ECR Feature: Purabi Deshpande on habitat use by over-wintering birds

Purabi Deshpande is undertaking her PhD at the University of Helinksi. She is an urban ecologist, with an interest in understanding how climate change and anthropogenic disturbance affect bird communities. Purabi shares her recent work on the interaction between climate and habitat on over-wintering bird abundance in Finland.

Purabi, watching early spring migrants in winter whilst surrounded by tens of centimeters of snow on the ground. (Photo credit: Ricky Nencini)

Personal links. Twitter

Institute. University of Helinski

Academic life stage. PhD

Major research interests. Urban ecology, ornithology

Current study system. I study the response of birds to changing environments at the intersection of urbanisation and climate change. Human impacts on ecosystems are often studied at a local scale (e.g. habitat destruction due to a city’s growth) or at the global scale (e.g warming temperatures due to anthropogenic climate change). I am interested in understanding how birds respond to both these local- and large-scale changes caused by humans. Part of my research is carried out in Bangalore, a megacity in India, and the other part in Finland, which at 60 to 70 degrees north faces the brunt of climate change.

Recent paper in JBI. Deshpande, P., Lehikoinen, P., Thorogood, R., & Lehikoinen, A. (2022). Snow depth drives habitat selection by overwintering birds in built‐up areas, farmlands and forests. Journal of Biogeography. 10.1111/jbi.14326

Motivation for this paper. Snow cover in Finland, especially in the south of the country, is decreasing drastically as a result of warming climates. At the same time in human inhabited areas across the country, there is a lot of supplementary feeding, either directly, indirectly (think garbage), or in the form of introduced plant species. Species that would typically be classified as “migrants”, which would leave Finland during the winter, are now seen overwintering in Finland. This change in migratory behaviour is possibly due to milder climates and/or constant food supply. We therefore wanted to explore how different environmental variables and their interaction with different habitats affected the abundance of overwintering birds in Finland.

A brambling, seen in a snowy winter (Photo: Petteri Lehikoinen)

Key methods. We explored if abundances of birds in three different habitats (built-up, farmland and forest) changed with snow depths and temperature across 32 winters and whether species traits could explain the observed changes. We expected most variation in abundance to occur in built-up habitats as snow depths were likely to be lower and food availability higher, which would allow more birds to overwinter here. This work would not have been possible without brilliant long-term climatic monitoring datasets that are maintained in Finland. The Finnish Meteorological Institute maintains mean daily snow depth data for 10 by 10 km grids across the country (among other climatic variables). More importantly, the Finnish winter birds census which is an effort undertaken by citizen scientists every winter for more than half a century is a mind-blowing effort. This is especially true when you consider that some of the data collection is done at temperatures as low as minus 30 degrees centigrade!

Major results. There are two major results from this recent paper. First, there is an interaction between habitat and climatic conditions. As expected, decreasing snow depth led to increased bird abundance in farmlands and forests. However, as snow depth increased, there was increasing abundance in built-up areas. These results indicate that built-up areas could provide refuges for birds to over-winter when climatic conditions become less favourable. With climate change there are expected to be more extreme weather events. Overwintering species that can occupy urban areas might benefit, compared to those species that avoid built-up areas. Secondly, we found that snow depth is a better predictor of bird abundance than temperature. Even though there is a correlation between temperature and snow depth, snow depth may better reflect climatic harshness because food or roosting sites will be covered at high snow depths. However, collecting snow depth data is more difficult than temperature, so it is often overlooked while studying the effect of climatic factors on species.

Unexpected outcomes. As I was interested in seeing how urban environments are affecting birds, I had expected that the largest changes in abundances of overwintering birds would be observed in built-up areas, due to low snow depths and easy access to food. On conducting the analyses, we discovered that this was not the case and most of the changes were driven by farmland areas! The most exciting finding of this work is that the variation in bird abundances is explained better by snow depths rather than temperature. Data pertaining to snow depth is often difficult to collect at a level that is relevant to study animal ecology. So, most research uses temperature instead. Few studies investigate how habitat preferences of animals change with changing snow depths.  Here we show that even though temperature and snow depth are often correlated they might be affecting animals differently and warrant separate investigation.

Barnacle geese foraging on a thawing farmland.

Next steps. As a result of warming climates we know that many species are moving their ranges along latitudinal and altitudinal gradients. Most of this work is focused on movements in the spring, However, weather is more variable in the winter. We are currently working on a manuscript which explores not only the poleward shifts in wintering bird communities in Finland, but also whether birds are moving poleward faster in certain habitats, and how changing snow depths are affecting these shifts.

