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.

ECR Feature: Felipe Vieira de Freitas on bee diversity

Felipe is a postdoc at Washington State University. He uses phylogenetics to study the evolution of bees. Felipe shares his recent work on the origins and unusual antitropical diversity of Eucerinae bees.

(left) Collecting bees in the Atacama Desert – Chile. (right) At the USDA bee lab in Utah, trying to understand the protocols for UCE work.

Personal links. Twitter | ResearchGate

Academic life stage. Postdoc

Institutes. Department of Entomology, Washington State University, Pullman/WA, USA

Research themes. Historical biogeography, Entomology, Phylogenomics, Phylogenetics, Insect systematics, Bee diversity.

Current study system. I study bees, which are impressive because of their diversity in body form, color, biology, and behavior. They are also some of the most important groups of insects as providers of ecosystem services. There are over 20,000 species of bees distributed throughout all zoogeographical regions of the world, most of them acting as pollinators. Despite being a relatively well-studied group of insects, there are still several open research questions related to the evolutionary origin of bees. Notably, some open questions have to do with origin in the Late (~100Mya) or Early (130Mya) Cretaceous, and with their origin in Africa, South America, or both (during the period when these continents were connected). Biogeography is a crucial aspect of the interpretation of the evolution of any taxon, and bees are not an exception.

Ancyloscelis sp. on a flower of Convolvulaceae (photo credit: Adriana Tiba and Julio Pupim).

Recent paper in JBI. Freitas, F. V., Branstetter, M. G., Casali, D. M., Aguiar, A. J., Griswold, T. & Almeida, E. A. B. (2022). Phylogenomic dating and Bayesian biogeography illuminate an antitropical pattern for eucerine bees. Journal of Biogeography. https://doi.org/10.1111/jbi.14359

Motivation behind this paper. Eucerinae is a group of solitary bees in the family Apidae that comprises more than 1200 species. Bees within this group exhibit a peculiar distribution, in which most of the diversity is concentrated in mid latitudes. This pattern is described as an ‘antitropical pattern’ (diversity increases away from the equator), contrasting with the typical pattern in which diversity increases toward the equator observed in most other taxa. This concentration of mid-latitude diversity is exceptionally high in areas of open vegetation in the New World, although there are several species in the Old World. The lack of a comprehensive historical biogeographic investigation of eucerine bees motivated our study. In this work, we sought to identify the processes that have led to an antitropical distribution in this group of bees based on a reliable phylogenomic framework.

Methodology. Our primary motivation was to infer the underlying species tree from eucerine bees across most of their range using a 2500 UCE (ultra-conserved element) loci dataset. A thorough phylogenomic framework is essential to dive into the past and investigate biogeographic events responsible for shaping how ranges changed through time. UCEs are highly conserved gene regions that provide reliable phylogenomic reconstruction across many animal groups. We hoped that by sampling UCEs across 197 species of eucerine bees, we would obtain robust estimates of their divergence times. We evaluated hypotheses that (1) Eucerinae originated from South America, (2) Eucerinae originated from Africa after these continents had separated, or (3) Eucerinae originated in both South America and Africa when these continents were connected in the supercontinent, Gondwana. An additional goal of our study was to understand the minimum amount of data for reliable phylogenomic-based divergence time estimation. Our full UCE dataset of 2500 loci (1.3Mb) is extensive and computationally demanding. So, we tested whether subsets of UCEs could produce comparable estimates to the entire dataset: 127 (~70kb), 83 (~50kb), and 31 (~20kb) UCE loci, chosen according to features that could reflect their quality for phylogenetic inference.

A male of Thygater analis on a flower of Ipomoea sp. (Convolvulaceae) (photo credit: Adriana Tiba and Julio Pupim).

Major results. Our main analyses support the hypothesis that eucerine bees emerged in South America. Following their origin in South America, there was likely a northward range expansion into North America, which was facilitated by the increase in open habitats. Although the main eucerine radiation occurred within South America, there is also evidence that some species, for example, the subgenus Eucera (Synhalonia), may have dispersed from Eurasia to North America. We believe that movements between South and North America were facilitated by large stretches of open habitat. However, with the rewarming of the planet during the mid-Miocene, forests would have reestablished, closing intercontinental connections and isolating the movement of bees over the equator. We suggest that these processes led to the antitropical pattern of distribution that we see today in eucerine bees.

Unexpected outcomes. Interestingly, we found the positive effect of adding more loci to estimate divergence times rapidly plateaus. With only 31 loci (~20 Kb), we achieved the same results as when using 127 loci (~70 Kb). We needed to select these subsets once the whole dataset (2500 loci) for these analyses would take months to conclude. And more than that, there is evidence suggesting that there is not a need for large datasets to reach good estimates of divergence times.

A female of Exomalopsis sp. on a flower of Asteraceae (photo credit: Adriana Tiba and Julio Pupim).

Next steps. The next steps are more related to improving our knowledge about smaller taxonomic groups of eucerine bees (the six tribes and their component genera). Understanding better the peculiarity of each one of them will probably help us to refine our interpretation of the broader scenario of Eucerinae as a whole. Our team continues to work on eucerine bees: we have projects in progress with Eucerini, the most species-rich of the tribes composing Eucerinae, Tapinotaspidini, and Emphorini.

If you could study any organism on Earth, what would it be? I would love to study other groups of Hexapoda, like Entognatha, especially Diplura and Protura. Because most species are associated with soil and caves, they probably have most of their diversity undescribed, and most of their behavior and natural history are still unknown.

ECR feature: Waleska Elizangela dos Santos Barbosa

Waleska Barbosa is a PhD student at the National Institute of Amazonian Research in Manaus, Brazil. She is an ecologist interested in the evolutionary history of Amazonian birds. Here, Waleska shares her recent work on species historical demography and habitat associations along Amazonian floodplains.

Waleska Barbosa on the observation tower at the Amazonian Museum (Museu da Amazônia – MUSA)

Personal links. Twitter | Instagram

Institute. National Institute of Amazonian Research (INPA)

Academic life stage. PhD student

Major research themes. Biogeography; Evolutionary history of birds; Climate change

Current study system. Bird species with different habitat associations are interesting systems to investigate the history of landscapes and their environments. Life habits make some birds intrinsically related to specific vegetation types; through the study of species’ evolutionary history, we can infer the past dynamics of these natural communities. In our recent paper, we study Synallaxis albigularis and Mazaria propinqua, a sympatric and closely related pair of ovenbirds; S. albigularis occurs mostly along the floodplains on the river banks, using more diverse habitat types, while M. propinqua is specialized on early succession vegetation of river islands.

Recent JBI paper. Barbosa, W. E. S., Ferreira, M., Schultz, E. D., Luna, L. W., Laranjeiras, T. O., Aleixo, A., & Ribas, C. C. (2022). Habitat association constrains population history in two sympatric ovenbirds along Amazonian floodplains. Journal of Biogeography, 49, 1683– 1695. https://doi.org/10.1111/jbi.14266

Motivation behind this paper. This paper emerged from a larger project, in which one of the main objectives was to improve our knowledge about birds associated with flooded Amazonian environments and their biogeographic history. Wetlands represent almost 15% of the total area of Amazonia. They include permanently and seasonally flooded areas and many distinct habitat types, which are quite dynamic, controlled by the continuous processes of sedimentation and erosion driven by precipitation patterns, river discharges and local topography. During sedimentation processes, channel changes may occur, modifying existing habitats and creating new ones, resulting in isolation or contact among populations. Some bird species prefer specific habitat types within the floodplains, as it is the case of M. propinqua and S. albigularis. Thus, in our recent paper we wanted to understand how did these species (which are co-distributed in the floodplains, but exhibit environmental differences) respond to the evolution of these environments, taking into account spatial/ecological heterogeneity.

