.
So far our studies were focused entirely on the fungal partner of the symbiosis. One obvious way to proceed in the future is to study the algal partners of our species to see whether association with genetically different strands helps them to adapt to different ecological conditions. We already know that lichens can associate with genetically different partners and that lichen photobionts are shared among different species in the same habitat (“lichen guilds”). The implications of these phenomena must be very different in vegetatively and sexually reproducing species. This is another field, which has virtually not been studied in Antarctica and where we are almost certain to meet with surprising results. Grant reviewers, unfortunately, have so far not swallowed the bait. But as long as the Western Antarctic Ice Shield has not collapsed there is hope!
Cetraria aculeata from Bale Mts., Ethiopia. (Photograph by Christian Printzen.)
Written by: Elisa Lagostina, PhD Christian Printzen, Head of Cryptogams Section Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt/Main, Germany.
João Pedro (JP) Fontanelle is a postdoc at the Institute of Forestry and Conservation at the University of Toronto in Canada. He is an evolutionary biologist interested in how spatial and temporal eco-evolutionary dynamics affect micro- and macroevolution. Here, JP shares his recent work on how stingrays invaded the freshwaters and diversified in South American basins.
João Pedro (JP) Fontenelle getting ready to fish in the Amazon.
Institute. University of Toronto, Institute of Forestry and Conservation
Academic life stage. Postdoc
Major research themes. How changes in environmental properties and connectivity affect the evolution of organisms at micro and macroevolutionary scales, their biogeography, and diversification patterns.
The unique sunset of the Amazon river basin.
Current study system. The Neotropical freshwater stingrays (subfamily Potamotrygoninae) is the only extant lineage of elasmobranchs that is exclusive to freshwater environments. They are morphologically diverse, presenting beautiful dorsal color patterns, making them very famous in the aquarium trade. It is really interesting that this subfamily achieved a high diversity and a broad distribution across almost all South American basins in a relatively short period of evolutionary time (25-20 my). That is especially cool when we think they are a marine-derived lineage, meaning their closest related lineage is found in marine environments.
Recent JBIpaper. Fontenelle, J. P. Marques, F. P. L., Kolmann, M. A, Lovejoy, N. R. (2021). Biogeography of the Neotropical freshwater stingrays (Myliobatiformes: Potamotrygoninae) reveals effects of continent scale paleogeographic change and drainage evolution. Journal of Biogeography, 48(6), 1406-1419 https://doi.org/10.1111/jbi.14086
JP (left) and Jonas Batista (Instituto Mamirauá) getting ready to fish in the Amazon.
Motivation behind this paper. It started during my MSc back at the University of São Paulo in Brazil. I was working on the taxonomy of a species-complex of these stingrays (Fontenelle et al. 2017), and I started to notice the correlation between stingray species and their distribution patterns. To try to understand the processes that led to the diversification of these stingrays, I started reading more about the evolution of the group, and consequently the biogeography of Neotropical freshwater fishes, especially Lovejoy et al. (1998), Albert et al. (2006) and Albert and Reis (2011). It was fascinating to see the intimate relationship between fish groups’ diversity, South American geography, and the abiotic properties of the environment, such as water chemistry. Trying to understand a bit more about how environmental and landscape characteristics affect the evolution of freshwater lineages was the biggest inspiration for my PhD. For the stingrays, it was widely accepted that their lineage had invaded freshwater habitats through the Caribbean. However, there were still questions about the age of this event and how the group had colonized the rest of the continent. Fortunately, we were able to compile more than two decades of samples collected all over South America, which allowed us to investigate biogeographical patterns for the whole group at a continental scale.
Key methodologies. We first needed a phylogeny (relationship hypothesis tree) with a good taxonomic representation of the freshwater stingrays. We compiled the most taxonomic rich phylogeny to date, with molecular data from more than 350 specimens, accounting for over 90% of the species and sampling most of the group’s distribution. We then combined geological data and fossil evidence to calibrate key nodes in this phylogeny to produce an age hypothesis for the diversification of the group. Then, based on the literature on biogeographical areas for Neotropical freshwater fishes, we cross-referenced the distribution of our specimens to selected biogeographical areas of relevance. Finally, we reconstructed ancestral ranges over the phylogeny using six different biogeographical models and then tested their fit to our data. These models apply different parameters, such as dispersal, range expansion, vicariance, and extinction, to interpret the differences observed in reconstructed distribution patterns. Our dataset allowed us to identify changes in river connectivity over evolutionary time and how paleogeographical events were fundamental in the dispersal and diversification of the group.