If you could study any organism on Earth, what would it be? I have always been excited about birds and I am quite happy sticking with them! More than particular organisms I would like to get my hands on some long-term monitoring datasets of different taxa and explore similar questions with all of them.

Anything else to share? My PhD journey so far has been a real adventure. Before I moved to Finland (from India), I had only seen snow once before. Carrying out fieldwork in sub-zero temperatures, thinking about winter ecology and shifting my “home-range” has been an excellent experience!

Climate and environment shape jackal diet

Dietary flexibility promotes range expansion: The case of golden jackals in Eurasia.

Above: Golden jackal in carcass cleaning role (with raven Corvus corax). According to the literature, the consumption of wild ungulates and domestic animals are mainly due to scavenging. Photo: Zoltán Horváth.

Global changes can lead to the expansion of a species geographical range. Exploring the causes and potential effects of predatory mammalian expansion is also relevant from a scientific, wildlife management, animal husbandry and conservation perspective

The golden jackal (Canis aureus) is a 10-15 kg canid that is one of the most successful carnivore species in Europe. Its original range included Central and Southeast Asia, the Arabian Peninsula, the Middle East and Eastern Central Europe. Isolated populations lived along the Mediterranean and Black Sea coastal regions until the middle of the 20th century. The species range then rapidly expanded to encompass the entire Balkans in the 1970s-1980s, and further to the north and west such that it is now found across Europe. Within this wide geographic range, the golden jackal also occurs in temperate, sub-Mediterranean, Mediterranean and subtropical climates. It occurs in habitats from grasslands to wetlands to deciduous forests to near-natural and highly artificial anthropogenic habitats, and even in the vicinity of large cities.

Cover image article: (open access)
Lanszki, J., Hayward, M. W., Ranc, N. & Zalewski, A. (2022). Dietary flexibility promotes range expansion: The case of golden jackals in Eurasia. Journal of Biogeography, 49, 993– 1005. 

The limiting and facilitating factors driving this range increase are of particular interest given the present rapid population expansion in Europe. The occupation of the jackal, previously considered to prefer a warm climate and it has recently been observed beyond the Arctic Circle. The species expansion may have been triggered by various factors, such as changes in land use or climate change, the abundance of anthropogenic food sources or a historic decline of the grey wolf (Canis lupus) as apex predator and competitor. The jackal’s population growth and range expansion are likely facilitated by the species’ dispersal potential, its ability to live in human-dominated environments and flexible social behaviours.

During range expansion, wildlife must adapt their foraging and trophic niche to the new biotic and abiotic conditions. In this study, based on 40 published datasets, we analysed which climatic and environmental factors affected/shaped the dietary composition of golden jackals. Furthermore, we compared these drivers in the species’ historic and recently colonized distribution ranges.

Golden jackal dietary study sites have occurred across Eurasia. White circles – Reviewed studies, black circles – studies of sufficient quality to be included in our analyses. Orange colour indicates the current geographical range with established, reproducing jackal populations. A blue dashed line separates the study sites of the recently colonized and historic ranges. Golden jackal photo by Zoltán Horváth.

Our analyses revealed that three main food groups dominate the golden jackal’s diet – small mammals, domestic animals and plants – but the proportions of each vary greatly. Other food types (for example birds, wild ungulates, reptiles, waste) may only be significant locally. We found that the jackal diet composition is shaped by climate, habitat productivity and habitat composition in similar way in both historic and recently colonized range. The proportion of small mammals in the golden jackal diet decreased with annual mean temperature, whereas the consumption of wild ungulates increased with environmental productivity (NDVI).

The jackal diet composition and trophic niche are shaped by climate and habitat productivity

The recently colonized distribution range of golden jackals in Europe had a lower mean temperature but higher environmental productivity compared to the species’ historic range in Eurasia. In the recently colonized range, jackals consumed small mammals and/or wild ungulates (mostly from scavenging or viscera eating) more frequently, and fewer plants and/or domestic animals (again, mostly from scavenging or feeding on the remnants of domestic animal slaughter).

That is, climatic and environmental factors shape the golden jackals’ diet composition and trophic niche breadth, which, in a changing environment, greatly enhances the opportunities for jackals to colonize new areas successfully.

Written by:
József Lanszki (1), Matt W. Hayward (2), Nathan Ranc (3) & Andrzej Zalewski (4)
(1) Full professor, Department of Nature Conservation, Hungarian University of Agriculture and Life Sciences, Kaposvár Campus, Hungary
(2) Professor of Conservation Science, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, Australia
(3) Research Engineer, Université de Toulouse, INRAE, CEFS, Castanet‑Tolosan, France
(4) Full professor, Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland

Additional information:

ECR feature: Amelia Bridges on deep-sea ecological gradients

Amelia Bridges is a postdoc at the University of Plymouth in the UK. She is a marine biologist interested in deep-sea ecology. Here, Amelia shares her recent work on seamount benthic community gradients.