Flooded forest in Juruá River; the dark line in the trees shows the inundation height (Credits: Marina Maximiano).

Key methodologies. We started by compiling occurrence records from online databases and scientific collections to corroborate the previously described distribution patterns and habitat affinities of our study species, building a new and more complete dataset that improves our knowledge on their entire distribution areas. Then, we used genomic data (UCE- Ultraconserved Elements, SNPs, mitogenome) to understand the evolutionary history of the two species. For this, we analysed their genetic structure, phylogenetic relationships, divergence times and demographic history.

Unexpected challenges. The biggest challenge that I experienced was becoming a mother during my Master’s degree, and to have another baby during the process of reviewing this paper. Luckily, I had a lot of support from my family and the BioGeoAm study group team, as well as from my supervisor Camila Ribas and colleagues, who helped me during all stages of research and publication of this paper. They also helped me to overcome all obstacles and inspired me to continue investigating the evolution of Amazonian birds. Another challenge was learning how to process genomic data, but this is part of the learning process, and nothing is more difficult than raising a baby.

Major results. We found differences in population histories related to distinct habitat associations along Amazonian floodplains. More resilient habitats, which are inhabited by S. albigularis, may sustain local populations, generating and maintaining diversity. In contrast, M. propinqua’spreference for more ephemeral island habitats may favour local extinctions, leading to demographic change, low genetic variability, no population structure, and smaller effective population size. Our results suggest that climatic variations during the late Pleistocene and Holocene caused changes in distribution and connectivity of the different habitats types along the Amazonian floodplains, affecting gene flow and population sizes of associated bird populations.

Synallaxis albigularis in a river bank vegetation (Credits: Tomaz de Melo).

Next steps for this research. We are currently investigating the effects of historical climate changes on bird populations associated with different environments across the Amazonian sub-basins of Negro River and Xingu River. Paleoclimate studies have shown that climate variations along the Amazon basin were not homogeneous; for instance, the climate history of the western Amazon seems to be more stable than the eastern part. At present, the Amazon landscape is made up of a mosaic of different types of environments. Climate variations during the Quaternary may have affected bird populations associated with these different environments distinctly, and it is here that our current research goals lie.

If you could study any organism on Earth, what would it be? It could be any organism that helps me understand how the Amazon was in the past and how it evolved. The Amazon is a magical place. Unfortunately, it is extremely vulnerable and terribly endangered. But I love birds and I am very happy to study them. When I was a child, like any child, I loved dinosaurs and now I study their living descendants! This is so cool! And I could study anything about birds, like their plumage, vocalizations, behaviour, and so on. Birds are incredibly interesting!

Anything else to add? I am wishful to go on an expedition into the Amazon. Even though I was born and currently live there, I feel that I know too little about this incredible biome. When I read about the expeditions of the first naturalists that visited the region, like Wallace and Bates, I start to think about how much I crave this experience.

Aridification-driven evolution: Three lineages, two data sets, one story

We tested the hypothesis that aridification of Australia during the Pleistocene promoted the isolation and divergence of three lineages of a migratory fish. We found support for this using an integrative framework of environmental and genomic modelling.


Above: Golden perch, Macquaria ambigua. Photo credit: Peter Unmack.

The Australian landscape has not always been so arid. In fact, if you travelled back to the early Cenozoic, in place of the central deserts you would find rainforests and lavish wetlands supporting very different ecosystems than we see today. But over millions of years, the plants and animals of Australia have had to adapt to a gradually drier climate, with heightened aridification during the glacial phases of the Pleistocene (~2.6 million to 11.7 thousand years ago) having caused major changes to the distribution and connectivity of populations. Despite having a good understanding of how this aridification has impacted terrestrial species, less is known about how it has affected the diversification of freshwater taxa.

Cover article (free-to-read for two years):
Booth, E. J., Sandoval-Castillo, J., Attard, C. R., Gilligan, D. M., Unmack, P. J. & Beheregaray, L. B. (2022). Aridification-driven evolution of a migratory fish revealed by niche modelling and coalescence simulations. Journal of Biogeography,   49,  1726– 1738. https://doi.org/10.1111/jbi.14337

In this study, we were curious to understand how historical aridification of Australia has influenced the evolution of an iconic freshwater fish, the golden perch (Macquaria ambigua). Specifically, we wanted to find out whether the divergence of three lineages of golden perch from three different river basins has been driven (or at least reinforced) by aridification. Previous research has found strong genetic differentiation between these lineages, and it has been proposed that they are actually three different ‘cryptic’ species. Clarifying this taxonomic ambiguity is important for the management and conservation of golden perch, especially since the species is regularly stocked from hatcheries into rivers and impoundments to support its recreational fishery.

We already had a ton of genome-wide data from previous work, so we thought we’d repurpose it to run some complex ‘coalescent’ models to better understand when these lineages diverged and experienced demographic changes. But what we needed first were some specific hypotheses to test. Rather than making hypotheses up out of thin air (or should I say water?), we used an environmental data set to develop contemporary and historical species distribution models. These models allowed us to predict how the amount of suitable habitat for golden perch has changed over time and theorize about how population sizes and connectivity of the lineages might have fluctuated between glacial and interglacial times.


Species distribution models for three golden perch lineages that are endemic to three major Australian drainage basins: Fitzroy (FIT), Lake Eyre (LEB), Murray–Darling (MDB). We found support for reduced habitat availability during the Last Glacial Maximum (~21 ka) compared to the present day.

What’s really cool is that our two independent data sets (environmental and genomic) found support for the same story. We discovered that during the Last Glacial Maximum (~21 thousand years ago), all three lineages had much smaller population sizes compared to the current day. Furthermore, the connectivity of suitable habitat between drainage basins was reduced at that time. This supports the idea that aridification caused the isolation (and facilitated the divergence) of the three golden perch lineages. We also found phylogenetic support for the delimitation of these lineages as separate species.

Our paper provides an exciting new insight into the diversification of freshwater taxa in Australia, and this integrative analytical framework could be applied to other study systems in the future. This research also has relevance for understanding how anthropogenic climate change might affect the connectivity of freshwater lineages, but that’s a story to explore elsewhere … 

Written by:
Emily Booth
PhD candidate, Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia

Additional information:
Twitter: @molecolflinders; @EmilyJBooth
https://molecularecology.flinders.edu.au

Will Geogenomics change the future of Phylogeography?

Phylogeography is celebrating its 35th birthday; Geogenomics its 8th. We asked authors of papers in a recent special section of Journal of Biogeography to reflect on how these two approaches can increase our understanding of the distributions of genetic diversity.

Above: Cover for the Geogenomics virtual issue .

Biogeography is an integrative discipline, as is reflected in familiar conjunctions including bio⋅geography, phylo⋅geography, and macro⋅ecology. One recently introduced term — geo⋅genomics — represents interdisciplinary approaches using “large-scale genetic data to test or to constrain geological hypotheses” (sensu Baker et al. 2014, p.38). Geogenomics is eight years young, arguably in its foundational phase, and its relationship with other disciplines in biogeography is developing. A special section in the Journal of Biogeography — which is running for the three months (v.49.9–49.11) and being compiled into a virtual issue — reviews the origins of geogenomics and compiles a suite of new studies that reflect geogenomics’ current purview (as practiced by biogeographers). A major contention of this special section is that Geogenomics has potential to substantially change the way we combine genetics and geology to increase rigor and insight when answering biogeographic questions. Here, we provide perspectives from some of the authors of papers in the special section on what they see in the future for Geogenomics. We posed three questions to them:
– What are the predominant limitations on (or opportunities for) advances in Phylogeography?
– What do you find new and exciting about Geogenomics?
– Can Geogenomics change the future of Phylogeography? (And/or what else will be needed?)