Gentle trawling the bottom of the Rio Tapajós.
Unexpected challenges. One big challenge was how to interpret the ages and the reconstructed ancestral ranges for many nodes of the tree over such a large timescale and geographic area. We had to rely on geography and geology dense papers to identify and properly interpret the biogeographical patterns. These papers helped us narrow down and interpret major events for the biogeography of the stingrays and other fishes and aquatic groups with similar distributions. This led to another series of challenges regarding contrasting biogeographical patterns among different fish groups. By exploring the literature on different fish lineages, we were able to identify evidence for the same paleogeographical event affecting the fish community, but with different outcomes depending on the group. That is, the same paleogeographical event can influence the evolution of distinct groups in different ways, and this can be attributed to differences in their biology and evolutionary history.
Major results. We provided biogeographic evidence for major changes in the paleogeography of South America across 30 million years, especially for the Amazon and associated river basins, which can be used by many other biogeography studies. We presented evidence of how changes in the connectivity between and within river basins are very important to the diversification patterns of aquatic groups and how these changes may affect different freshwater groups differently. From a more fish-focused perspective, we have highlighted the importance of marine incursions on strict freshwater dominated regions for the adaptation and diversification of marine-derived lineages (MDLs) and the importance of the Pebas Mega Wetlands acting as a facilitating route for the dispersal of the stingray lineage and possibly other MDLs, from fishes like drums and pufferfishes, for example, to mammals, molluscs and even plants. It was really nice to interpret the biogeographic patterns and explain the colonization of the South American continent by this interesting group of fishes.
Retrieving longlines at dawn, after the stingrays feed time.
Next steps for this research. By extrapolating the results from this research, we are investigating macroevolutionary patterns involving biogeography, ecology, diversification, and phenotypic changes related to changes in environment and distribution. We are also working on how paleogeographic changes in the South American landscape have influenced the evolution of other fish groups and the signals in their phylogeny. Finally, we are exploring the relationships of these stingrays at a population level to study population dynamics and their relationship to taxonomic and phylogenetic diversity.
If you could study any organism on Earth, what would it be? The easy answer for that is fishes! They are fascinating solely by the fact that what we call ‘fishes’ covers more than half of the vertebrate diversity, and are found in a crazy variety of sizes, shapes and biologies. As one of my undergraduate professors used to say: “there is probably a fish example for that”. It is really hard to choose one group of fish, though. I’m particularly interested in rapidly evolving and diverse groups, and their relationship to changes in habitat; however that still accounts for a bunch of them!
A juvenile stingray in a basin for transportation (right); an adult stingray and its beautiful color pattern, fresh on the boat (left).
Anything else to add? This manuscript is the first published chapter of my PhD thesis. That adds an extra layer of satisfaction as this research is also one of the main reasons I pursued my PhD. I’ve been questioned before about how long it took us to get this manuscript in good shape and out. Still, all the years of intense work have been a real reminder of how difficult it is to work with a diverse group in a diverse area, especially when the evolution of the group is still not very well understood and the taxonomy is very complicated (which is the case of the Neotropical freshwater stingrays). It is great to provide a very important contribution to the study of these fish and the Neotropical region and its biogeography. It has been challenging from start to finish, but so worth it! We have learned a lot.
Chaim Lasmar is a postdoc at Universidade Federal de Lavras. He is an ecologist with a particular interest in ants and their contribution to ecosystem function. Chaim shares his recent work on the variable foraging behaviour of ants across large spatial scales and across different ecoregions in the neotropics.
Research themes. Community Ecology, Macroecology, Biogeography, Landscape Ecology, Ants.
Current study system. Ants play important roles in the ecosystem by interacting with several abiotic and biotic factors to obtain resources. Through their foraging activities, ants are important components of terrestrial ecosystems as seed dispersers, granivores, scavengers, predators and for the cycling of nutrients. Additionally, they are mega abundant and diverse, easy to sample and present different feeding habits and diets by consuming several nutrients such as sugar, amino acids, lipids and sodium. Therefore, they are an excellent model organism to understand diversity patterns such as foraging behaviours that may give us insights into the ecosystem functioning.
