Featured

Introducing: Journal News

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. The journal 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.

To attain these goals, we made several changes at the journal since September 2019:
Cover Image: published for free to highlight research in each issue
Editors’ Choice: will be ‘full access’ for two years at no cost to the author
– Social media: new team to increase visibility and achieve broader reach
– Updated our statement of the journal’s scope

Other improvements are in the works. Watch for announcements in the coming months.

Featured

Introducing: Featured Researchers

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, jbiogeography@gmail.com. To help you get started, the questionnaire is provided below. Check out recent contributions for examples and ideas!

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Questionnaire format:

Name

Links to social media and/or personal website(s)

Institute

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.

Featured

Introducing: Highlighted Papers

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.

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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.

Life in the “dead heart” of Australia

It was the desolation of Australia’s deserts and dried-up rivers, contrasted with the fossil legacy of giant extinct marsupials and birds, that led the British explorer JW Gregory to label this region ‘the dead heart of Australia’. In fact, despite its harsh and unforgiving climate, the Australian deserts are teeming with life.

Above: The red desert sands of a vegetated dunefield in the Great Victoria Desert near Yulara in the Northern Territory, Australia (photo credit: Stephen Zozaya)

The Australian arid zone comprises more than 70% of the continent and is one of the largest arid systems in the world. In much of the literature, the arid zone is drawn as a homogeneous blob in the center of Australia – a rough oval shape comprising the “deserts”. Indeed, the topography of the region is generally subdued and superficially featureless. But anyone who has visited or flown over the center of Australia will know there are isolated rugged mountains in the northwest, center and south – flat topped mesas and razor-back ridges that rise up from the surrounding lowlands, they conjure up quintessential images of the Aussie outback, glowing red in the late afternoon sun. Even the vast intervening desert lowlands, far from being homogeneous, comprise a discontinuous mosaic of sandy dunefields with unwaveringly consistent longitudinal dunes, stony gibber deserts, clay plains, ephemeral rivers and salt lakes.

Cover image article: (Free to read online for a year.)
Pepper, M, Keogh, JS. Life in the “dead heart” of Australia: The geohistory of the Australian deserts and its impact on genetic diversity of arid zone lizards. J Biogeogr. 2021; 48: 716– 746. https://doi.org/10.1111/jbi.14063 

It was the desolation of the deserts and dried-up rivers, contrasted with the fossil legacy of giant extinct marsupials and birds, that led the British geologist and explorer JW Gregory to label this region ‘the dead heart of Australia’. In fact, despite its harsh and unforgiving climate, and contrary to Gregory’s unflattering description, the Australian deserts are teeming with life. I have been working with Scott Keogh on the evolutionary history of lizards in the Australian arid zone for 16 years – the diversity of lizards here is higher than anywhere else on earth! My original training as a geoscientist has been instrumental in driving my research towards understanding how changes in the landscapes and climate across Australia over the past 15 million years have structured genetic diversity between and within species that live here. Over this relatively short period of geological time, previously wet and humid landscapes across Australia were radically transformed. The late Cainozoic saw wide-scale contraction of tropical and temperate forests, unprecedented levels of erosion, cessation of major drainages and the disappearance of extensive inland lakes, with intensifying aridity culminating in the development of dunefields across most of the central continent.  How has this geohistory of the Australian desert landscapes harbored and structured the diversity in plants and animals that we see today? Which areas of Australia’s deserts have the most biodiversity? Which areas have the least? And how old (or young) are the species that live there?


Stony desert country with flat-topped mesas from the Kanku-Breakaways near Coober Pedy in South Australia

(photo credit: Damien Esquerré)

The very cool thing about working on the biogeography of the Australian arid zone is that the mountain range systems here are ancient – they have been geologically stable for a hundred million years, which means the contribution of geological uplift to speciation is negligible. Trying to understand speciation processes and drivers is hard enough, so removing mountain building from the speciation equation simplifies things immensely (as a comparison, our close neighbor New Zealand has built its enormous mountain ranges in the last 5 million years, so you can imagine the impact this would have had/has on organisms evolving there!). Equally cool about the Australian landscapes is that the vast deserts that dominate the interior of the continent are thought to have formed as recently as one million years ago during the height of the Pleistocene glacial cycles. This complete transformation of landscapes across so much of the continent would have had unprecedented consequences on the evolutionary history of plants and animals living there  – some would have gone extinct, unable to tolerate the drier and more inhospitable conditions. To survive, others would have been forced to contract their distributions to wetter, more climatically stable areas where they could persist (typically mountainous regions) until arid conditions eased. Other more generalist species may have been preadapted to aridity and sand and instead were able to expand their distributions and diversify in these new environments.

Currently we don’t know very much about the evolutionary forces at play in Australia’s deserts (compared to those in Australia’s forested fringe). It is amazing what the genes of living species can reveal about the evolution of ancestors that haven’t existed for millions of years. However, without knowledge of past landscape and climate change in Australia’s deserts, evolutionary biologists cannot make sense of the genetic patterns they see in the plants and animals today.  As the geohistory of Australia’s arid zone is not widely understood by biologists, we wanted to review its geological development and contemporary landscapes in an accessible way (not many biologist want to spend their time deciphering the lingo of the geology literature!), and in doing so we describe a series of biogeographical hypotheses centered on how geomorphology, evolutionary history and contemporary ecological factors interact to shape diversification patterns in Australia’s desert lowlands.


An aerial drone photo of vegetated dunes in the northern Simpson Desert in the Northern Territory
(photo credit: Paul Hesse)

The main message from our review is that for much of Australia’s biota living in the broad centre of the continent, their deeper history was shaped by an environment characterized by vast fluvial systems, feeding enormous volumes of water into permanent mega-lakes and transporting large quantities of sand across the landscape. This extensive surface water dried out first in the west, and elsewhere fluvial systems switched to an ephemeral state and progressively became saline. But wet pulses in history would have reactivated these inland rivers from time to time as precipitation waxed and waned with glacial cycles (even during the driest period in the Last Glacial Maximum there were large rivers in the southeast and enhanced run-off from the highlands). When they were dry, their sand filled valleys could be blown out by wind, forming extensive sandplains across the continent that would have been stabilized by a vegetation progressively shifting to dry woodlands, and open shrublands and grasslands. Geochronological evidence suggests that the formation of dunefields began in the mid-Pleistocene, accelerating as the climate became increasingly arid in later glacial cycles. These dunes reflect episodic accumulation, and patchy, rather than widespread, activity, so the deserts in Australia never looked like the vast mobile dune landscapes of the Sahara. With this in mind, it becomes more apparent how species could have persisted and diversified in the arid zone despite the enormous and turbulent climatic changes of the Pleistocene. Indeed, human populations were faced with the same severe climatic conditions, and likely responded in a similar way. From renowned Australian archaeologist Mike Smith: “… if we take the desert as a whole, the archaeological evidence is more consistent with a pattern of widespread ‘cryptic’ refugia than with a geographic division into refuges, corridors and barriers. People appear to have survived across much of the desert, but as scattered occurrences and at low densities—in effect, in pockets of microhabitat. Some regions may have been abandoned, including some areas of sandy desert and parts of the Pleistocene coast, but direct evidence for abandonment of large parts of the interior is more limited than once thought. ‘Each desert has its own barriers, corridors and refuges,’ says Cane, ‘and one should look to this inner variability in order to understand the true nature of desert colonization and settlement’ (1995:49)”.