Their answers, and links to their papers, are provided below. We hope the special section and this discussion provoke thought and stimulate advances in this rich area. We look forward to publishing more on these topics in the coming years!

Editorial: (Free to read online for a year.)
Dawson, M.N., Ribas, C.C., Dolby, G.A. and Fritz, S.C. (2022) Geogenomics: Toward synthesis. J Biogeogr. 49(9):1657–1661. https://doi.org/10.1111/jbi.14467 

The special section on Geogenomics was conceived and edited by Paul Baker (Duke University, USA), Greer Dolby (University of Alabama at Birmingham, USA), Sherilyn Fritz (University of Nebraska – Lincoln, USA), Anna Papadopoulou (University of Cyprus, Cyprus), and Camila Ribas (Instituto Nacional de Pesquisas da Amazônia, Brazil) in association with the chief editors.  


Key attributes in geogenomic thinking include the bidirectionality of process and inference, and the integrative iteration of ecological, evolutionary, and earth processes, scaling from generational to geological times. See Dawson et al. (2022) for more detail.

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Barbosa, W. E. S.,  Ferreira, M.,  Schultz, E. D.,  Luna, L. W.,  Laranjeiras, T. O.,  Aleixo, A., &  Ribas, C. C. (2022). Habitat association constrains population history in two sympatric ovenbirds along Amazonian floodplains. Journal of Biogeography,  49,  1683– 1695. https://doi.org/10.1111/jbi.14266

Molecular biology has advanced a lot in the last decade, and the development of new sequencing techniques and a decrease in sequencing costs made a lot of phylogenomic studies possible. Given the availability of different sequencing platforms and sequencing strategies, strategic planning in phylogenomic studies has become more difficult, and analysis of all these data remains at a high cost. In addition, such complex data analysis requires scientists to be trained in bioinformatics, which makes them capable of solving the problems that arise throughout the stages of data processing and analysis.

What I find most exciting about geogenomics is the possibility of comparing dates of geological or climatic events with biological data at various scales with robust data, which allows even more accurate reconstructions of Earth‘s history.

Geogeonomics can make phylogeographic studies more interdisciplinary. In phylogeographic studies, biologists use dating and geological interpretations to understand the processes governing the distribution of closely related lineages. Meanwhile, in geogenomics, geologists can use genomic data as a proxy for their earth history studies. Thus, through bioinformatics, biologists and geologists can work together to test hypotheses as well as formulate new ones and obtain increasingly robust reconstructions.

– Waleska Barbosa




Northern chamois (Rupicapra rupicapra) inhabit steep terrain in Central Europe and are well-adapted to cold climate. They recolonized the European Alps after the glaciation. Photo credit: Flurin Leugger. 

Leugger, F.,  Broquet, T.,  Karger, D. N.,  Rioux, D.,  Buzan, E.,  Corlatti, L.,  Crestanello, B.,  Curt-Grand-Gaudin, N.,  Hauffe, H. C.,  Rolečková, B.,  Šprem, N.,  Tissot, N.,  Tissot, S.,  Valterová, R.,  Yannic, G. &  Pellissier, L.(2022).  Dispersal and habitat dynamics shape the genetic structure of the Northern chamois in the Alps. Journal of Biogeography,  49,  1848– 1861. https://doi.org/10.1111/jbi.14363

Phylogeographic studies at the very beginning were purely descriptive, linking molecular data to geography, e.g., investigating the spatial distribution of genotypes (Avise et al., 1987[1]). Early phylogeographic studies were based on mtDNA markers which included only few 100s base pairs and only describe female-related patterns (Avise 1998[2], 2009[3]). Compared to the multi-locus or more recently used whole genome analyses (see also response below), they provide limited insights into the history of the study organism. Advances in statistical approaches and modelling helped to overcome some limitations, i.e., to receive more realistic estimations or investigate additional species-environment relations (Knowles, 2009[4]) and test hypothesis of genetic diversity over time. The spatio-temporal resolution of genetic and/or geographic data is until now often a limiting factor in phylogeographic studies.

The connection of genomic (i.e., data from entire genomes and not only from a very restricted marker) data and landscape evolution at large spatial scales is exciting in the field of Geogenomics. Although initially defined as way to investigate geological patterns based on biological data (Baker et al., 2014[1]), Geogenomics is often perceived in a reciprocal illumination: geological or geographic data is used to improve our understanding of biodiversity and biological properties (Dawson et al., 2022[2]). New insights can be obtained by combining genomic with geographic data (and various models) compared to classical genetic analysis. For example, we[3] used genomic data of chamois across the European Alps in combination with several hundred landscape connectivity models over 20,000 years to test hypothesis on chamois’ dispersal which would not have been possible with distribution data or genetic data alone. Given that many researches use the reciprocal definition of Geogenomics (e.g., Barbosa et al., 2021[4]; Luna et al., 2021[5]; Ortego et al., 2022[6]), I argue that Geogenomics should be considered as part – or rather advancement – and not opposite of Phylogeography, where whole-genome data is used compared to the single or few genetic markers used during the emergence of Phylogeography. The core of Geogenomics is to test various hypothesis using genomic data in combination with both models and landscape data to gain new insights into biodiversity (e.g., migration) and landscape evolution (e.g., formation of migration barriers). Understanding how biodiversity evolved facing past environmental changes is paramount to predict and/or mitigate adverse effects of the current global changes where Geogenomics can contribute valuable information.

The core of Geogenomics is the hypothesis-driven approach using large-scale genomic data to improve our understanding of geological or biological properties. Advancements in genetic analysis and computational modelling are likely to foster Geogenomics in the next years and result in ever more hypothesis which can be addressed. Additionally, the tools of Geogenomics offer new possibilities to study biodiversity and landscape evolution at a finer scale than ever before. Genomic (whole-genome) data, i.e., SNP-based approaches, allows for more detailed analysis compared to classical phylogeographic studies, that is for example, on population level instead and over shorter time to estimate anthropogenic impacts. Using ancient DNA (aDNA) from fossils will offer new insights into Phylogeography. For example, aDNA could improve models about historic population changes and connectivity between populations.

– Flurin Leugger




(Left) The Striped Woodcreeper (Xiphorhynchus obsoletus, Dendrocolaptidae), a bird species with wide distribution in the Amazon floodplains. Photo: João S. Barros. (Right) Amazonian floodplains of the Rio Branco, at the foot of the Serra Grande, Roraima, Brazil. Photo: Thiago O. Laranjeiras.

Luna, L. W.,  Ribas, C. C., &  Aleixo, A. (2022).  Genomic differentiation with gene flow in a widespread Amazonian floodplain-specialist bird species. Journal of Biogeography,  49,  1670– 1682. https://doi.org/10.1111/jbi.14257

Modern phylogeography still lacks conceptual and methodological definitions in incorporating multivariate data (e.g., environmental, biotic, behavioral, climatic, and geological variables) into biogeographic models. In this context, the predominant limitation is how we can incorporate information from multiple species traits and historical changes in the landscape (constrained by dated geological events) into a statistical framework that can infer the current distribution of genetic diversity of the species and communities. Another issue is that the incorporation of whole genomes into the discipline has just begun, and several new tools and approaches will have to be developed or adjusted to fully incorporate the massive amount of data provided by this type of DNA sequencing. 