Recent paper in JBI. Lasmar, C.J., Bishop, T.R., Parr, C.L., Queiroz, A.C.M., Schmidt, F.A. and Ribas, C.R. (2021), Geographical variation in ant foraging activity and resource use is driven by climate and net primary productivity. J Biogeogr. https://doi.org/10.1111/jbi.14089
Motivation behind this paper. Studies in the lab and a few in the field have demonstrated how ants can change their resource use according to the climate and the availability of plant resources. However, most field studies have been performed at small spatial scales. The remaining large spatial scales studies mainly focused on effects of temperature and productivity in similar habitats or evaluated only a few resource types (e.g., sugar and amino acids or sugar and sodium). Thus, there are still knowledge gaps in terms of whether previous findings hold when assessing foraging behaviour at large spatial scales in different ecoregions. Thus, we decided to assess ant foraging behaviour at large spatial scales and in different ecoregions in the neotropics, which are generally poorly studied in terms of ant foraging behaviour.
Chaim placing baited tubes in the Cerrado savannah forest.
Key methodologies. We used a classic baiting approach to assess the influence of climate and productivity on ant foraging activity and resource use. We provided ants four types of resources, sugar, lipids, amino acids and sodium in 60 transects distributed in six Brazilian biomes that were distinct in terms of climate and productivity. By placing 1500 baited tubes for ants, we obtained estimates of overall ant foraging activity and we could also assess the relative use of each resource type in comparison to the other three. We also assessed the current weather and annual and monthly climate and productivity for each of our transects.
Major results. We made a step forward in our understanding of foraging behaviour by demonstrating how ant foraging activity and resource use was driven by climate and primary productivity at large spatial scales. We suggest that precipitation, temperature seasonality and productivity influence the availability of resources. This resulted in patterns of relative resource use that we considered largely as a trade-off between sugar (where energy availability was low), and amino acids and sodium (where energy availability was high). Temperature likely influenced relative amino acid and lipid use by acting on the physiology of ants. Given that ant foraging activity and resource use involves numerous biotic and abiotic interactions, we suggest that it is conceivable that global climate change and changes in productivity may shift these patterns in foraging behaviour. In turn, changes to foraging could result in changes in ant-mediated ecosystem functions.
Pheidole fracticeps workers (left) and Ectatommabrunneum (right) visiting baited tubes with a cotton ball soaked with lipids in Pantanal
Challenges overcome. Although I had a lot of fun traveling to, and experiencing, the Brazilian biomes, it was challenging to perform the fieldwork at some places. Our research required a huge sampling effort. Sometimes it was not easy to walk along a 750 m transect in the forest while carrying heavy bags full of baited tubes. Some study areas were in very remote places. In the Amazon, for example, there was no road to access the areas and we had to set all transects by foot. This research would not have been possible without the help of many other researchers in the field, and I would like to thank them for their efforts.
Next steps. There are some remaining knowledge gaps concerning the foraging behaviour of ants at large spatial scales. Ant foraging activity is intimately liked to species richness and we were not able to disentangle the direct influence of ecological drivers on foraging activity from the influence of ant species richness. Additionally, it is known that ant resource use also changes across different habitat strata at local scales. Thus, disentangling the relationship between ant species richness, foraging activity and their relation to ecological drivers across habitat strata will certainly contribute to understanding ant foraging behaviour.
Pampa forest habitat.
If you could study any organism on Earth, what would it be? Well, I think I am very satisfied studying ants and intend to keep studying them for a long time. Recently I started to study (besides ants) other invertebrates (e.g., other insects and spiders) and large mammals, which I also enjoyed. But it would really be great if one day I could also study trees to comprehend more broadly the ecosystems through different taxa.
Anything else to add? As ecologists, we are used to travelling to incredible wild places all over the world, as we try to understand the systems and processes of our natural environments. Yet once our fieldwork is done and our samples are collected, we leave little for the people who live in and around the natural areas we have visited. It was with this in mind that, in addition to our ecological data collection on ant communities in protected areas, we also included scientific dissemination of our work to local people living around these areas. We targeted rural and municipal schools, speaking to students about the importance of biodiversity conservation in Brazil and highlighting the significant role ants play in the ecosystem. We feel this is critical work, particularly as we face a strong wave of science denialism and because Brazil hosts between 15-20% of the world’s biodiversity which has been under severe attacks.