We hope that our review and the hypotheses we outline stimulate further studies of arid zone biogeography. In particular, we look forward to the ways in which future biological collections will open the vast “dead heart” of the continent, to further our understanding of how life has been able to persist and flourish amidst the formation of the largest desert in the Southern Hemisphere.


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The quintessential Australian arid zone lizard, Moloch horridus 
(photo credit: Damien Esquerré)

Written by:
Mitzy Pepper
Postdoctoral researcher, Division of Ecology and Evolution, The Australian National University

Additional information:
https://keoghlab.com/
https://sites.google.com/site/drmitzypepper/about-me
Twitter: @Keogh_Lab

ECR Feature: Josep Padullés Cubino

Josep is a postdoc in the Department of Botany and Zoology at Masaryk University. He is a biogeographer and macroecologist interested in plants and their community structure. Josep shares his recent work on developing maps of phylogenetic structure of plant communities across Europe.

Josep Padullés Cubino with Mediterranean sclerophyllous evergreen forests in the back (Mare de Déu del Mont, Catalonia; Author: Laura Guerrero).

Name. Josep Padullés Cubino

Personal links. ResearchGate | Orcid | Twitter | GoogleScholar

Institute. Department of Botany & Zoology, Masaryk University, Brno, CZ

Academic life stage. Postdoc.

Research themes. Plant biogeography and macroecology, both in natural and anthropogenic habitats.

Current study system. I study forest plant communities across all Europe. Forests represent up to 40% of Europe’s land surface making it important to understand their ecology and biogeography. Our recent study was novel because until then most studies examining the phylogenetic structure (i.e., the degree of species phylogenetic relatedness) of forest plant species had either focused on specific clades or life forms (mainly trees), and used either floras or regional checklists, thus omitting the effect of fine-scale processes, such as species interactions, at the plant community level. Our study was the first providing maps of the phylogenetic structure of forest plant communities at the European scale.

Recent paper in JBI. Padullés Cubino, J., et al. 2021. Phylogenetic structure of European forest vegetation. Journal of Biogeography, 48, 903-916. https://doi.org/10.1111/jbi.14046.

Mediterranean evergreen Quercus suber forest with accompanying shrubs (e.g., Phillyrea angustifolia, Pistacia lentiscus, Myrtus communis) in Lago di Burano, Italy (Author: Gianmaria Bonari).

Motivation behind this paper. We used vegetation-plot data from the European Vegetation Archive (EVA; http://euroveg.org; Chytrý et al., 2016, Journal of Vegetation Science), which has recently been launched and contains more than 1.5 million vegetation plots sampled across Europe. This, along with environmental data and novel analytical methods and tools, has created unprecedented opportunities for exploring fine-scale patterns of phylogenetic structure at large spatial scales and understanding their determinants. Studying these spatial patterns and relationships is important because they provide insights into the mechanisms that determine the coexistence of specific groups of plant lineages and help us explain why some lineages (and not others) thrive under certain environmental conditions at certain locations. Furthermore, while we have a relatively good understanding of the spatial patterns and drivers of plant species richness in European forests, less is known about their phylogenetic structure. Our study can be used to compare hotspots of species richness and phylogenetic diversity across Europe, and serve as a basis for more regional or local-scale studies.

Mediterranean Pinus pinaster forest with Erica arborea and Calluna vulgaris in the understory in Monticiano, Italy (Author: Gianmaria Bonari).

Key methodologies. To investigate the phylogenetic structure of European forest vegetation, we considered alternative metrics either sensitive to basal (ancient evolutionary dynamics) or terminal (recent dynamics) branching in the phylogeny. Then, we compared the observed values of these metrics against the expected values obtained from a null model. As a result, we classified vegetation plots with respect to the phylogenetic relatedness under random expectations: (1) those that did not differ from random expectations; (2) those with more closely related species than random (phylogenetic clustering); and (3) those with more distantly related species than random (phylogenetic overdispersion). We also determined what plant lineages where overrepresented in particular forests across Europe, and tested factors that might drive phylogenetic clustering. The general expectation was that increased environmental stress combined with phylogenetic niche conservatism would select for a subset of closely-related (clustered) lineages adapted to these extreme environments.

Temperate oak-hornbeam (Quercus petraeaCarpinus betulus) forest with Galanthus nivalis in the Moravian Karst, Czech Republic (Author: Milan Chytrý).

Unexpected outcomes. One challenge was to deal with the large amount of data. We initially had more than 140,000 vegetation plots in our dataset. We resolved it by performing stratified resampling of the plots throughout the study area, which allowed us to use a smaller yet still representative dataset. The calculations of the metrics of phylogenetic structure were also computationally demanding. Luckily for us, some recently developed R packages, like ‘PhyloMeasures’ (Tsirogiannis & Sandel, 2016; Ecography), made our lives easier.

Major results. We found that plant species in forests located in areas with higher climatic stress and instability were more phylogenetically related than random (i.e., more phylogenetically clustered). Clustered forest communities also occurred in Fennoscandia, particularly in areas that were glaciated during the Pleistocene, likely reflecting limited postglacial migration of certain plant linages after deglaciation. In contrast, forest communities whose plants were more distantly related than random (i.e., phylogenetically overdispersed) were relatively common in the hemiboreal zone in Russia, which could reflect the effect of the transition between the boreal and temperate biogeographical regions. Overdispersed forest communities were also relatively more common in some areas around the Mediterranean Basin, which partially overlapped with areas considered as refugia for many lineages during the Pleistocene glaciations. We also found that the families Ericaceae, Poaceae and Fagaceae were overrepresented in forests in different regions in Europe.

Hemiboreal spruce forest with Picea abies in Norra Kvills National Park, Sweden (Author: Milan Chytrý).

Next steps. We are now exploring how different axes of plant trait variation (i.e., the leaf economic and plant size spectra) differ in forest understories across Europe. Forest understories play a vital role in ecosystem functioning (e.g., litter decomposition and nutrient cycling) and the provision of ecosystem services (e.g., habitat provisioning, tree regeneration, and pollination). We believe that combining both studies (i.e., phylogenetic vs. functional diversity) will give us a better understanding of the biogeography of European forest plants. We are also planning on applying our approach to other European habitats such as grasslands or shrublands.

If you could study any organism on earth, what would it be and why? I like to think of life on Earth as a complex network of interactions among different organisms. Ideally, I would like to investigate more about these interactions, particularly between plants and fungi, and between plants and humans, in both directions. I have a special predilection for Mediterranean plants, the region where I am originally from.