Geogenomics can be seen as a step forward in phylogeography in terms of concept and methodological approach. This advance comes from defining the study design more rigorously, using geological constraints and high-throughput genomic technology to tackle biogeographic hypotheses. That is, it adds the context of geological history into the investigation of biogeographic patterns, or vice versa, using known biogeographic patterns to illuminate geological processes at both regional and intercontinental scales.

Explicitly using dated geological events within phylogeographic approaches can help refine the hypotheses being tested. For the past two decades, phylogeography relied on the description of spatial genetic patterns as a posteriori explanation of possible events that shaped the evolutionary histories of taxa. With the addition of concepts from geogenomics, phylogeography can be profoundly changed, whereby the addition of an explicit historical/geological context into sampling designs will help illuminate complex evolutionary and biogeographic patterns.

– Leilton Luna & Alexandre Aleixo




The thermophilous grasshopper Dericorys carthagonovae. Photograph by Francisco Rodríguez.

Ortego, J.,  González-Serna, M. J.,  Noguerales, V., &  Cordero, P. J. (2022).  Genomic inferences in a thermophilous grasshopper provide insights into the biogeographic connections between northern African and southern European arid-dwelling faunas. Journal of Biogeography,  49,  1696– 1710. https://doi.org/10.1111/jbi.14267

In my opinion, an important limitation is the difficulty to integrate geological information into process-based phylogeographic inference, which is particularly challenging when ancient events are involved. Geology and phylogeography illuminate each other, but what is probably needed is more active collaboration between researchers of the two disciplines. Among others, this could help to consider more carefully uncertainty surrounding geological reconstructions when interpreting phylogeographic evidence (e.g., dating of events).

Something I find very exciting are the discrepancies between geology/geography and phylogenomic evidence, as such findings can provide important counterintuitive insights into disregarded phenomena governing species distributions and geographical diversification. For instance, mounting biogeographical evidence – including our study published in this special issue – suggests that the colonization of semiarid areas of Iberia by thermophilous organisms of African origin most likely took place from the central Maghreb region (Algeria or Tunisia). This indicates that the exchange of terrestrial organisms between Iberia and Africa did not exclusively take place across the strait of Gibraltar (i.e., through the shortest geographical distance) and suggests that long-distance overseas dispersal might be much more common than previously thought.

Understanding the processes shaping species distributions and their spatial patterns of genomic variation requires the effective integration of multiple disciplines and, as such, geogenomics will be instrumental to the advance of phylogeography. However, organismal traits (i.e., dispersal capacity, interspecific interactions, ecology, etc.) must be also considered to formulate and test phylogeographic hypotheses, as not all taxa are expected to respond in the same way to a shared abiotic background and only certain geological events (e.g., Quaternary climatic oscillations) but not others (e.g., landmass/ocean configuration) might explain their demographic and evolutionary trajectories depending on species-specific attributes. Phylogeographic studies on geophilic organisms with low dispersal capacity might particularly benefit from a “geogenomic approach” and provide insights that, in turn, could contribute to refine geological hypotheses, particularly when developed within a multi-species comparative framework.

– Joaquín Ortego


Additional information:
Virtual issue on Geogenomics: https://onlinelibrary.wiley.com/doi/toc/10.1111/(ISSN)1365-2699.Geogenomics

REFERENCES
[1] Baker, P. A., Fritz, S. C., Dick, C. W., Eckert, A. J., Horton, B. K., Manzoni, S., … & Battisti, D. S. (2014). The emerging field of geogenomics: constraining geological problems with genetic data. Earth-Science Reviews, 135, 38-47.
[2] Dawson, M.N., Ribas, C.C., Dolby, G.A. and Fritz, S.C. (2022), Geogenomics: Toward synthesis. Journal of Biogeography, 49, 1657-1661.
[3] Leugger, F., Broquet, T., Karger, D. N., Rioux, D., Buzan, E., Corlatti, L., … & Pellissier, L. (2022). Dispersal and habitat dynamics shape the genetic structure of the Northern chamois in the Alps. Journal of Biogeography 49,  1848– 1861. https://doi.org/10.1111/jbi.14363
[4] Elizangela dos Santos Barbosa, W., Ferreira, M., de Deus Schultz, E., Willians Luna, L., Orsi Laranjeiras, T., Aleixo, A., & Cherem Ribas, C. Habitat association constrains population history in two sympatric ovenbirds along Amazonian floodplains. Journal of Biogeography, 49, 1683-1695.
[5] Luna, L. W., Ribas, C. C., & Aleixo, A. (2021). Genomic differentiation with gene flow in a widespread Amazonian floodplain‐specialist bird species. Journal of Biogeography, 49, 1670-1682.
[6] Ortego, J., González‐Serna, M. J., Noguerales, V., & Cordero, P. J. (2022). Genomic inferences in a thermophilous grasshopper provide insights into the biogeographic connections between northern African and southern European arid‐dwelling faunas. Journal of Biogeography, 49, 1696-1710.

Ecological traits matter

Differences in dispersal abilities and habitat specialization determine the postglacial range expansion of three high-elevation plants

Above: Steep limestone cliffs in the Pre-Pyrenees, a glacial refugium for the study species.

When I first visited the Pyrenees as a child from the Mediterranean lowlands, I got fascinated by the accordion-like folded landscape, the green and dense meadows, and the amount of unknown colorful flowers which painted the entire picture. In the coming years, I began to understand what processes and conditions produced that landscape and vegetation, and the original fascination slowly turned into questions. Inspired by classical and more recent literature about glacial refugia for plants from the European Alps, the question started to burn inside me: what about the Pyrenees? What happened in these mountains that create an almost perfect border between the Mediterranean and the template climate? As claimed in some classical studies, did mountain plants in the Pyrenees have more possibilities of surviving the cold stages than their counterparts in the Alps? And looking in the opposite temporal direction, what possibilities do they have to cope with climate change in the near future? To date, the lack of a critical mass of molecular data for Pyrenean mountain plants does not allow us to answer these questions, and that is the reason why we started the project in which our publication is framed.

Cover image article: (Free to read online for a year.)
Carnicero, P., Wessely, J., Moser, D., Font, X., Dullinger, S. & Schönswetter, P. (2022). Postglacial range expansion of high-elevation plants is restricted by dispersal ability and habitat specialization. Journal of Biogeography, 49,  1739– 1752. https://doi.org/10.1111/jbi. 

In this project entitled Conserving intraspecific diversity in a warmer world, we aimed at tackling the above mentioned questions and to understand the impact of past and current changes in the diversity within species. Nine species endemic to the Pyrenees were selected for this purpose, and in this first publication of the project, we present the results for three species with preference for carbonate bedrock. In the general trend of searching for individual examples, which could be a proxy for a wider group of ecologically similar species, I expected these three species to be good models to explain what happened to other species with similar bedrock preference. Nothing further from the truth. Our results showed two different responses to the end of the cold stage: one expanded rapidly, while the other two showed postglacial stasis; they remained in the areas where they survived the cold stages, with only a few colonizations of areas previously under the ice. Why?