Dr Amelia Bridges presenting her research at the National Marine Aquarium.

Personal links. Twitter | Website | Research Gate | Linkedln

Institute. University of Plymouth

Academic life stage. Postdoc

Major research themes. Benthic ecology, marine spatial planning, fundamental ecology of the deep sea, habitat mapping.

Current study system. The deep sea represents an immensely vast area of our planet, and yet comparatively little is known about ecosystems within it. Throughout my career I’ve been lucky enough to work on a number of deep-sea ecosystems including the Pheronema carpenteri sponge aggregations of the North Atlantic, and the cold-water coral reefs and gardens in the South Atlantic. What I find so interesting and engaging is that we’re still learning about the fundamental ecology of these ecosystems. For example, what functional roles do they have? How do these fit in with the wider biosphere, global cycles and ecosystem services?

Recent JBI paper. Bridges, A. E., Barnes, D. K., Bell, J. B., Ross, R. E. & Howell, K. L. (2022). Depth and latitudinal gradients of diversity in seamount benthic communities. Journal of Biogeography, 49(5), 904-915

The RRS James Clark Ross coming into Jamestown, St Helena (Credit: Nils Piechaud).

Motivation behind this paper. Shifts in diversity over environmental gradients represent one of the most fundamental ecological fields of study, with research dating back centuries. Investigation of diversity gradients in the deep sea began in the 1900s, but samples were only available from soft-substrate ecosystems due to the technologically challenging nature of data collection. Just like in terrestrial and shallow marine ecosystems, we know that different substrate types support different communities in the deep sea. Additionally, certain features that provide hard substrates, such as seamounts, are also exposed to different hydrodynamic regimes that alter key environmental drivers of diversity such as food availability. Here, we wanted to investigate whether diversity gradients described for the deep sea, but hypothesized from soft-substrate data, applied to hard-substrate ecosystems also. Understanding diversity gradients of communities living on hard-substrate is important as seamounts and oceanic islands often serve key ecological roles such as stepping stones for dispersal and providing nursery habitat and refugia.

Key methodologies. We used regression modelling to investigate the relationship between α- and β-diversity, depth and latitude, and other ecologically/biologically relevant parameters correlated with them. Whilst some previous studies have characterised these relationships over individual or small chains of seamounts in close proximity, our data comes from nine different features across a 32-degree latitudinal range, and therefore represents the most broadscale study of such relationships. These data were collected aboard large, ocean-going research vessels equipped with high-resolution camera equipment and sensors collecting environmental data. This approach has allowed us to provide insight on gradients and drivers that are relevant at broad ocean-basin-scales as opposed to regionally, finer-scale relationships. Additionally, the investigation of α- and β-diversity within a single dataset is not often undertaken, but our results show that differences in the two indices are important to consider, particularly through the lens of sustainable management.

Some example seabed images from the cruises around St Helena, Ascension and Tristan da Cunha (Credit: British Antarctic Survey/Centre for Environment, Fisheries and Aquaculture Science).

Unexpected challenges. As many who work in deep-sea science will attest, characterising the diversity of ecosystems from imagery can be particularly challenging. Not only is the initial annotation process manual and slow, but the taxonomic resolution achieved is often below what could be reached if physical specimens were examined using traditional taxonomic approaches like dissection. However, when working with fragile ecosystems like cold-water coral gardens, there is an important balance to strike between non-invasive scientific sampling and taxonomic resolution. This is why we used an Operational Taxonomic Unit (OTU) approach in our study, given that we can rarely identify an individual to species level. Still, we can say that this group of individuals is very similar morphologically. Therefore, an OTU is treated as a species (or morphospecies) in diversity analyses.

Major results. Whilst patterns in the data we collected aligned with previously described parabolic latitudinal diversity gradients per hemisphere in the deep sea, likely driven by productivity regimes, we did not detect shifts in α-diversity gradient caused by depth that are commonly reported from soft-substrate ecosystems. This demonstrates that ecological ‘rules’ based on data from one ecosystem may not be transferable to other ecosystems, particularly where key characteristics such as substrate type are different. Although the number of ‘species’ (OTUs) didn’t change with depth, upon further data exploration, we found that the ‘species’ present across the depth range did vary significantly, aligning with a small number of studies that have hypothesised the high species richness of seamount features in the deep sea derives from a turnover, or change in, species as you progress down the slope into deeper water (β-diversity gradient). The difference in α- and β-diversity gradients observed here shows the importance of considering both metrics when characterising seamounts and determining sustainable management strategies in the future.