Anything else? This project was like a dream come true. I am honoured that I had the opportunity to work with these data. Many people before me had spent a lot of time to collect it and put it together. Furthermore, I felt like I owed this effort to the forests. I always go to the forest when I need to relax and recharge my batteries. It is where I feel most connected to the Earth.

Hotspots and diversity patterns of Arabian squamate reptiles

While some areas of the world are renowned for their high diversity of life, such as the tropics, others, such as deserts, are generally perceived as deprived of diversity. This is, however, very far from the truth.

Above: The Saudi Dwarf Gecko, Tropiocolotes wolfgangboehmei, whose phylogenetic position was unknown until our study. Picture by Al Faqih Ali Salim.

Biodiversity is not distributed evenly across the world and understanding the factors that generate common patterns is of fundamental importance to the study of evolutionary biology. While some areas of the world are renowned for their high diversity of life, such as the tropics, others, such as deserts, are generally perceived as deprived of diversity. This is, however, very far from the truth. Deserts all over the world are abundant with species that are perfectly adapted for their harsh environmental conditions.

Cover image article: (Free to read online for a year.)
Šmíd J, Sindaco R, Shobrak M, Busais S, Tamar K, Aghová T, Simó-Riudalbas M, Tarroso P, Geniez P, Crochet P-A, Els J, Burriel-Carranza B, Tejero-Cicuéndez H, Carranza S (2021). Diversity patterns and evolutionary history of Arabian squamates. Journal of Biogeography, 48: 1183–1199.https://doi.org/10.1111/jbi.14070 

Deserts tend to be very difficult to access for researchers and Arabia is no exception to this rule. Although we have been studying various aspects of the diversity of Arabian squamates for more than fifteen years now, from conducting exhaustive field trips, collecting new genetic, environmental, and distribution data, revising the taxonomy and systematics of many groups, to continuously discovering new species along the way, we felt that a broader picture was still missing.

To understand the general patterns, evolutionary history, and drivers of the diversity of Arabian squamates we compiled all available distribution records to derive range maps for all the species, and we reconstructed their evolutionary relationships. This included species that had been known only from their taxonomic descriptions (like the Saudi dwarf gecko, Tropiocolotes wolfgangboehmei, depicted here) or species that have not yet been formally described. This allowed us for the first time to produce a detailed map of squamate species richness of the Arabian Peninsula. By including the evolutionary component, we were able to identify main hotspots where long evolutionary history is concentrated. We found that the mountains that rim the peninsula support rich and unique communities that are dominated by local radiations. In particular, the Asir Mountains of southwestern Arabia, the Dhofar Mountains of extreme eastern Yemen and southern Oman, and the Hajar Mountains of northern Oman and UAE show unprecedented levels of squamate endemism and phylogenetic endemism. The mountains can thus be viewed as diversification hubs that generate new species and maintain their high diversity. The deserts in the interior of the Arabian Peninsula are generally inhabited by widely distributed generalist species.


In suitable habitats, some lizard species can attain high local population densities, like the endemic Sharqiyah Toad-headed Agama, Phrynocephalus sakoi, from the Sharqiyah Sands, Oman. Picture by Jiri Smid.

How can the mountains harbor so many species when they cover only a minor part of Arabia in sharp contrast to the vast inland deserts? The key variable seems to be topographic complexity or, in other words, heterogeneity of different environments. Heterogeneous environments provide a large number of available habitat types and thus numerous opportunities for niche partitioning, population isolation, allopatric speciation, and ultimately the coexistence of multiple divergent lineages.

Our study not only sheds light on the processes that have helped to generate and maintain the diverse and unique fauna of Arabian squamates, but it may also be used to direct future conservation efforts that would focus on the preservation of the evolutionary history of the Arabian fauna.

Written by:
Jiri Smid; Associated Researcher; Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
Mohammed Shobrak; Professor; Department of Biology, Faculty of Science, Taif University, PO Box 11099, Taif 21944, Saudi Arabia
Salem Busais; Associated Professor; Department of Biology, Faculty of Education, University of Aden, Aden, Yemen
Karin Tamar; Postdoc; Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
Johannes Els; Head of Department; Herpetology and Freshwater Fishes, Environment and Protected Areas Authority, Sharjah, UAE
Bernat Burriel-Carranza; PhD student; Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
Salvador Carranza; Director; Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain

Additional information:
Jiri Smid: https://scholar.google.cz/citations?user=vsAjzyYAAAAJ&hl=en
Mohammed Shobrak: https://scholar.google.com/citations?user=-SsOYv0AAAAJ&hl=en; @mshobrak; https://www.facebook.com/mshobrak
Salem Busais: http://www.arbiodiversity.academia-srt.net/; https://scholar.google.com/citations?user=yv4t5B0AAAAJ&hl=en; @SBusais
Karin Tamar: https://scholar.google.co.il/citations?user=j_Nx_5oAAAAJ&hl=en&oi=ao
Johannes Els: https://scholar.google.cz/citations?user=h3sJUiYAAAAJ&hl=en&oi=ao
Bernat Burriel-Carranza: https://scholar.google.es/citations?user=k1QIuk4AAAAJ&hl=es
Salvador Carranza: http://molevol.cmima.csic.es/carranza/index.html; https://scholar.google.es/citations?hl=en&user=AOP1VxMAAAAJ&view_op=list_works&sortby=pubdate

Connections between ploidy and environment in South American frogs

Polyploid frogs occur mainly in the SE corner of South America to the apparent exclusion of closely related diploids, a trend that persists across genera.

Above: Occurrences and range maps of all the frogs included in the study,
grouped by genus and colored by ploidy

Genome duplications are one of the most extreme mutations that can be found in nature. Lineages that undergo genome duplication (called polyploids) experience traumatic changes on the molecular and cellular level that are known to incur significant fitness costs. However, the increase of genetic material also provides the opportunity for adaptation. Polyploids experience more mutations per gene, allowing now-redundant gene copies to develop new functions. The various potential costs and benefits of genome duplication combine to create a unique evolutionary trajectory for polyploids. In particular, many polyploid species are known to inhabit new, challenging or disrupted environments that are subject to greater environmental extremes than experienced by their diploid counterparts. For example, polyploid species are often found in areas that have been recently glaciated and they also make up a large proportion of invasive plant species.

Editors’ Choice article: (Free to read online for a year.)
David, K.T. and Halanych, K.M. (2021), Spatial proximity between polyploids across South American frog genera. J Biogeogr. 48: xxx–xxx. https://doi.org/10.1111/jbi.14067 

Much of my PhD dissertation work focuses on the evolutionary consequences of gene and genome duplication on the molecular level, but while reading I started to become more interested in this relationship between environment and ploidy. I decided to focus my investigation on frogs, a group with lots of publicly available locality data, and restrict my search to South America which has a large number of polyploid frog species across multiple clades.