Arthur Boom is a PhD student at the Université Libre de Bruxelles. He is interested in the biogeography of African plants and the application of genomic approaches to study their evolutionary. Arthur shares his recent work on trees from the Brachystegia genus to understand the history of miombo woodlands in Africa through sequencing of their plastid genomes.
Institute. Evolutionary Biology & Ecology unit, Université Libre de Bruxelles (Belgium)
Academic life stage. PhD student.
Research themes. Phylogenomics, Phylogeography, and Biogeography of African plant taxa.
Current study system. My co-authors and I are currently studying the evolutionary history of Brachystegia tree species. This genus is particularly emblematic of southern African savannas and woodlands. With roughly twenty species, it is one of the most dominant tree genera in the vegetation belt stretching from Angola to Tanzania: the miombo woodlands (c. 2.7 million km²). Additionally, eight Brachystegia species are also distributed in the African Guineo-Congolian rain forests. This spatial distribution and diversity of species allow the investigation of global biogeographical questions. Namely, how, and when, tree species diversified in African biomes and how plant lineages may have shifted between biomes. Consequently, Brachystegiaas as a broadly distributed genus is a useful system to explore the onset of current African biodiversity. However, Brachystegia is also a taxonomically challenging taxon to work with, as several species are morphologically variable in addition to having blurred species boundaries. Little is known about what influences patterns of morphological variation for these species and may be due either to hybridization, ecotypic differentiation, or phenotypic plasticity.
Recent paper in JBI. Boom, AF, Migliore, J, Kaymak, E, Meerts, P, Hardy, OJ. Plastid introgression and evolution of African miombo woodlands: New insights from the plastome‐based phylogeny of Brachystegia trees. J Biogeogr. 2021; 48: 933– 946. https://doi.org/10.1111/jbi.14051
Motivation behind this paper. Molecular-dated phylogenies using either large taxonomic coverage, or focusing on some key plant taxa, are essential to understand the tempo and modalities of species diversification. In plants, such phylogenetic investigations have been extensively conducted in Europe and northern America, such that generation of major phylogeographic hypotheses on factors affecting lineage diversification in plants are geographically biased. In the Afrotropics, we are increasingly testing these hypotheses developed on other continents to determine their global generality. In comparison to Europe/northern America, African woodlands and savannas are still poorly investigated despite their wide spatial distribution, their functional properties and unique biodiversity, and their key role in Hominid evolution. Brachystegia genus is typical, dominant, and diverse in the miombo woodlands of Africa and is a potentially useful system to gain new insights on the history African savannas and woodlands. We aimed to explore the phylogenetic relationships and corresponding divergence timing at the genus scale among Brachystegia species.
Some of the specimens that were collected in the frame of this study (A, B, and C: Brachystegia spiciformis, B. longifolia and B. boehmii). In addition to herbarium vouchers, we also collected leaflets and dried them using silica gel (in D, left to right: B. spiciformis, B. longifolia and B. taxifolia). DNA is generally better conserved using the latter approach.
Key methodologies. Our approach used African field collections and herbarium vouchers in combination with high-throughput sequencing technologies. We took advantage of recent advances in molecular biology to extract DNA from ancient plant material and to assemble plastid genomes of 25 different Brachystegia tree taxa. Bioinformatic tools were thus essential to reconstruct the Brachystegia plastid phylogeny, using Bayesian and Maximum-Likelihood methods. To infer the temporal dynamics of Brachystegia diversification, we conducted a two-step dating approach. Firstly, a dated phylogeny covering the Fabaceae family allowed the use of multiple fossils for time calibrations and to estimate the divergence time between Brachystegia and a near-relative genus, Julbernardia. We then applied this divergence time estimate to calibrate the Brachystegia plastid phylogeny.
Major results. Our main contribution is a proposed scenario for the past history of Brachystegia settlements, allowing us to better understand the history of miombo woodlands. In our JBI paper, plastid genomes proved to be very informative for tracking the past dynamics of the genus Brachystegia. In southern Africa, Brachystegia plastid clades appear older in eastern regions than in western ones, suggesting a possible historical westwards expansion of miombo vegetation, during the Plio-Pleistocene. Our results bring explicit insights of the past distribution of one of the largest African woodland types.