Sunrise at sea near Tristan da Cunha (Credit: Nils Piechaud).

Next steps for this research. The next steps would be to conduct similar studies on other seamounts/oceanic island features within the South Atlantic to determine if the identification of key drivers holds true, but also in other ocean basins for the same reason. The global south is extremely understudied compared to the northern hemisphere, and as we have shown, caution needs to be taken when applying ecological ‘rules’ to less studied ecosystems/areas. Through equitable scientific exploration of the global south, I hope we will further understand the fundamental ecology of deep-sea ecosystems, their distribution, and how we can best ensure their sustainable management going forward.

If you could study any organism on Earth, what would it be? I know I’m biased, but I really do love deep-sea ecosystems! I think the fact that we still have so much to learn about them is the most exciting aspect – the only comparison I can think of would be turning the clock back and being a terrestrial ecologist centuries ago. Also, from a management perspective, we still have the chance to ensure robust environmental regulations are in place in the deep sea before mass exploitation happens.

Anything else to add? Although I wasn’t present, during one of the cruises the fibreoptic cable connecting the camera system to the ship snapped (possibly due to a shark bite!) leaving the camera system totally unconnected on the seafloor, hundreds of metres below the surface. Luckily, thanks to the clever work of Captain and crew, it was retrieved… on the first attempt!

ECR feature: Pieter Sanczuk on plant range shifts under climate change.

Pieter Sanczuk is a PhD student at the Ghent University in Belgium. He is a botanist interested in forest microclimates. Here, Pieter shares his recent findings on the understorey plant species range dynamics under climate change.

Pieter searching for bluebells transplanted 60 years ago (and 35 years before he was born). Although GPS coordinates were available, small bluebell populations can be hard to find in a 1,500 ha sized forest.

Personal links. Google Scholar

Institute. Forest & Nature Lab, Bioscience, Ghent University, Belgium

Academic life stage. PhD student.

Major research themes. The effects of forest microclimates and biotic interactions on understorey plant species range dynamics under climate change.

Current study system. In my PhD, I study the effects of small-scale environmental variation and biotic factors (e.g., competition or herbivory) on understorey species range shifts due to climate change in temperate forests of Europe. Many species are shifting their distributions towards higher latitudes and elevations. However, such a trend remains somehow elusive for forest understorey species, mostly due to the importance of processes operating at small spatial scales. For example, trees are ecosystem engineers, buffering the climatic extremes for species living within and below tree canopies. By including environmental variation related to small spatial scales into predictive models, I aim to obtain more accurate projections of future species ranges.

Recent JBI paper. Sanczuk, P., De Lombaerde, E., Haesen, S., Van Meerbeek, K., Van der Veken, B., Hermy, M., Verheyen, K., Vangansbeke, P. & De Frenne, P. (2022). Species distribution models and a 60-year-old transplant experiment reveal inhibited forest plant range shifts under climate change. Journal of Biogeography, 49(3), 537–550

The Hallerbos in Belgium is nicknamed ‘the blue forest’ because of the carpets of spring-flowering bluebells, which attract yearly more than 100,000 visitors (Photo by Sanne Govaert).

Motivation behind this paper. Bluebell (Hyacinthoides non-scripta) is one of the most well-known species in the European forest understorey. During spring, this species can form a blue carpet that covers the understorey layer. For this reason, tourists worldwide are attracted to large flowering populations in France, Belgium and the UK. However, reports indicate that the colonization rates (i.e., the speed a plant population can move) in this species can be five orders of magnitude slower than the velocity of contemporary climate change. If climate change negatively impacts bluebells’ performance, this species is potentially vulnerable to local extinction, and range shifts that are fast enough to track the shifting isotherms are highly questionable. In our paper, we aimed to find out how climate change will affect range dynamics in bluebell and whether this species will be able to track the projected distribution shifts.

Key methodologies. The most emblematic part of our methodology was the experiment. That is, as far as I know, our experiment is among the longest running transplant experiments in the world. In 1960 (more than 60 years ago!), bluebells were transplanted from three natural source populations to several forest sites beyond its natural distribution in Belgium. Both the source and transplanted populations were resurveyed 45 and 60 years after the installation of the experiment, which allowed us to analyse temporal trends in the population performance and estimate colonization rates. Because long-term experimental research is typically done at smaller scales, we combined the results from the experiment with species distribution models to assess potential range dynamics across a broader spatial extent. The combination of experimental research with predictive modelling is highly powerful and often provides complementary insights not possible to obtain when using only one of the methods.