When we were seeking an answer to this incongruent pattern, we went back to basic questions that a biologist should never forget: where and how do our study species live, disperse, reproduce, etc.? And these indeed brought us to a reasonable explanation. Salix pyrenaica, the species, which rapidly expanded and colonized previously glaciated areas, is a very good disperser and often able to find a place to grow provided a carbonate bedrock. In a way, we can call Salix pyrenaica a generalist of carbonate bedrocks. This ecological trait allowed it to rapidly and efficiently explore the newly available terrain after glaciation, by dispersing many fruits, and a considerable amount of them finding a proper spot to grow. Instead, Cirsium glabrum and Silene borderei showed a much more static picture. The areas where, according to our genetic and climatic data, they survived the cold stages are almost a perfect match to the areas where they occur nowadays. In contrast, they barely occur in potentially suitable areas that were under the glaciers during the ice ages. Silene borderei has no particular adaptations for long-distance dispersal, but Cirsium glabrum does. While it is true that Silene borderei indeed showed a more static postglacial history than Cirsium glabrum, something still has to explain why both expanded so little after the glaciations as compared to Salix pyrenaica. In contrast to the latter, Cirsium glabrum and Silene borderei are microsite-specialists in terms of habitat selection, which imposes a severe drawback in terms of colonization of new areas: even if dispersing seeds efficiently, only a very small portion of them will find a suitable habitat to grow, rendering the colonization of new areas an extremely slow process.


Schematic representing the impact of habitat specialization in range expansion. In the left panel, a generalist like Salix pyrenaica showing multiple successful dispersal events. In the right panel, for a micro-site specialist like Cirsium glabrum, most of the dispersal events will not succeed.

How close do these results bring us to inferring where the glacial refugia for high-elevation species in the Pyrenees actually were? Despite the uncertainties conferred by the above mentioned results, we are in the position of formulating some statements and, of course, new questions. On the one hand, Salix pyrenaica shows the expected behavior of contraction-expansion of glacial refugia: survival of a harsh period in refugia, and posterior expansion from there. Unfortunately, this expansion seems to have been so fast and involved a high degree of exchange of genes between expanding populations, that the signal for identifying the refugia in detail is too weak. In this case, we can state that there were at least two refugia in the east and the west. Instead, for Cirsium glabrum and Silene borderei we can clearly state that the eastern and western Pre-Pyrenees played an important role for the survival of the species during the ice age. The Pre-Pyrenees have already been suggested as a main refugium for species with carbonate bedrock preference, and our results confirm this.

In conclusion, our results show that species-specific ecological traits play a major role in the recent history of the studied species. Thus, for species like Cirsium glabrum and Silene borderei, refugia remained their permanentdistributions, while others, like Salix pyrenaica, started remarkable range expansions from the refugia. Ecological traits therefore strongly impact which species have narrow or widespread distributions. Future molecular data coming from our and other projects will provide further evidence to confirm, reject or reformulate the general applicability of the hypotheses formulated here.

Written by:
Pau Carnicero, PhD, Department of Botany, University of Innsbruck

Additional information:
@CarniceroPau
https://www.uibk.ac.at/botany/staff/scientific_staff/carnicero-campmany_pau.html.en

Acknowledgements
I would like to thank Peter Schönswetter for his relevant feedback on this blog post.

ECR feature: Leilton Willians Luna

Leilton W. Luna is a postdoc at the Pennsylvania State University. He is a biologist with a broad interest in how species adapt, diversify, and become extinct. Here, Leilton shares his recent work on birds of the Amazonian floodplains.

Leilton Luna doing research or just having fun bird watching.

Personal links. Twitter | Personal website

Institute. Department of Ecosystem Science and Management, Pennsylvania State University, USA

Academic life stage. Postdoc

Major research themes. Connections between the evolution of Earth and living organisms, ecological drivers of biological diversity, and the application of population genomics to the conservation of endangered species.

Current study system. I am currently studying the birds of the Amazonian floodplains. These river-created environments have a unique diversity of species, in contrast to adjacent habitats, such as upland (terra firme) forests. To me, the coolest thing is to understand how a riverine landscape produces such a wide variety of species. Perhaps one of the keys to understanding this question is to investigate the past, using genomic technologies. Using genomic data, I can explore the relationships between floodplain bird populations and the historical events in the Amazon that possibly made these populations so differentiated today.

Recent JBI paper. Luna, L. W., Ribas, C. C. & Aleixo, A. 2022. Genomic differentiation with gene flow in a widespread Amazonian floodplain-specialist bird species. Journal of Biogeography 49(9): 1670-1682. https://doi.org/10.1111/jbi.14257

Motivation behind this paper. The biogeographic history of floodplains is poorly known in comparison to other Amazonian environments. Therefore, we would like to understand what factors are responsible for generating diversity in Amazonian floodplains. Could it be differences between flooded environment types, such as blackwater igapó versus white-water várzeas forest? Or changes in the riverine landscape caused by past climate changes? Or even an interplay between these factors? To answer these questions, we study the Striped Woodcreeper (Xiphorhynchus obsoletus), the most common and widely distributed bird in the Amazonian floodplains. The tight relationship of this bird to the floodplains could tell us a little bit about the history of the environment, and for this purpose, we analysed its DNA. Another motivator was to underscore the importance of collections and expeditions for biodiversity research. Our study used tissues deposited in genetic resource collections, in museums from Brazil and the USA, which are the result of more than two decades of expeditions into the Amazonian floodplains.

Left: The Striped Woodcreeper (Xiphiorhynchus obsoletus). What can its DNA tell us about the history of the Amazon floodplains? (Credit: João Barros). Right: The igapó flooded forest of the Demini River, a tributary of the Negro River. The watermark on the tree trunk shows the height of the river during the flood (Credit: Thiago Laranjeiras).

Key methodologies. To investigate the structure and connectivity of Striped Woodcreeper populations, we sequenced a small amount of the bird’s genome. Along with genomic data, we used environmental information to test whether genetic differences between populations were associated with steep environmental gradients, specifically between igapó (habitats bordering clear- and black-water rivers) and várzeas forests (associated with white-water rivers). In addition, we tested different evolutionary scenarios based on information from geomorphological changes that occurred in central Amazonia during the Late Pleistocene. Here, the novel approach was to combine environmental and geologic information to gain insights into the drivers of genetic diversity in Amazonian floodplains.

Unexpected challenges. The main challenge was to cover the sampling of the Striped Woodchopper in the huge area of the Amazon basin. Even with tissue bank contributions from several past expeditions into the flooded forests, there were still important gaps. Thus, in August 2017, we undertook a navigation expedition on the Solimões River, in the heart of the Amazon. Spending 30 days on a boat, waking up early in the morning to enter the jungle and search for the Striped Woodcreeper and other floodplain birds, was a thrilling and frightening experience. The apprehension of not getting the samples was a constant companion. However, with the help of an extraordinary team of ornithologists from the National Institute for Amazon Research (INPA) and the Emilio Goeldi Museum (MPEG), we were able to succeed.

The team of ornithologists (also biogeographers) from INPA and Museum Emilio Goeldi navigating between Amazonian riverine islands during an expedition on the Solimões River in August 2017.

Major results. We found that genetic variability in a bird endemic to the Amazonian floodplains is more related to the history of changing riverine connections associated with Late Pleistocene climate change, rather than strong contemporary environmental gradients. Also, by comparing our results with others previously published, we found that the type of habitat a species uses can possibly determine the levels of genetic differentiation between populations. These findings add a new layer of information about the formation of the Amazonian biodiversity, which involves complex interactions between species’ ecological traits and the dynamic history of their environments.

Next steps for this research. The next step is to investigate the genetic diversity of more floodplain birds! This time, the idea is to gather a collection of bird species with different habitat specializations and test whether habitat use determines the structure and levels of genetic differentiation across species. Understanding these interactions is critical for highlighting the uniqueness of Amazonian floodplains, since many of these habitats are intensively destroyed in parts of the Amazon basin by logging and hydroelectric dam construction. These human activities are already affecting the occupancy of floodplain birds, but little is known about the effects on genetic diversity and connectivity at both population and community scales.