The preliminary results were striking. Not only were polyploid and diploid species ranges largely separate from one another, there seemed to be a recurring pattern across genera of polyploid lineages occurring in the southeast region of the continent. To us, this suggested a particular environment that was conducive to the formation and/or maintenance of polyploid species. This pattern was corroborated with range overlap analysis which indicated greater overlap between polyploid lineages than diploid lineages across the phylogeny. Indeed, on average polyploid species occur closer to other polyploids of different genera than they do to diploids of their own genus. To explore this idea further we collected all the information we could on the environmental and climatic conditions of the region. Polyploids seem to overwhelmingly prefer temperate climates (84.7% of occurrences) whereas the most popular climate for diploids was tropical (42.6%), which polyploids almost entirely avoid (6.6%). Similarly, polyploids have less than half the relative frequency in forested biomes (31.1%) than diploids (63.2%). Instead, polyploid occurrences are more common in grasslands, savannas and shrublands (58.7%). In addition to biome classifications, we also looked at whether or not any continuous environmental variables were significantly different between polyploid and diploid species. Using a phylogenetic ANOVA test, we found that temperature seasonality (standard deviation of temperature over the course of the year) was the only variable significantly different between polyploids and diploids. Temperature fluctuations have been linked to fish and amphibian polyploids before, possibly connected to their ability to resist environmental disruptions. However, changes in temperature could also result in an increase in polyploid formation, as temperature shocks are a well-documented method for inducing whole genome duplications in many aquaculture species, as well as frogs.


Heatmaps of temperature seasonality and cropland usage alongside occurrence and range maps of all frogs included in the study

Another difference between polyploid and diploid occurrences appears to be human impacts. Southeastern South America has experienced rapid agricultural development over the last century, resulting in one of the largest biodiversity declines in the world. As polyploids are thought to be more adaptable or resistant to challenging/disrupted environments its possible they are able to survive in this transformed landscape in ways diploids are not. In each of the sampled genera, polyploids were more frequent in areas with higher cropland usage, fertilizer application, and pesticide application compared to diploids between every comparison with statistical significance. Importantly, phylogenetic ANOVAs comparing these variables were not significant, meaning that we cannot discount the possibility that differences are the result of shared ancestry between occurrences rather than ploidy alone. As a result, we considered the human impact hypothesis to be a little more speculative than the temperature seasonality hypothesis, but still merits further investigation, as there does appear to be a strong correlation between ploidy and human impacts in at least some of the genera under study. We hope that our findings prove useful in understanding how polyploid lineages are formed and persist in nature, and lead to further investigations into the relationship between ploidy and environment.

Written by:
Kyle David

PhD candidate, Auburn University, USA

Additional information:
Twitter: @KyleTheDavid
https://kyletdavid.github.io/

ECR feature: Elie Gaget on riparian birds community changes

Elie Gaget is a Postdoc at the International Institute for Applied Systems Analysis (IIASA) – Austria. He is a community ecologist interested in understanding how climate warming and land-use change affect bird communities. Here, Elie shares his recent work that uses a long-term survey to understand latitudinal and altitudinal shifts in riparian birds due to climatic change.

Long-term studies require field monitoring (Photo of Elie Gaget by Pauline Gohier).

Personal links. Research Gate

Institute. International Institute for Applied Systems Analysis (IIASA) – Austria

Academic life stage. Postdoc

Major research themes. Community ecology, Conservation biology, Climate change adaptation

Current study system. Birds! They are amazing! Birds are not only an iconic group easy to monitor and to study, but also fantastic living organisms, relaxing and sources of inspiration. My work partly focuses on birds in wetland ecosystems, which have suffered severe damages because of human activities. Wetlands are spectacular, hosting a high diversity of species and showing different faces following the seasons – at least in Europe where I live. Combining bird observations and wetland ecosystems for scientific conservation purposes is a great satisfaction to me.

Recent paper in JBI. Gaget, E., Devictor, V., Frochot, B., Desbrosses, R., Eybert, M. C., & Faivre, B. (2021). Disentangling the latitudinal and altitudinal shifts in community composition induced by climate change: The case of riparian birds. Journal of Biogeography, 48(3), 526-536. https://doi.org/10.1111/jbi.14016

The great crested grebe (Podiceps cristatus) needs a peaceful place to breed (Photo: Elie Gaget).

Motivation behind this paper. Birds are often used as sentinels of the impact of human’s pressure on ecosystems. This study takes advantage of a very special long-term bird monitoring program that sampled bird communities from upstream to downstream along three major French rivers for 31 years. We investigated whether temporal bird community changes were responsive in a similar way to climate warming and land-use change at different locations along the rivers. The main hypotheses were regarding community elevational shifts over time and how bird communities can adjust to an accumulation of human’ pressures. In theory, climate niche tracking (i.e., local change of relative abundance of species-specific thermal preferences) by high elevation species should closely match a local change in temperature to a higher elevation because species only need to move small distances to find cooler temperatures. Conversely, lowland species must make a greater latitudinal shift to compensate for a local change in temperature – thus, there should be a time lag between climate niche tracking and local change in temperatures for these species.

Key methodologies. We used the Community Temperature Index to reflect the relative abundance of species-specific thermal preferences to measure the temporal lag accumulated by communities according to temperature increase, the so-called climatic debt. In addition, we quantified the temporal changes in the abundance of habitat specialists and generalists using the Community Specialization Index. These metrics allowed us to investigate whether and how the composition of riparian bird communities in lowland versus highland can be related to recent climate warming and reveal a biotic homogenization response. We also assessed the interaction between the thermal and homogenization responses of the communities by calculating species’ contributions (percentage of change related to a specific species) to both community index temporal trends. By doing so, we compared whether the same species drove the shift in Community Temperature Index and Community Specialization Index.

The white wagtail (Motacilla alba) is a fairly common species in Europe, sometimes benefiting from human-made habitats (Photo: Ghislain Riou).

Unexpected challenges. One challenge concerns the spatial design, with three rivers sampled along their stream at different locations. Streams may have their own characteristics and particularities in terms of environmental factors and pressure exposition, which might obscure congruent patterns. We were very impressed by the fact that we observed a remarkably consistent pattern among the rivers for each biodiversity metric used. Not saying that n=3 is a perfect design to investigate spatial heterogeneity, but having such a similar response was important for the conclusions of our study.

Major results. Surprisingly, climatic debt was larger in the highland than in the lowland community, even though temperature increased at a similar rate in both areas. This finding was not primarily expected given thermal niche tracking can be achieved with smaller distances in the highland by performing elevational shifts than in the lowland that requires latitudinal tracking. In other words, for riparian birds, the thermal community adjustment to climate warming was better in lowlands than in highlands. However, a strong homogenization signature was detected in both areas. Interestingly, community changes relative to climate warming and land-use change were uncorrelated, meaning that the species responsible for the community adjustment to climate warming were not the same as those responsible for the community homogenization. In addition, we found a decline in bird abundance in the highlands compared to lowlands that were stable over time. Together, these results highlight the vulnerability of highland species to the accumulation of anthropogenic pressures, particularly in the context of climate warming.