Two of the transplanted populations in 2020. Several traits were measured on ten flowering individuals within each population.

Unexpected challenges. One of the largest challenges was relocating the transplanted populations. Although GPS coordinates, maps, and descriptions of the overstorey structure were available for each population, relocating ~1 – 10 m² patches of bluebells in a 1,500 ha forest is difficult. Our first attempt was actually in 2019. However, this field campaign failed because we were too late in the growing season. We could only relocate one population, from which the flowers and leaves were in a senescent phase. Timing really matters! So, in 2020, we returned just right within the flowering period. This was a good decision, as we relocated all populations that were also found in the first resurvey of the experiment (except for one, where the forest was clear-cut). Finding the populations is really satisfying if you think that someone (actually, not just someone, but the pioneer of Belgian forest ecology) planted the individuals 60 years ago – that is, 35 years before I was born!

Major results. Unfortunately, we found clear signals that the populations in the source and transplanted areas have decreased. The species distribution models also predicted a similar decreasing trend in habitat suitability due to climate change. Hence, the decrease predicted by the models has already started in the study populations. Moreover, based on the colonized distance from the transplanted populations since 1960, we estimated that the average colonization rate was only 2 cm per year. Currently, this is 17,500 times slower than the velocity of climate change (the temperate isotherms for broadleaf and mixed forests are shifting at a rate of 350 m per year). Given the slow colonization rate presented by the plant, range shifts that are fast enough to track the shifting climate are virtually impossible. In essence, bluebell’s climatic envelope is currently running away from its natural distribution.

Bluebell is adapted to grow in deep shade below closed tree canopies of Beech (Fagus sylvatica), and therefore successfully occupies forest patches that are too stressful for many other plant species to grow. Picture from the Vecquée forest wherein the transplanted populations are located.

Next steps for this research. Luckily, forests are natural climate regulators. Depending on the forest structure, overstorey temperature can be buffered up to 8 °C, resulting in cooler microclimates. This buffering can attenuate climate change impacts on forest understorey species. If we want to predict understorey range dynamics under climate change accurately, we need to integrate the variation in understorey temperature conditions. Currently, we are running predictive models on a suite of common forest understorey plant species to investigate the effect of forest microclimates on their range dynamics under climate change. We aim to generate guidelines for forest managers to help mitigate climate change effects on forests.

If you could study any organism on Earth, what would it be? Herbs are great study organisms: they are easy to measure and perform experiments with and often show fast responses to experimental treatments under changing environmental conditions.

Anything else to add? In short: combining multiple methodological approaches is really cool! It can take a bit longer to familiarize yourself with the analyses, but you learn a lot from them, and it often provides novel insight into your study system. If you doubt it, go for it!

Historical biogeography in recent evolving Neotropical mammals

Oligoryzomys is an intriguing genus of sigmodontines that is distributed in almost all ecoregions of South America and continental Middle America. How did it get to be so diverse and distributed so broadly?

Above: A Patagonian specimen of Oligoryzomys longicaudatus, a species representative of one the fastest and geographically wide radiation of Neotropical mammals (photo credit: Dario Podesta).

Recent studies about the diversity of New World rodents, especially the mice and rats of the subfamily Sigmodontinae, show that their diversification started at the end of the Middle Miocene (ca. 12 Mya; Parada et al. 2021), reaching an impressive diversity of more than 400 living species in this period of time. Sigmodontine species richness is far from being completely characterized as shown by the frequent descriptions of new living species and even genera. Among sigmodontines, there is an intriguing genus that can be found in almost all ecoregions of South America and continental Middle America, the genus Oligoryzomys. This large distribution is only compared among mammals with that of the medium- and large-sized genera Conepatus (skunks), Didelphis (opossums), Procyon (raccoons) and Puma (cougar). Oligoryzomys encompasses 32 living species of long tailed mice; this species richness is among the largest among sigmodontine genera but is far below those of the genera Thomasomys, mainly distributed in the Tropical Andes and formed by 47 species, and Akodon, distributed in most of South America except Amazonia and most of Patagonia and formed by 31 species. Remarkably, Oligoryzomys is a much younger lineage (ca. 2.6 Mya old) than Thomasomys (ca. 4.22 Mya) and Akodon (ca. 3.8 Mya old). Another issue of interest is that several species of long tailed mice are the primary reservoir of distinct strains of hantaviruses that in humas cause Hantavirus Pulmonary Syndrome.

Cover image article: (Free to read online for two years.)
Hurtado, N. & D’Elía, G.(2022). Historical biogeography of a rapid and geographically wide diversification in Neotropical mammals. Journal of Biogeography, 49, 781–793. 