Unexpected outcomes. We were particularly surprised that the Brachystegia clades revealed by the plastid phylogeny exhibited a strong geographical structuring independently of their species delineation. Specimens from the same species were rarely monophyletic, except when they were geographically close. This unexpected tree topology could be explained by hybridisation with subsequent backcrosses. This highlights possible cytoplasmic introgression between species that co-occur in the same area and share closely related plastid genomes. To our knowledge, our study is one of the first to report such a phenomenon of spatially dependent introgression in a tree genus from the Afrotropics, but such introgression has been observed in Quercus and Eucalyptus trees in Neartic, Paleartic and Australasian realms.
(left) Miombo woodlands have a closed but not overly dense canopy, allowing the growth of an herbaceous layer. They are dominated by trees such as Brachystegia, Isoberlina, and Julbernardia (Lubumbashi surroundings, Democratic Republic of Congo). (right) Collection of branches and leaves from a Brachystegia tree using a long-reach pruner.
Next steps? Using plastid genomes, we now have a better view about the miombo spatial and temporal dynamics. However, further investigations are needed to provide a dated species phylogenetic tree of the Brachystegia species. We are thus currently sequencing several hundred low-copy nuclear genes, using a targeted enrichment genomic approach. Additionally, by increasing our geographical cover, we would like to deeply investigate the Brachystegia genus developing continuous phylogeographic and phylodynamic inferences using additional plastid sequences. Such investigations would be conducted in a comparative framework using other emblematic trees from miombo woodlands such as Julbernardia and Isoberlina.
If you could study any organism on Earth, what would it be?Without surprise, if I could study any organism on Earth, it would be trees! Through my ongoing PhD thesis, I was particularly surprised by the large knowledge gaps in the phylogeographic history of trees! I am especially interested in tropical trees, which are poorly studied despite their ecosystem engineer role in most of the hotspots of biodiversity. Among the questions coming to my mind: how do tropical and dominant trees diversify? How is such diversity maintained through time? These questions reflect a more global interest on hybridisation and the concepts of plant species. Oaks are particularly interesting in this context as recent genomic and ecological investigations have broader implications on how dominant trees diversify, coexist, cooperate and compete. I am also convinced that tropical taxa can be very promising in evolutionary ecology. Apart from plants, I am also fond of jellyfish, bumblebees, and dinosaurs!
Anything else to add? Collecting plant materials from tropical African species, like Brachystegia, distributed on such a wide spatial scale (18 countries), including narrowly and disjunctly distributed taxa was definitively a challenging aspect of this study. It was also a unique opportunity to discover unforgettable landscapes in Democratic Republic of Congo, to explore precious herbarium collections (BR, BRLU, FHO & LISC), and to develop innovative genome skimming sequencing. Even fairly old vouchers can be of use with such an approach. Indeed, one of the samples used in this study was collected in 1933! Finally, we were helped in many ways during this study, and I’d like to take the opportunity to thank all the people that made this study feasible, researchers, those involved in the field collections, curators and lab colleagues.
Felip Camurugi is a postdoc at Universidade Federal do Mato Grosso do Sul. He is a biogeographer with an interest in anurans and their diversity. Felipe shares his recent work on gladiator treefrogs from South American and his tests for the presence (or absence) of cryptic lineages in this species.
Felipe Camurugi in the field, collecting herps. Photo credit: Sandro Paulino.
Institute. Universidade Federal do Mato Grosso do Sul
Academic life stage. Postdoc
Current study system. My main research focus is to explore the roles of landscape heterogeneity on the genetic divergence of anurans from open and dry environments of South America. The gladiator treefrog, Boana raniceps, is distributed at a continental scale, occurring in lowlands of the South American open and dry formations. Therefore, it is an interesting organism to study how past and current landscape changes can affect species’ distributions and gene flow across these environments. In addition, Boana raniceps is a generalist species associated with lentic water bodies of almost all major river basins, which enables the testing of several hypotheses on diversification in the Neotropics.
Recent paper in JBI. Camurugi, F., Gehara, M., Fonseca, E.M., Zamudio, K.R., Haddad, C.F., Colli, G.R., Thomé, M.T.C., Prado, C.P., Napoli, M.F. and Garda, A.A., 2021. Isolation by environment and recurrent gene flow shaped the evolutionary history of a continentally distributed Neotropical treefrog. Journal of Biogeography. 48: 760-772 https://doi.org/10.1111/jbi.14035
Motivation behind this paper. The seasonally dry tropical forest Caatinga, the Cerrado savanna, and the Chaco have a complex geomorphological and climatic history. Only in the past few years have we begun testing the main promoters of genetic divergence and testing new hypotheses about diversification processes for the region. Given the wide distribution of Boana raniceps, which occurs across a broad environmental gradient, we were curious as to whether this “species” actually exhibited cryptic diversification (undescribed species forming a species complex), or, conversely, was an uncommon case of an anuran species with a broad, continental-level distribution. Additionally, this species provided a good system to test classical biogeographic hypotheses of how landscape features have shaped historical and contemporary patterns of genetic variation.