Next steps for this research. Overall, our results support the development of long-term surveys and conservation actions dedicated to riparian bird communities. Not only are these riparian assemblages among the richest in Europe, but they are also highly exposed to both land use and climate change.

The impressive northern giant petrel (Macronectes halli), a sub-Antarctic scavenger characterized by massive nasal tubes (Photo: Elie Gaget).

If you could study any organism on Earth, what would it be? My dream species is the Northern Giant Petrel. Sometimes considered ugly, this bird leaves no one indifferent. Giant Petrel behaviour is amazing, especially on land when feeding as vultures on carrions. This apex species has a great potential for studies investigating the impact of fisheries on the Antarctic and sub-Antarctic food webs, bird olfaction, movement ecology and disease regulation.

Synthesis, Perspective, Commentary: A call to all authors!

Biogeography is a rapidly moving research area that intersects with many other scientific disciplines and contemporary environmental issues. Moreover, the biogeographic literature is diverse, scattered across disciplinary journals and continually expanding. Making sense of this ever-changing landscape of scientific discourse is challenging, but can be greatly facilitated by accessible and readable synthesis and discussion articles. Such articles have often been seen as the exclusive preserve of senior scientists – the ‘silverbacks of biogeography’. This is categorically incorrect; good ideas, novel viewpoints and compelling writing are not age-dependent and we actively encourage enquiries and submissions from scientists at all career stages.

Journal of Biogeography (JBI) has three article types (Synthesis, Perspective, and Commentary) that allow authors to develop new themes and concepts, re-assess and revisit standard models and frameworks, and to contribute to current debates. Each article format has slightly different aims:

Synthesis articles have the aim of reviewing or reassessing a timely area of biogeographical research. We use ‘Synthesis’ rather than ‘Review’ to emphasize that such articles should ideally contribute to an integrated understanding, resolving misunderstandings and apparent contradictions and, often, presenting new conceptual frameworks or categorizations. Synthesis papers may take the form of traditional narrative reviews or more formal meta-analysis (e.g., Gurevitch et al. 2001).

Perspective articles offer a forum for more personal perspectives on key research fields, concepts and issues within biogeography. Such a format is ideal for developing and substantiating new ideas and arguments (and for highlighting flaws and inconsistencies in traditional/standard models and concepts). 

Commentary articles are comments on the latest original research in biogeography. This could be criticisms of the articles, but could equally be used to draw attention to implications or interpretations that were not considered in the original article.  

While we welcome submissions in these categories from all authors, we want to take this time to particularly encourage junior authors.

There are a lot of very good reasons to give serious thought to writing a review (Synthesis) or discussion (Perspective/Commentary) article. Firstly, they are enormous fun to develop and write. Freed from the standard research article format you have much greater freedom to develop strong, compelling narratives, and to bring in your own ideas and informed speculations. Most articles are collaborations, and much of the enjoyment stems from the exchange of ideas and thoughts with colleagues rather than the actual process of writing – although, if you are like me, this can also be strangely enjoyable.

Secondly, they can have a major impact on your career. Review and discussion articles are often highly cited, can generate high levels of debate and interest among the scientific community. I always advise my PhD students and post-docs to adopt a mixed publication strategy, combining standard research articles with other more discursive article types. This strategy is one of the best ways to boost your CV, your scientific visibility and your publication metrics.

Finally, there is a common but incorrect perception among many early career-stage researchers that these sorts of articles are much more difficult to write than standard research articles. This is related to the common view that review and discussion articles are the domain of senior scientists. Many of us on the chief editorial board at JBI can personally testify this is not the case. My first published article (Ladle 1992), for example, written during the 2nd year of my PhD, was a Review. I was extremely fortunate that one of the reviewers – the late, great Leigh Van Valen – realized that I was new to the publishing world and provided some of the best feedback I have ever received on how to make a good scientific argument.

We believe it is important to follow that example at JBI, making review-type articles accessible to all. To meet this goal, JBI has created a new Research Highlights Editor position on the chief editorial board. Nearly thirty years after that first review, I am about to start work in this position, and I would like to begin with an open invitation to the global biogeographical community: if you have ideas for writing a Synthesis, Perspective or Commentary we would be delighted to hear from you. I am very happy to receive direct enquiries (richardjamesladle@gmail.com or via jbioffice@wiley.com) or, if you have a manuscript, please consider submitting it to us (https://onlinelibrary.wiley.com/journal/13652699 see “submit an article”). We can’t guarantee publication, but we will do everything we can to ensure that it is fairly reviewed and to offer constructive advice on structure, content and style.


Written by:
Richard Ladle
Research Highlights Editor

References
Gurevitch, J., Curtis, P. S., & Jones, M. H. (2001). Meta-analysis in ecology. Advances in Ecological Research32, 199-247.
Ladle, R. J. (1992). Parasites and sex: catching the Red Queen. Trends in Ecology & Evolution7, 405-408.

Different paths of success in the sea – what we can learn from seaweeds

Closely related clades of brown marine seaweeds display different patterns of geographical distributions and diversifications.

Above: Meadow of the brown seaweed Lobophora in the Canary Islands. Photograph by Jan Ranson

In studying the factors and processes structuring marine biodiversity and distribution patterns, an unconscious (perhaps inevitable) bias towards animals vs. seaweeds is often reflected in the literature. The emphasis is essentially made on what usually are considered emblematic taxa such as corals, sponges and fishes. This trend somewhat echoes what we observe in society, where seaweeds go mostly unnoticed by the general public even though they play a crucial and irreplaceable role in the functioning of coastal marine ecosystems as primary producers.

Editors’ choice: (Free to read online for a year.)
Vieira, C, Steen, F, D’hondt, S, et al. Global biogeography and diversification of a group of brown seaweeds (Phaeophyceae) driven by clade‐specific evolutionary processes. J Biogeogr. 2021; 48: 1– 13. https://doi.org/10.1111/jbi.14047 

Seaweeds include a heterogeneous set of organisms, which have diverged into evolutionary independent lineages (brown, green and red algae). Despite their ecological importance, our knowledge on seaweeds’ biodiversity, biogeography and evolution is still very fragmentary. Not even that long ago it was not particularly uncommon for seaweed experts to claim that many seaweeds have biogeographic ranges spanning all major ocean basins and that they were present in temperate as well as tropical regions. However, truly cosmopolitan species were thought to be rare, for these needed to be present also in Arctic and Antarctic regions. Needless to say that the use of DNA-assisted species identification radically altered our view on seaweed diversity. Two decades later many so-called widespread species turned out to be species complexes sometimes comprising over a hundred individual species (e.g. Lobophora, Portiera). Alongside the development of a more accurate view of species diversity, a much improved view on distribution ranges and diversity patterns emerged with some clades conforming to a textbook latitudinal diversity gradient, while other clades displayed inverse latitudinal patterns.