Amazed by the large diversity and geographic distribution of Oligoryzomys and their epidemiological relevance, which we collaborate to uncover and characterize the genus in previous studies, and here we designed a new study aimed to explain how this genus reached its enormous distribution and diversity in such a short period of time. After gathering samples from our own fieldwork, loans from museum collections and colleagues, we collected sequences of five genes. Then, we reconstructed the phylogenetic relationships among long-tailed mouse species using coalescence methods and dated their divergence times and found the biogeographic model that best describe the type and sequence of biogeographic events to explain the genus’ diversification.

Historical biogeography of the genus Oligoryzomys.

We corroborated that Oligoryzomys has a higher diversification rate than that of the Thomasomys and Akodon, the most species rich genera of the subfamily. We found that the most recent common ancestor of the genus, which lived ca. 2.6 Mya, was distributed in a large area in the lowlands of northern South America. Then, this ancestor, after a series of vicariant and dispersal events, colonized southern South America, the Andes and part of Middle America. This fast and geographically wide Pleistocene radiation is complex and involves events previously suggested for other groups of rodents (e.g., Andean diversification) and Neotropical fauna (e.g., connection between Amazonia and Atlantic forests), and others that are novel for rodents and for the most part for the South American mammals (e.g., the identification of the Chaco as a center of diversification).

However, much remains to be learned about the diversification of Oligoryzomys. One key fact that keeps us motivated and curious to understand why long-tailed mice constitute such a marvelous radiation is which trait or set of traits, either physiological, life history or morphological, has/have prompted this fast and geographically broad radiation? We hope that in the near future, with the analysis of additional data (hopefully at a genomic scale, conducted by us and several other colleagues, we will gain a deeper understanding of the radiation of Oligoryzomys. And then, we hope to explain how this radiation is related with the diversification and presence of strains of hantaviruses in several species of Oligoryzomys.

Written by:
Natali Hurtado (1) and Guillermo D’Elía (2)
(1) Research Associate, Centro de Investigación Biodiversidad Sostenible – BioS. Lima, Perú.
(2) Professor, Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile; and Curator, Mammal Collection at the Universidad Austral de Chile, Valdivia, Chile

Hurtado, N. & D’Elía, G.(2022). Historical biogeography of a rapid and geographically wide diversification in Neotropical mammals. Journal of Biogeography, 49, 781–793.
Parada, A., Hanson, J., & D’Elía, G. (2021). Ultraconserved elements im- prove the resolution of difficult nodes within the rapid radiation of Neotropical Sigmodontine rodents (Cricetidae: Sigmodontinae). Systematic Biology, 70(6), 1090–1100.

Additional information:
@NataliHurtadoMi; @GuillermoDElia,

ECR Feature: Paulina Meller on factors shaping diversity in geoxyles

Paulina Meller is finishing her PhD at the University of Hamburg, Germany. She studies the evolutionary forces that generate diversity in plants. Paulina shares her recent work on the environmental factors that have given rise to diversity in geoxyles, plants with disproportionately high below-ground woody biomass.

Paulina Meller taking a break from digging in the Afromontane grasslands of Tundavala, Angola. Photo credit: Manfred Finckh (Twitter: @ManfredFinckh)

Personal links. Twitter | Webpage

Institute. Institute of Plant Science and Microbiology, University of Hamburg, Germany.

Academic life stage. PhD (but finishing soon!).

Major research themes. Patterns and drivers of diversity, with a research focus on tropical vegetation (and a personal interest in birds).

Current study system. I study geoxylic plants (geoxyles) in Afrotropical grasslands. Geoxyles have a low growth form and disproportionally high belowground woody biomass. Many geoxyles evolved from tree species in response to environmental changes that proceeded the Miocene. Emerging fire occurrences have been hypothesised as the evolutionary driver of geoxyles. Hundreds of geoxyle species exist in Africa, and there are more in other tropical grasslands. They can be so diverse and abundant that they form “underground forests”. The belowground storage organs and bud banks enable geoxyles to resprout again after environmental disturbances. Their abundance, diversity and resilience make geoxyles a key element of tropical grassy ecosystems.

Recent paper in JBI. Meller, P., Stellmes, M., Fidelis, A., & Finckh, M. (2022). Correlates of geoxyle diversity in Afrotropical grasslands. Journal of Biogeography, 49, 339–352.

Motivation behind this paper. Geoxyles have been mostly overlooked in studies on tropical grassy ecosystems, probably due to the fact they are hidden underground. Despite some very good studies on geoxyles in Southern Africa and the Cerrado in South America, the main narrative remains that they all evolved from trees in response to fire. However, this narrow focus neglects other environmental factors that might have shaped the evolution of geoxyles and their taxonomic diversity. As a result, the knowledge on geoxyles has been rather fragmentary and one-sided so far.