Gladiator treefrog (Boana raniceps) in northeast Brazil.
Key methodologies. The combination of phylogeographic and landscape genetics tools has increased in the past few years, providing new opportunities to disentangle the relative roles of historical and contemporary processes of landscape changes on connectivity and genetic diversity among populations, and divergence among species. Using several complementary approaches, such as population assignment tests, species distribution models, approximate Bayesian computation, and niche comparisons, we could identify the geographical break of lineages and infer the main mechanisms involved in the processes of population/species diversification.
Major results. Our study suggests that the evolutionary history of the gladiator treefrog, Boana raniceps, was mediated by climatic shifts during the Pleistocene and topographic complexity in central Brazil. We identified two lineages that occupied different environmental niches. These lineages diverged during the mid-Pleistocene (~340,000 years ago) and kept gene flow until Last Glacial Maximum (LGM: ~21,000 years ago). During the dry and cold periods, such as the LGM, areas facilitating connectivity between populations probably shrank, reducing historical gene flow. In addition, Boana raniceps lives in lowland areas, which means that areas with a very complex topography may have hindered the migration of individuals over thousands of years, and together with the contraction of open and dry biomes during LGM, have reinforced the genetic differences within this species. Areas with this profile are located, for example, in the Brazilian Central Plateau region, which coincides with the geographical division between the two lineages. However, the environmental factors that restricted gene flow over years were clearly semipermeable, as the overall genetic divergence among populations was shallow.
Landscapes of open and dry environments of South America: Caatinga.
Challenges and unexpected outcomes. To evaluate divergence among populations of Boana raniceps, we of course needed to obtain specimens from across most of the South American continent! This involved collaborations across many institutes to obtain samples covering most of the species’ distribution. In the end, we obtained a collection of approximately 300 individuals at 115 localities encompassing four countries. Anurans typically have high phylogeographic structure due to their life history strategies, such as a tendency towards philopatry and expected low dispersal ability. Consequently, species of frogs widely distributed are frequently expected to potentially show high levels of cryptic diversity. We were surprised to find that in South American, B. raniceps is a single species that is widely distributed across the continent. Despite evidence of unique, spatially structured lineages, the amount of divergence was weak and shallow. Therefore, this pattern of intense and recurrent gene flow in a highly complex landscape was unexpected.
Landscapes of open and dry environments of South America: Chaco.
Next steps of this research. The acoustic communication in anurans is an important component in the evolution of these organisms. Thus, the next step in this research is to investigate whether does trait divergence correlates with genetic divergence and whether sexual selection can have reinforced the geographic structure in Boana raniceps. Testing whether B. raniceps females prefer calls from males of their own lineage, or if they can mate indiscriminately, can give us a clue if behavioral isolation is a possible driver of genetic differentiation, in addition to landscape features.
If you could study any organism on Earth, what would it be? I would continue to study amphibians! I am very curious about salamanders. In South America, they are relatively less diverse but still little studied. Since I saw my first Bolitoglossa salamander in the Brazilian Amazon, I’ve wondered about the ecological and historical factors that have shaped the evolutionary history of the genus in the continent. However, my curiosity about salamanders is not regionalized and it would be really cool to study them in any part of the globe.
Water bodies where Boana raniceps can typically be found.
Anything else to add? This research is part of my thesis on the biogeography and evolution of acoustic signals of Neotropical anurans, particularly the gladiator frogs of the Boana albopunctata group. Besides biogeography of amphibians at different scales (from taxa, lineages, and genealogies, for example), the frog calling behavior and its consequences on the evolutionary histories of species is a thrilling theme for me, and having water up to my waist whilst recording and collecting frogs always makes for a great time in the field. Currently, I am combining my interests in the natural history of amphibians with genetic data to explore the roles of landscape features and biotic interactions as drivers of genetic divergence at a community level.