Marine brown seaweeds covering the seafloor — in this case a vertical wall — in the Baleares Islands, Spain. Photograph by Christophe Vieira.

Studies focusing on large-scale biogeographical patterns in seaweed are particularly uncommon. Moreover, the factors underlying these patterns have been only rarely addressed. Generally, because species diversity was insufficiently characterized for many groups of seaweed or datasets were too small to allow rigorous statistical testing of alternative diversification hypothesis. This forced phycologists to address macroecological or evolutionary questions at genus-level, as a proxy for species level diversity. However, species- and genus-level diversity patterns and diversification dynamics do not necessarily align well, leaving many questions unanswered with respect to clade-specific drivers of diversification.


The brown marine seaweed Dictyota in the Keys, Florida, USA. Photograph by Ana Tronholm.

In this sense, the driving force behind writing this paper was the long-brewing idea of overcoming the aforementioned impediments and addressing patterns of diversification in seaweeds. To this end, we put together a consortium of phycologists with access to local seaweed diversity and joined efforts for data acquisition (collecting and barcoding). This study illustrates how patterns in distributions and diversification diverge among closely related clades as a result of contrasting evolutionary mechanisms, using the brown seaweed order Dictyotales as an example of successful diversification in the marine realm. This work marks a milestone in the study of global biogeography and diversification of marine seaweeds.


Sampling of seaweeds in Tenerife, Canary Islands. Photograph by Ana Tronholm.


Written by:
Olivier De Clerck (1), Christophe Vieira (2), Ana Tronholm (3)

1) Professor, Phycology Researh Group, Biology Department,  Ghent University. (2) Postdoctoral Fellow, Kobe University Research Center for Inland Seas, Japan. (3) Researcher, Department of Biological & Environmental Sciences, University of Gothenburg.

Additional information:
https://phycology.ugent.be/;
https://www.facebook.com/groups/Phycology.UGent/

Speciation research in Bombina: a 40 years story

Hybrid zones can be abrupt and leaky

Above: From the cover: Fire‐bellied toad (Bombina bombina) from southern Poland, where they form a famous hybrid zone with their sister species the yellow‐bellied toad (Bombina variegata). Photo credit: Christophe Dufresnes.

I was not even born when Jacek Szymura and Nick Barton initiated their pioneering research on the hybridizing fire-bellied toads Bombina bombina and Bombina variegata in the late 1970s / early 1980s. These tiny amphibians are quite distinctive in looks, sounds and habitats, but still they utterly hybridize wherever they get the chance along an extensive area of contact in Central Europe. This area soon became a playground to study hybrid zones and understand how different species are maintained apart despite interbreeding and gene flow, a major question in evolutionary biology. Dozens of papers on this iconic system, some highly influential, were published in subsequent decades.

It thus felt natural to include the B. bombina/variegata pair in my post-doc project a couple of years ago: a comparative framework of amphibian hybrid zones analyzed with high-throughput sequencing data to characterize the genetic and biogeographic features of speciation. For Bombina, we specifically aimed at testing whether the two species kept their genetic integrity everywhere they hybridize, or whether there was noticeable variation linked to their dynamic biogeographic history. And simply to revisit this famous speciation model for the first time with genome-wide markers.

Cover article: (Free to read online for a year.)
Dufresnes C, Suchan T, Smirnov NA, Denoël M, Rosanov JM, Litvinchuk SN. 2021. Revisiting a speciation classic: Comparative analyses support sharp but leaky transitions between Bombina toads. Journal of Biogeography 48(3): 548-560. https://onlinelibrary.wiley.com/doi/full/10.1111/jbi.14018  

To get fresh samples, Dr. Tomasz Suchan and I initially went into the field near Krakow in Poland, home of the first Bombina hybrid zone ever documented. But decades after Jacek Szymura cycled around these once abundant populations, most of them had since disappeared following landscape changes. Exploration of suitable habitats along the Carpathian foothills led us to discover a new contact, although now fragmented by … the E40 highway, which was precisely built along the foothills!

In parallel, we were able to resurrect a forgotten collection of specimens sampled in the 1990s by Drs. Spartak Litvinchuk and Juriy Rosanov across a wide transition zone in the Ukraine Transcarpathians, and Dr. Nazar Smirnov recently documented another area of hybridization in the Ukraine Ciscarpathians. Combined with previous literature – thanks to the support of Prof. Alexey Yanchukov – new and published data could be gathered across no less than 11 contact zones!


Fine-scale distributions of the two species in Central Europe, and admixture analyses of toads collected across two parapatric ranges in Poland (left) and Ukraine (right), based on genome-wide markers. In these examples, most individuals (= horizontal bars) are either pure B. bombina (blue) or B. variegata (green), but with slight admixture by the other species. Credit: Prof. Christophe Dufresnes.

Finally, to properly reconstruct the history of hybrid zone formation, we had to map the numerous lineages of each species. Dr. Mathieu Denoël spent days buried under amphibian atlases to accurately delimit range extents, which were then exploited to predict past distributions and routes of expansions from the various glacial refugia.

We were quite amazed that in all contact zones, the exact same pattern stood out: sharp but leaky transitions (hence the title of our paper), in the sense that the genomes of the two species always locally admix, but only a few alleles made it far into the foreign ranges. This means that species boundaries between B. bombina and B. variegata remain robust despite the ongoing gene exchange, probably because the hybrids are not that fit. Based on hundred-times more loci than the classic Bombina research, our study thus provides decisive empirical evidence that hybridization should not be viewed as a force of “despeciation”, as long as reproductive barriers that prevent hybrids to spread are strong enough, in the form of developmental problems or maladaptation.


Dr. Nazar Smirnov taking notes on a B. variegata site in Western Ukraine. Credit: Dr. Ihor Skilsky.

Moreover, our results also implied that the biogeographic history of these numerous hybrid zones did not really influence how the toads mixed in the end. This was surprising since in other amphibians, we had shown that hybrid zones could have quite different genetic structures depending on the lineages involved, the time since contacts, etc. Here, such replicability indicates that when two species are sufficiently differentiated, hybrid swarms remain geographically restricted, no matter how and when the contact is established.

What next? In parallel to this publication, we have pushed analyses further to look at the genomic architecture of reproductive isolation, i.e. the number of barrier loci that cause incompatibilities between species, by comparing multiple pairs of European frogs and toads. It turns out that with their sharp transitions, the Bombina pair lies at the upper edge of the speciation continuum, where many parts of the genome ceased to admix. Another team has also been working on a reference genome, from which they have already identified the sex chromosomes. These developments mark the advent of a new exciting era for evolutionary research in the timeless Bombina model!


A precious finding a few hundred meters south of the E40 highway in southern Poland: a B. variegata individual (slightly admixed by B. bombina) in a forest track puddle. Credit: Prof. Christophe Dufresnes.


Written by:
Christophe Dufresnes

LASER, College of Biology & the Environment, Nanjing Forestry University, Nanjing, China.