As part of my PhD, I was working on a geoxyle species list for Angola when a nice paper by Pausas et al. (2018)* came out, providing a framework to classify belowground plant structures. It was therefore an exciting opportunity to combine the species list with analyses on their ecology, belowground functionality, and taxonomic and biogeographical origin, linking the fragmented knowledge together to better characterise geoxyle evolution.


Caloncoba suffruticosa (Achariaceae) resprouting and flowering shortly after fire. The belowground woody storage organs and bud banks are partly excavated, typically only the green parts and flowers are visible aboveground.

Key methodologies. Our recent paper is quite complex because we measured so many facets of geoxyle biology, which was necessary to understand how heterogeneous and diverse this group of plants is. Each facet of geoxyle biology required a different analysis. Our study is the first to integrate different kinds of data – from field-derived functional traits, over literature research on origins, to large scale spatial and environmental modelling – to show how the facets of geoxyle biology interlink with one another. We took the vivid discussion on the main drivers of geoxyle evolution – fire versus frost – as an incentive to test for correlations between belowground traits, spatial distribution, and environmental pressures. Strikingly, some species seem to be more fire dependent than others, and most geoxyles had a strong link to frost-prone sites. So both frost and fire are important evolutionary drivers.

Major results. It was important to show that the geoxylic life form is much more diverse, complex and heterogeneous than previously assumed. The focus so far has been on the species with close tree relatives, which is totally reasonable since they are the most striking geoxyles. But they make up less than 50% of the geoxyle pool studied so far. In order to better understand tropical grassy biomes, and manage these often-threatened ecosystems sensibly and sustainably, it is crucial to characterise the diversity in geoxyles. Another important point to me was to reconcile whether fire or frost is the one driver of geoxyle evolution. We showed that there is no single driver, as implicit in previous discussion on the overarching importance of fire. Although some geoxyles clearly evolved in response to fire, there are species that have evolved in response to dry season frost events, and likely some also evolved in response to edaphic conditions. By recognizing that geoxyles are diverse and heterogeneous, determining an ultimate evolutionary driver of their diversity becomes less important.

Unexpected results and challenges. A particularly surprising finding was that many species in our study sites exhibit considerable belowground woody biomass. We had to include almost every species we looked at, and the more species we excavated, the longer grew our list of geoxyles. We therefore show that it is not sufficient to describe and understand an ecosystem by its visible, aboveground parts alone. Moreover, it was hard work to excavate all these over 100 different species, as some formed tubers big as a football in 1.2 m depth, others grew in particularly rocky ground. Our field assistant Segunda was a great help in this regard! Neither have I had so many blisters on my hands before, nor dirty finger nails, than during this campaign. But afterwards I lost some 5 kg and had hands as tough as a sailor’s.

Paulina in the field. This is a drone image of a geoxyle grassland near Chitembo, Bié province, in Central Angola. Geoxyles resprout and colour the landscape brightly at the end of the dry season, long before grasses or trees do.

Next steps. There are still so many open questions, but I would like to compare the geoxyle diversity hotspots of Africa (Miombo) and Brazil (Cerrado) more closely. Our Brazilian colleagues have done some amazing work on geoxyles, and often on different aspects to what we have done with African geoxyles. A combined, intercontinental analysis would fill many knowledge gaps and yield important new insights. For instance, whether similar families or genera produce geoxyles, thereby hinting at a phylogenetic predisposition to evolve this life form, or whether species and functional diversity are dependent on similar environmental factors on both continents.

If you could study any organism on Earth, what would it be? I don’t know if I am competent enough, but I would like to study big birds like the Southern Ground Hornbill (Bucorvus leadbeateri), or the Great Blue Turaco (Corythaeola cristata). I have seen both during my trips to Angola, and I love to see and hear them, they make me happy. There is something magic in waking up in the early morning to the bass sound of a foraging group of Ground Hornbills. They always look like the Blues Brothers on a stroll.

Anything else to add? Doing research in Angola is exciting and exhausting, beautiful and bizarre, endearing and endangering – but you come home the wiser and more experienced, and you will always be able to tell an interesting story. So even after 7 years of countless blisters, sunburns, malaria, and a barely survived crocodile attack I still enjoy digging in Angolan grasslands, and collaborating with our Angolan colleagues and friends.