If you could study any organism on Earth, what would it be? Rather than an organism, I would like to study an interaction between organisms. I find it fascinating how species that compete for the same resources can adapt and evolve to this competition. Or even how two species find a way to coexist in intimate dependence, “cooperating mutualistically” throughout their evolutionary history. What could be the genetic basis behind the adaptation of such interactions? In this case, I would continue to study birds, which exhibit several interesting interactions with other groups of organisms. Be it hummingbirds selecting their favorited flowers by smell, or birds parasitizing the nest of other birds so that their offspring can survive (even at the expense of their foster siblings).

Anything else to add? As someone born in Amazonia, it is impossible not to be impressed by the number of species – especially bird species. A casual walk on the edge of a forest, or even in city parks, is enough to realize that there is something special about this region. Therefore, having the opportunity to study the Amazonian biodiversity is something rewarding. A lifetime is not enough to understand the evolutionary, ecological, and ecosystem complexity of this green wonderland. But unfortunately, that clock is ticking against this biodiversity, as levels of destruction, habitat conversion, and climate change are driving the Amazon rainforest to its tipping point. But despite this grim prospect, I still see that there is much to be done, both in science and in international conservation policies, to keep this huge forest, the number of species, and the native peoples who live in it standing.

The flooded Amazonian forests differ according to the “color” of the river. Meeting of the waters between the Negro River (igapó black-water) and the Solimões River (várzea white-water) (Credit: Thiago Laranjeiras).

ECR feature: Emily Booth on the evolution of Australian freshwater fishes

Emily Booth is a PhD student at the Flinders University in Australia. She is a molecular ecologist interested in understanding the effects of climate changes on the evolution of species. Here, Emily shares her recent work on the ‘genomic vulnerability’ of Australian freshwater fishes to climate change.

Emily Booth during fieldwork in Australia.

Personal links. Twitter

Institute. Flinders University, Australia

Academic life stage. PhD candidate

Major research themes. I am interested in understanding the effects of climate change (both historical and contemporary) on the evolution of species, particularly freshwater fishes.

Current study system. I am currently working with four species of Australian freshwater fish: golden perch (Macquaria ambigua), Murray cod (Maccullochella peelii), Murray River rainbowfish (Melanotaenia fluviatilis), and southern pygmy perch (Nannoperca australis). These species exhibit a variety of different life history and ecological traits; I am incredibly fascinated by the amount of biodiversity hidden away in our river systems! My PhD aims to assess the ‘genomic vulnerability’ of these species to anthropogenic climate change — that is, to predict how much adaptive genetic change is needed for populations to keep up with climate change. My recent JBI paper focussed on golden perch, which is a large-bodied, socioeconomically important species. Golden perch have evolved to tolerate a broad range of hydroclimatic conditions, including the Australian arid zone where river flow is highly variable. Golden perch undergo seasonal migration and have an amazing dispersal capacity, making them ideal for studying the effects of environmental change on highly vagile freshwater species.

The Murray River, Australia, is home to a variety of freshwater fishes (Photo credit: Kade Storey-Byrnes).

Recent JBI paper. Booth, E. J., Sandoval-Castillo, J., Attard, C. R., Gilligan, D. M., Unmack, P. J. & Beheregaray, L. B. (2022). Aridification-driven evolution of a migratory fish revealed by niche modelling and coalescence simulations. Journal of Biogeography, 49, 1726– 1738. https://doi.org/10.1111/jbi.14337

Motivation behind this paper. This paper is derived from my Honours thesis (equivalent to a MSc thesis in several other countries). My co-authors and I wanted to understand the processes that have led to the divergence of three golden perch lineages from three different river basins. Previous research had found these lineages to be so genetically distinct that they could be considered as separate species, but further investigation was needed. Since golden perch are extensively stocked from hatcheries into rivers to support the recreational fishing industry, it is important that we clarify how many species we are dealing with! We tested the hypothesis that historical aridification of Australia during the Pleistocene caused reduced habitat connectivity between river basins and facilitated the divergence of the three lineages.

Key methodologies. A cool thing about this study is that we used two independent data sets (genomic and environmental) to investigate the biogeographic and demographic history of golden perch. We began by using genome-wide SNP data to reconstruct the phylogenetic relationship between the three major golden perch lineages. Next, we built species distribution models (SDMs) based on environmental data to estimate the contemporary and historical ranges of those lineages. The SDMs allowed us to develop hypotheses (for example, about the historical size and connectivity of populations), which we then tested using genomic-based coalescent modelling.

Unexpected challenges. The most challenging part of this research was definitely the coalescent modelling. As somebody who was brand-new to coding, it certainly took some time to get my head around how to use the program fastsimcoal. But once I got the hang of it, it was difficult to know when to stop! In the end, I tested somewhere around >30 different models. It was a good thing I had hypotheses from the SDMs to keep me on track about which scenarios to test…otherwise I would have been there forever.

Major results. Our research found phylogenetic support for the delimitation of three golden perch cryptic species, each endemic to one of three major drainage basins. We discovered that aridification of Australia during the late Pleistocene likely played a role in facilitating the divergence of these lineages. Our SDMs found that during the Last Glacial Maximum (~21 thousand years ago) the amount of suitable habitat for golden perch was extremely reduced and there was far less connectivity between drainage basins. This theory was also supported by our coalescent models, which found that population sizes were much smaller during the Last Glacial Maximum compared to the current day. It was remarkable to find such a similar signal from two independent data sets. This work strongly highlights the benefit of integrating multiple types of data and analyses to develop and test biogeographic hypotheses.

Golden perch, Macquaria ambigua (Photo credit: Peter Unmack).

Next steps for this research. The evolution of arid zone species, especially obligate freshwater organisms, is a poorly studied topic in the literature. Many Australian freshwater species exhibit cryptic diversity between drainage basins, yet little research has been done to understand how this has arisen. I would be interested to use a similar analytical framework for other taxa to determine some broader scale patterns regarding the influence of historical aridification on the evolution of Australian freshwater diversity.

If you could study any organism on Earth, what would it be? I think it isn’t so much a question of what I want to study, but where. During undergrad I fell in love with island biogeography after reading David Quammen’s book The song of the dodo. Islands provide amazing natural experiments for testing evolutionary theories, and I am fascinated by processes like adaptive radiation and body size change that frequently occur on them. It might sound cliché for a biogeographer, but I would love to study species from the Galapagos Islands. Maybe marine iguanas (Amblyrhynchus cristatus) to start with, they’re pretty cool!

ECR Feature: Raphael S. von Büren on range limits in alpine plants

Raphael S. von Büren recently completed his Masters at the University of Basel, Switzerland. He is an alpine ecologist with particular interests in the ecophysiology of plants. Raphael shares his recent work on the environmental factors influencing the range distribution of alpine plants.

(left) Portrait Raphael von Büren. Photo credit: Raphael von Büren. (right) Research in alpine environments: Raphael von Büren in his preferred habitat during field work for his master’s thesis. Background: Rhone glacier, Switzerland. (Photo credit: Raphael von Büren)

Personal links. ResearchGate

Institute. Department of Environmental Sciences, University of Basel, Basel, Switzerland; Department of Research and Monitoring, Swiss National Park, Zernez, Switzerland

Academic life stage. Masters (completed 2021).