Additional information:
https://chrisdufresnes.wixsite.com/laser

Mariana M. Vasconcellos on diversification and phylogenetic relationships of pajama frogs

Mariana Vasconcellos is a postdoc at the Universidade Federal do Rio de Janeiro. She is interested in the environmental correlates of diversification and climatic adaptation, with a large focus on amphibians and reptiles. Mariana shares her recent work on unravelling the drivers of diversification in South America’s pajama frog group, revealing some surprising phylogenetic relationships and the effects of past climates.

Mariana Vasconcellos in her natural habitat. Photo credit: Mario Van Gastel.

Personal links. Google Scholar | ResearchGate | Twitter

Institution. Universidade Federal do Rio de Janeiro

Academic life stage. Postdoc

Major research themes. Diversification and climate adaptation of Neotropical species and populations to environmental changes. My research mainly focuses on amphibians and reptiles, but occasionally plants as well.

Current study systems. How have populations and species responded to environmental changes in the past, and based on that, how will they likely respond to ongoing climate change? These questions are at the core of my research. To answer them, I first turned to the Cerrado savanna of central Brazil, where I studied the pajama treefrogs, an interesting group of which most species are endemic to this savanna. They got their name because of the stripes along their bodies, which make them look like they are wearing striped pajamas. Our goal for this study was to understand the factors that explain the occurrence of this species group in very different habitats, such as grasslands, savannas, and rainforest regions. I am now addressing signatures of environmental changes in other herps and plants in the Brazilian Atlantic Forest as well.

The Cerrado landscape with gallery forests meandering in the background, following small rivers, where one pajama treefrog species is found.

Recent JBI paper. Vasconcellos, M. M., Colli, G. R., Cannatella, D. C. (2020). Paleotemperatures and recurrent habitat shifts drive diversification of treefrogs across distinct biodiversity hotspots in sub-Amazonian South America” Journal of Biogeography. 48:305-320 https://doi.org/10.1111/jbi.13997

Motivation behind this paper. Pajama treefrog species occur in very contrasting habitats of open/dry or forest/humid ecoregions across South America, but the group is most diverse in the Cerrado savanna. This is quite curious, as treefrogs are mostly associated with humid habitats and are usually more diverse in forest regions. When we started our research, their phylogenetic relationships and diversification patterns were relatively unknown. Therefore, we thought that a good place to start would be to resolve the phylogenetic relationships in this group to reconstruct their biogeographic history and understand when and how they diversified in the Cerrado savanna. We noticed a very unusual biogeographic pattern of closely related species or clades distributed in regions of contrasting vegetation and climate. Based on phylogenetic niche conservatism, it is expected that closely related species inhabit similar habitats, so we decided to test the effect of eco-similarity across areas in the dispersal of these frogs over time. We also evaluated the contribution of past environmental changes, such as paleotemperatures, in their temporal pattern of diversification.

A male pajama treefrog (Boana buriti) calling to attract females. Photo credit: Gabriel Horta.

Key methodologies. To better understand how the species have dispersed and diversified across different regions, we reconstructed ancestral areas along the phylogeny using the dispersal-extinction-cladogenesis (DEC) model. We evaluated six alternative scenarios of dispersal across the Neotropics using a different dispersal rate matrix for each of our six hypotheses. For example, we tested scenarios for the ‘center-of-origin’ in either forest or open areas, and we also tested whether dispersal was more frequent across ecologically similar areas vs. simply adjacent areas (regardless of ecological similarity). In addition, using species diversification models, we identified the factors that contributed most to the variation in speciation and extinction rates over time, taking into account the effect of past climate, time and species diversity (=ecological limits) upon them.

Major results. The evolution of the gladiator treefrogs, including the pajama treefrogs, is the product of repeated dispersal events between open/dry and forest/humid regions across South America. We did not find support for a single region acting as a ‘center-of-origin’ for the group. Instead, we inferred recurrent range shifts across adjacent dissimilar regions. We also uncovered a strong influence of past climates in their diversification, with speciation rates being temperature-dependent and showing higher rates of speciation during warmer climates. This highlights the very dynamic history of some Neotropical organisms, which might be triggered by environmental changes. These changes have promoted frequent habitat shifts among contrasting adjacent habitats and impacted the rate at which new species arise, possibly contributing to the great species diversity found in the Neotropics.

Unexpected challenges and outcomes. The first main challenge of our research was to sample all the pajama treefrog species. Since most of these species have very restricted distributions, we made extensive field trips across central and southeast Brazil to collect their DNA. These frogs mainly occupy highlands and plateaus with beautiful landscapes and astonishing waterfalls, so the search for specimens was very enjoyable indeed. But after sequencing our samples, our first results turned out to be very surprising: the pajama treefrogs are in fact not a single clade, but instead, three independent clades nested in the larger Boana pulchella group of gladiator treefrogs. This unexpected result meant we had to shift our investigation to a larger group comprising a much larger geographic area across South America (including the Andes, Araucaria Forest, Pampas grassland, in addition to the Cerrado and Atlantic Forest). This change also allowed us to explore an even more complex biogeographic history for the group and to focus on the temporal diversification patterns for the larger Boana pulchella group.

A gladiator treefrog (Boana ericae), part of the larger Boana pulchella group. Photo credit: Guilherme Santoro.

Next steps. The next step in this research is to better understand species limits and the speciation process in this group, of which we have barely scratched the surface, by compiling a more complete current phylogeny for the group. We focused most of our sampling efforts on filling gaps of species sampling. Therefore, our limited population sampling for many species prevented us from confidently addressing species limits in clades where the taxonomy has historically been complicated. With the help of new collaborators, I am now increasing our sampling of the main pajama treefrog clade to include more populations and individuals in a phylogeographic study. Our new goal is to investigate the factors that promote the frequent movement of species between the Cerrado savanna and the Brazilian Atlantic Forest, with a repetitive pattern of species interchange over time.

If you could study any organism on Earth, what would it be? Definitely frogs! They are extremely diverse in tropical regions, and they come in all kinds of sizes, shapes, and colors. Their great diversity of reproductive modes and behavioral mating strategies make them especially interesting organisms to study, not to mention the many habitat specializations for arboreal, fossorial, terrestrial, and aquatic environments that evolved multiple times across different continents. They are great study organisms to understand diversity patterns in the tropics, and to address many interesting biogeographic questions. But to me, one of the best features of frogs from a researcher perspective is how easy they are to observe and collect. If you visit any preserved area in the tropics at night, provided there is surface water (running or still), you can observe several species, within arm’s reach, without the need for complicated gadgets or skills to observe and collect them.

(left) Close-up of the preferred microhabitat for a pajama treefrog species. (right) Waterfalls were frequently visited places to collect treefrogs.