Major research interests. Alpine plant ecology and ecophysiology, field botany, plant identification.

Current study system. Currently, I am working on several plant ecology projects in alpine ecosystems: (1) Under review is a paper where we studied the influence of earlier snowmelt on above- and belowground growth and senescence of alpine grassland. (2) I am part of the current GLORIA (GLobal Observation Research Initiative in Alpine environments) field survey campaign, a worldwide project exploring vegetation changes on mountain summits. (3) In our latest project, we examine non-native species in the Swiss National Park, a protected area in the Central Alps, to set the basis for long-term monitoring, to anticipate potential future invasions and to discuss the implications for management in an alpine wilderness area.

I am fascinated by working in remote, pristine, alpine areas with harsh environmental conditions. High topographic heterogeneity leads to a mosaic of micro-habitats on small scales, resulting in high biodiversity and a variety of adaptations to the local micro-environment.

Recent paper in JBI. von Büren, R.S. & Hiltbrunner, E. (2022) Low winter temperatures and divergent freezing resistance set the cold range limit of widespread alpine graminoids. Journal of Biogeography, 49, 1562–1575. https:// doi.org/10.1111/jbi.14455

Field work. Cover Journal of Biogeography Volume 49, Issue 8. (Photo credit: Raphael von Büren)

Motivation behind this paper. Range limits of alpine plants are largely unexplored and unexplained. Studying the range limits mechanistically helps resolve the very basic ecological questions of why a certain species exists where it does, and why it is absent elsewhere. Understanding where the edges of an organism’s fundamental niche lie is essential for extrapolating its future distribution under changing conditions. Multidisciplinary approaches are needed that combine micro-climatology with plant ecophysiology at a high spatio-temporal resolution, focusing on the actual life conditions of alpine plants in situ.

Key methodologies. In an alpine grassland in the Swiss Alps, we selected 115 microsites (40×40 cm) within a 2 km radius that spanned a diversity of micro-climatic conditions. At each microsite, we assessed soil temperature 3 cm below ground, closest to the plant meristems, year-round with small temperature loggers and derived snow cover duration and thermal conditions from these data. Additionally, we determined soil chemistry and moisture, as well as vegetation characteristics (species composition, Landolt indicator values). Field data were combined with various freezing resistance analyses (electrolyte leakage, tetrazolium vital staining, regrowth capability) in individuals of the two most abundant alpine graminoids on acidic soils in the European Alps (Carex curvula, Nardus stricta) at 38 microsites by employing mixed regression models. Our approach allowed us to address where (field data) and why (freezing analyses) these graminoids occur or are absent. To our best knowledge, our study is the first to provide a mechanistic explanation of the cold range limit of alpine plant species.

Major results. The study demonstrates that low soil temperature extremes (freezing stress) during winter set the range limit of widespread alpine graminoids, and not the gradual action of temperature on growth and development (like it is the case for the treeline). This contrasts the common assumption that freezing resistance during the growing season is critical for plant species distribution. As clonal alpine plant species are very long-lived, a single clear, cold night without snow may set the scene for centuries. Understanding the edges of the fundamental niche is essential to extrapolate the current occurrence of a species to novel situations under climate change.

High micro-habitat diversity due to topography driven snowmelt pattern in the study area. Timelapse movie 2018. (Photo credit: Raphael von Büren, Erika Hiltbrunner)

Unexpected outcomes and challenges. Air temperatures extrapolated from weather stations do not accurately reflect the micro-climatic conditions alpine plant species are embedded in. Therefore, we measured soil temperature at high spatio-temporal resolution in situ to base our findings on ground-truth thermal conditions.

A common challenge in alpine environments is the limited accessibility of the study region in winter due to high avalanche risk. Hence, the freezing resistance was assessed throughout the growing season but not in winter. Taking away the insulating snowpack to access plant material in winter may also induce unwarranted plant responses.

Evaluating foliar freezing resistance in alpine graminoid species is demanding, because the leaves are often very narrow, and cell damages induced by frost injury are not clearly visible as tissue discolouration and necrosis. We employed an electrolyte leakage method with a miniaturized conductivity cell, which enabled us to reduce the water volume for leaking in order to gain high precision for detecting cell damages.

Next steps. As a next step, I propose to explore cold range limits of other alpine graminoid species, using the same methodology we used in our recent paper. Not only to resolve the very fundamental ecological question, why species occur where they do and why they are absent at other places; but also to explore my hypothesis that only some graminoid species reach the upper alpine grassline (restricted by the gradual action of temperature, in analogy to the treeline) and other graminoid species (which do not reach the grassline, e.g., Nardus stricta) are restricted by temperature extremes and freezing resistance (see Bürli et al. 2021, Alpine Botany; Körner 2021, Trends in Ecology & Evolution).

Lab work. (Photo credit: Raphael von Büren)

If you could study any organism on Earth, what would it be? I am interested in general ecological patterns. Therefore, I prefer studies with multiple species. My favourite taxa are vascular plants, or more generally, sessile organisms. It is fascinating to explore the various adaptations that these species have evolved to cope with diverse environments, given their sedentary lifestyle. Expertise in field botany and vegetation ecology enables the “reading” of landscapes. That is, by simply looking at the species composition, one can infer the environmental conditions at a location. In topographically rich alpine environments, steep micro-habitat gradients lead to different plant communities within a few meters only.

Anything else to share? The recent study in Journal of Biogeography represents a condensed piece of my master’s thesis. I conducted most of the fieldwork in summer 2020 close to the Furka pass in the Swiss Central Alps at 2200-2800 m asl. Fieldwork in remote alpine regions requires quite a bit of planning and the cooperation of people with good team spirit is of great importance. I was part of a research team that was working on various ecological projects. We spent 4 months at the Alpine Research Station Furka (ALPFOR, http://www.alpfor.ch), giving up the comforts of home for the sake of science. After this intense time of sharing almost everything, helping each other with field and lab work, surviving harsh weather conditions and being snowed in, cooking together, and having inspiring discussions, it only remains for me to express my appreciation to the entire team, and in particular to Erika Hiltbrunner, Christian Körner and Patrick Möhl. Thank you, folks!

Danish island biogeography

Danish islands help to disentangle how plant dispersal characteristics shape species richness patterns.

Above: The Danish coastline with the island Hjelm in the background. © Anders Sanchez Barfod.

Suppose you hear the names Galapagos, Hawaiian or Canary Islands. In that case, I am sure you have a picture in mind right away. These islands are well known in general and very popular in island biogeography. We have seen pictures and documentaries or read evolutionary and ecological studies about these islands. But have you every head of islands like Anholt, Egholm, Fur or Hjelm? These are islands scattered along the Danish coast, and I would like to convince you that such islands have great potential to help us solve pending questions in island biogeography.

Editors’ Choice article: (Free to read online for two years.)
Walentowitz, A., Troiano, C., Christiansen, J. B., Steinbauer, M. J., & Barfod, A. S. (2022). Plant dispersal characteristics shape the relationship of diversity with area and isolation. Journal of Biogeography, 49, 1599–1608. https://doi.org/10.1111/jbi.14454

Denmark has more than 1400 immensely diverse islands. Some are home to Danes while others are uninhabited; they are located in the North Sea, Baltic Sea or in bights and fjords and differ in size. My co-authors Prof. Dr Manuel Steinbauer (University of Bayreuth) and Assoc. Prof. Dr Anders Sanchez Barfod (Aarhus University) were intrigued by these islands and their flora. They raised the question: can the way plants disperse to islands help explain the species richness patterns on these islands?

Indeed, they can. For example, a plant like the common oak tree (Quercus robur) has heavy acorns dispersed by mammals or birds (zoochore dispersal). The chances are high for an acorn to reach and get established on a larger island. The transporting animal was looking for a spot with enough resources for survival and therefore decided to head for a larger island. For plants dispersed by water (hydrochore dispersal) like the common cordgrass (Spartina anglica), chances are high that these are adapted to habitats associated with coastal areas. Now simple mathematics can help to explain why larger islands have proportionally fewer hydrochore plant species than smaller islands: If the coastline doubles, island area roughly quadruples.

It was most astonishing to unveil such relationships between plant dispersal and island characteristics despite the human impact on plant communities on Danish islands for centuries. These patterns seem so fundamental and robust that anthropogenic encroachment could not overwrite them. However, if we additionally include human impact in our models, we can explain plant species diversity on islands even better.

While working with Danish Islands, I was highly impressed by two former botanists and scientists, who massively shaped this study, although I never had the chance to meet them. Eric Wessberg was a Danish botanist who inventoried numerous islands jointly with his team. His plant records built the baseline of our study. Such data are essential for the studies we conduct as island biogeographers. I was also profoundly impressed by the theories and thoughts developed by Alvar Palmgren, a Finnish botanist who lived from the late 19th until the mid-20th century. Back in his day, he developed first thoughts on how plant dispersal characteristics shape richness patterns on islands long before the discipline of island biogeography was established. Alvar Palmgren seems to suffer a bit from what I call the “Alfred Russel Wallace syndrome”, as his genius work is little remembered. Alfred Russel Wallace developed theories about evolution at the same time as Charles Darwin. Still, his counterpart is better known to be the founder of evolutionary biology. With our study, we hope to not only put Danish islands onto the map of island biogeographical research but also value the work of Eric Wessberg and Alvar Palmgren.

I learned from this study that numerous islands are out there whose potential for island biogeography has not been explored yet. We should continue to be on the lookout for such islands that help answer questions on how island biodiversity is being shaped by natural and anthropogenic forces.

Written by:
Anna Walentowitz, M.Sc., PhD candidate
University of Bayreuth
Department of Biogeography
Universitaetsstrasse 30 95447 Bayreuth

Additional information:
Twitter: https://twitter.com/ArchipelagoAnna

ECR Feature: Nicky Lustenhouwer on niche shifts in invasive plants

Nicky Lustenhouwer is a postdoc at the University of Aberdeen. She is an evolutionary ecologist interested in range expansions and invasive organisms. Nicky shares her recent work on the relative roles of climate change tracking versus niche evolution in the spread of an invasive weed.

Nicky Lustenhouwer with a particularly large individual of Dittrichia graveolens during fieldwork collecting seeds in California. (photo credit: Nicky Lustenhouwer)

Personal links. Scholar | Twitter | Github

Institute. School of Biological Sciences, University of Aberdeen, UK

Academic life stage. Postdoc

Research themes. Evolutionary ecology, range shifts, invasions, population spread

Current study system. I am currently studying the blue-tailed damselfly, Ischnura elegans, which is rapidly shifting its native range northward with climate change. A decade of previous work has shown all kinds of interesting evolutionary changes that have happened during this range shift in Sweden and Scotland, including changes in thermal tolerance, dispersal, and female morph frequencies. The aim of my current postdoc is to expand on this work with two new transects in Norway and Finland, so we can study how evolution varies along four parallel transects. I just returned from 7 weeks of exciting fieldwork travelling from pond to pond in Scandinavia.

Recent paper in JBI. Lustenhouwer, N. & Parker, I.M. 2022. Beyond tracking climate: Niche shifts during native range expansion and their implications for novel invasions. Journal of Biogeography. 10.1111/jbi.14395

Motivation behind this paper. This paper was part of my previous postdoc at the University of California, Santa Cruz, where I was studying the Mediterranean annual plant Dittrichia graveolens. This is a fascinating species because it is currently both expanding its European native range very rapidly, and invading several other continents, including California where it is considered a noxious weed. I had previously found that the native range shift of D. graveolens was promoted by rapid evolution of earlier flowering time (the species produces seeds in autumn and is constrained by the end of the growing season in the north). I was therefore really interested to ask whether this range shift was simply tracking climate change, or if the climate niche had shifted along the way, allowing for further range expansion. And if that was the case, how would this change our risk assessment of climatic areas that may be invaded elsewhere?

[left] Dittrichia graveolens is a typical ruderal plant and can be found in any kind of disturbed environment, like this crack in the pavement in its native range in southern France. [right] Highways are key range expansion corridors for Dittrichia graveolens, as shown here at the northern range limit in the Netherlands. (photo credit: Nicky Lustenhouwer)

Key methods. We collected occurrence data for Dittrichia graveolens across its native range in Eurasia and in two invaded ranges in California and Australia. We used these data to quantify the climate niche in both environmental space (using the COUE framework of niche centroid shift, overlap, unfilling and expansion) and in geographic space (using MaxEnt). A key step was to reconstruct the historic native range limit pre-expansion (1901-1930) using old maps and records. This allowed us to model the climate niche based on the historic range and climate, and then project it forward to the present (1990-2019) to see what the expected range shift would be when tracking climate change, and how this matched the observed current distribution of the species. We also modelled how D. graveolens’ climate niche changed over the course of the native range expansion. Finally, we used this information to ask which areas of California and Australia may be at risk of invasion if similar niche shifts were to occur in the exotic range.

Major results. We found that the native range expansion of D. graveolens in Europe went well beyond expectations based on tracking climate change alone, accompanied by a 5% niche expansion into more temperate climates over the course of this range shift. In contrast, the two invasions were still confined to climatic areas predicted by the historic native niche only, showing niche conservatism. This was especially surprising in Australia, where D. graveolens has been present for nearly 150 years. Our results highlight that niche shifts are not necessarily most common during invasions, which is where they have historically received most attention in the literature. They can also play an important role during native range shifts induced by climate change, with important consequences for the location of the new range limit.

Dittrichia graveolens growing at the edge of a salt marsh where the species was first observed in California (Alviso). (photo credit: Nicky Lustenhouwer)

Unexpected challenges. Our biggest challenge was dealing with the geographic bias in species occurrence records that are readily available, a very familiar problem in niche modelling. One way we mitigated this issue (apart from accounting for it in our models as much as possible) was by investing a lot of time in collecting extra occurrence records in under-sampled areas, from all kinds of data sources such as small botanical journals in local languages, old floras that the library had shipped over for me, and local databases. In the end about a quarter of our data points came from outside the Global Biodiversity Information Facility (GBIF – the major database for open biodiversity data). What I enjoyed most was directly contacting local experts in countries where we had minimal data, and these local experts provided a wealth of interesting anecdotes about their experience with this species in its recently expanded range.

Next steps. I will continue to collaborate with my colleagues in Santa Cruz, as we are writing up a series of greenhouse experiments and genomics work to investigate evolutionary changes during both the native range expansion of D. graveolens and the invasion in California. I am very excited to be able to compare a native and exotic range expansion scenario in the same species but against different backgrounds of genetic diversity, gene flow from the historic native range, and environmental gradients. We are for example studying how plant height, seed traits, and phenology shift from core to edge in each range.

If you could study any organism on Earth, what would it be? A plant that grows somewhere beautiful, like an arctic species – everyone always makes fun of me for picking study organisms that thrive in the most human-disturbed environments (both Dittrichia and Ischnura elegans do). During my PhD in Switzerland, I spent all my time on highway parking lots instead of in alpine meadows!