Anything else to add? The current featured research in the Journal of Biogeography is the result of the first chapter of my dissertation before my research started shifting to population genomics. This manuscript was first rejected by another journal (which was indeed not a good fit), and I did not find the time to address the criticisms I received while working on my following chapters and papers before graduation. With the start of a new postdoc position, diving into a new study system with different questions, this paper was sadly neglected for quite some time until I decided to take the time needed to develop it into a new submission. I addressed the criticisms we received, reanalyzed part of the results, and developed a more interesting framework to test the diversification pattern. I had to do quite a lot of re-writing and editing as well. But it was worth it! During the peer review process, the manuscript got even stronger, with a more solid conclusion. I recognize that many of us have papers that just need a final push to be submitted. I hope this can serve as an inspiration to those lacking motivation to work on that dusty, abandoned manuscript again.

ECR feature: Axel Arango on diversity of the Seasonally Dry Forests in the Neotropics

Axel Arango is a PhD student at the Instituto de Ecología A.C. (INECOL) – Mexico. He is a macroecologist interested in untangling the patterns and processes shaping biodiversity worldwide. Here, Axel shares his work on the biodiversity patterns of the Neotropical Seasonally Dry Forests.

Axel Arango presenting his poster during the International Biogeography Society’s Humboldt 250 Meeting in 2019 at Quito, Ecuador.

Personal links. Website | Twitter

Institute. Instituto de Ecología A.C. (INECOL), Mexico

Academic life stage. PhD student

Major research themes. Evolutionary Macroecology, Phylogenetic ecology, Biogeography, Biodiversity

Current study system. My ongoing research focuses on untangling the patterns and processes shaping biodiversity worldwide, mostly using phylogenetic and macroevolutionary tools to unveil the mechanisms generating biodiversity. When I began my graduate research on these topics, I was attracted by the outstanding diversity and endemism of the Neotropical Seasonally Dry Forests and the lack of knowledge on the processes shaping their patterns despite being one of the most threatened biomes in the world due to human exploitation. This motivated me to answer some of the long-standing questions about this biome by taking advantage of recently developed and open-access databases. During this process, I realized that answering such biodiversity questions does require detailed information on several ecological and evolutionary aspects of the clades under study. Driven by this realization, I’m currently pursuing my PhD studying birds as a model system to explore and evaluate the diversification and biogeographic history across the Americas.

Recent paper in JBI. Arango, A., Villalobos, F., Prieto‐Torres, D. A., & Guevara, R. (2021). The phylogenetic diversity and structure of the seasonally dry forests in the Neotropics. Journal of Biogeography48(1), 176-186.https://doi.org/10.1111/jbi.13991

The remnants of a Dry Forest in Veracruz, Mexico.

Motivation behind this paper. This paper derived from my Master’s thesis at INECOL, which came to light when my supervisors and I got interested in describing large scale biodiversity patterns of neglected biomes, such as the Neotropical Seasonally Dry Forests (hereafter NSDFs). For more than two decades, the NSDFs had been described to present an inverse latitudinal diversity gradient, showing higher species richness away from the Equator. Several hypotheses had been posited trying to explain this phenomenon, arguing from different origin and colonization times for this biome to long-term climatic stability facilitating the diversification and expansion of these forests. However, only a few attempts tried to evaluate these hypotheses. By taking advantage of recently developed databases and exploring the climatic dynamics since the Pleistocene, we tested the geographic and evolutionary processes responsible for driving this uncommon distribution of diversity shown by the NSDFs.

Key methodologies. We used available data on woody plants distribution in the NSDFs (http://www.dryflor.info/data) and a recently published phylogeny for seed plants to estimate diversity and relatedness metrics. More than 4000 species and 800 assemblages of woody plants were used to evaluate the latitudinal gradient of the NSDFs and test if climatic stability since the Last Maximum Glacial was driving this pattern. We used different phylogenetic metrics such as phylogenetic diversity, which describes the amount of history contained within an assemblage, and the Net Relatedness Index (NRI) that describes the degree of phylogenetic relatedness (closely, distantly or randomly related) among species within an assemblage. These phylogenetic patterns can infer ecological (environmental filters, local extinction) and evolutionary (phylogenetic niche conservatism, diversification) processes that shaped the distribution and diversity of the NSDFs in the Neotropics. As such, our work was ingenious in the way it approached and evaluated the hypotheses on NSDFs diversity and distribution mainly by using comprehensive databases and state-of-the-art phylogenetic methods to solve a long-standing question on NSDF biodiversity patterns.

Unexpected challenges. Initially, we focused only on phylogenetic diversity measures to understand the latitudinal gradient of the woody plants associated with the NSDFs. However, after analyzing the results, a new question arose about what processes drove the reverse latitudinal gradient in these biomes. We decided to expand our study and test one of the most famous hypotheses explaining this phenomenon: the Pleistocene Arc Hypothesis (PAH). This hypothesis argues that the current disjunct distributions of the NSDFs were once connected during the Pleistocene’s cold and dry periods, which can be tested using climate data and phylogenetic structure metrics. However, a challenge we often face when working with these types of large datasets published by different researchers at different times is to match the taxonomy between both information sources, which might have been the most labor-intense process in this study.

A lonely Huaziche (Vachellia sp.), a common species of dry habitats in a Veracruz NSDF.

Major results. We found that the reverse latitudinal gradient showed by the NSDFs is not a result of the climatic stability since the Last Glacial Maximum, challenging one of the most prominent hypotheses previously suggested (i.e., PAH). Instead, it is likely the outcome of more intricate and deeper-time evolutionary processes. However, the idea of widespread clades in the past that subsequently fragmented into isolated lineages and diversified in situ remained valid by the evidence of several separate and unique regions composed by closely related species. Still, these isolation events and evolutionary processes may have occurred long before the Pleistocene and were perhaps associated with different timings of radiation and adaptations of the woody plants in this biome.

Next steps for this research. As part of an ongoing collaboration, we will evaluate if there’s a differential Diversification Rate at the proposed source areas of the NSDFs to argue that these places are the drivers of NSDF’s current diversity and distribution. We will also calculate measures that assess the species’ influence in ecosystem functioning (i.e., Functional Diversity) of these forests to discern how much they depart from the Phylogenetic Diversity. This approach could give us insights into the biogeographic history in these forests by explaining, for example, if its expansion was either mediated by Phylogenetic Niche Conservatism or ecological convergence.

If you could study any organism on Earth, what would it be? Dinosaurs – other than birds, of course! More specifically, all the extinct clades that inhabited the Earth millions of years ago. Extinct species can provide us with a more robust idea of processes building up biodiversity, and how cool it would be to look at all those different kinds of organisms forgotten by time?

Anything else to add? When I started working on this project, although I had experience in statistics and population ecology, I hadn’t had that much exposure to programming and only had a vague idea about community phylogenetics. Fortunately, with the help of my advisors (Fabricio Villalobos and Roger Guevara), I picked it up and built a robust project that was awarded by the International Biogeography Society at the Humboldt 250 Meeting in 2019. In hindsight, I think this combination of skills helps me better formulate and tackle broad questions about biodiversity.