ECR Feature: Rodolfo de Oliveira Anderson on ecophysiology in skinks

Rodolfo is a PhD student at Monash University, Melbourne, Australia. He is a herpetologist with an interest in physiology and biogeography. Rodolfo shares his recent work on the ecophysiological strategies used by an Australian skink, Lampropholis guichenoti, to survive in diverse, variable climatic conditions.

Rodolfo on top of Cradle Mountain, Tasmania.

Personal. Twitter

Institute. School of Biological Sciences, Monash University, Melbourne, Australia.

Academic life stage. PhD student.

Major interests. Herpetology, Ecophysiology and Biogeography.

Current study system. I’m studying lizards. These amazing dry-skinned ectotherms depend on environmental temperatures to keep their own body temperature within suitable limits. They employ several strategies, such as thermoregulatory behaviour and tolerance to extreme temperatures, to cope with climatic variation. In my PhD, I’ve focused on an Australian genus, Lampropholis skinks, to study how the environment interacts with physiology, setting their distribution. Lampropholis skinks are small (1–4 g) and found all down the Australian east coast, spanning ~30 degrees of latitude, and must therefore cope with considerable climatic variation across their range. My work characterises the different ecophysiological strategies used by these skinks to cope with very different climatic regimes.

Recent paper in JBI. Anderson, R. O., Alton, L. A., White, C. R., & Chapple, D. G. Ecophysiology of a small ectotherm tracks environmental variation along an elevational cline. Journal of Biogeography.

The Garden-skink (Lampropholis guichenoti) foraging on the leaf litter. Photo by Jules Farquhar.

Motivation behind this work. The ecophysiology of species, that is, how organisms interact with their environment through their physiology, is key to understanding the limits of its geographic distribution. One species of Lampropholis (the Garden-skink, L. guichenoti) is found across different elevations in the Australian Alps, which are in the southern part of Australia. At the top of their distribution in the Alpine National Park (~1500 masl), in the state of Victoria, temperatures can go below zero and snow is present during the coldest months of the year. By contrast, in the lowlands, the climate is much hotter and drier. This huge disparity across an elevational gradient suggests that Garden skinks must have incredibly flexible physiological strategies. I wanted to know how the ecophysiology – which includes metabolism, thermal physiology, water balance, and locomotion – changes in response to climatic variation. Understanding how ecophysiology shifts across climatic gradients could help reveal how these small animals can inhabit contrasting environments, survive, and potentially expand their geographic range.

Key methodologies. This study comprised three parts. Firstly, I went to the field to collect the skinks, either by hand or by mealworm fishing. I went to four different sites, ranging from the lowlands (near the sea level) up to 1500 masl. Secondly, caught skinks were brought to the lab at Monash University, Melbourne, so I could quantify several ecophysiological traits (e.g., thermal tolerances, water loss, metabolism). Finally, I used the ecophysiological data to develop mechanistic models (NicheMapR) to predict the physiology and behaviour of the skinks in the field. This integrative approach provided interesting insights about the role of behaviour in the survival of these animals, especially in the cold highlands. I found that thermal physiology, metabolism, and rates of water loss, follow the demands of different climates. Skinks in the highlands are more cold tolerant and have a more efficient metabolism. In the drier and warmer lowlands, the skinks have to save their body water content, but they can reach higher locomotor performance. Finally, behavioural thermoregulation can maintain body temperature above freezing conditions and increase the activity time of skinks.

View of the Alpine National Park, Victoria. Garden skinks (Lampropholis guichenoti) can be found to altitudes of up to ~1500 m, where temperatures drop to below zero.

Garden skinks (Lampropholis guichenoti) were collected in dry woodlands across the elevational gradient in the Alpine National Park.

Major results. We demonstrated how an integrative approach can be very fruitful for biogeographical research. We showed that physiology as a whole is affected by climate, going beyond approaches that solely analyse thermal physiology. The environment is complex, and multiple interactions occur between the physical world and organisms. In the same study, we showed that in response to low temperatures, skinks increase their metabolic rate and energy efficiency, and elevate their cold tolerance. In dry and hot environments, skinks have to avoid water loss to prevent dehydration, but they have fewer fitness costs. Therefore, thermal physiology, metabolism and water balance are flexibly modulated to shape the fundamental niche of these skinks. Our work demonstrates that understanding the interaction between physiology and climate is key to understanding how organisms can survive in different types of environments, and hence the processes shaping their geographic distribution.

Unexpected challenges. The fieldwork was certainly the hardest challenge in this project. My field assistants and I had to actively search for the lizards for several days in areas with hard access. The fieldwork was also carried out in late summer/early Autumn, when the temperatures in the highlands drop dramatically at night. In a few instances, we had to refuge in emergency huts to spend the night in the field. Fortunately, all of us survived and we found a sufficient number of skinks for my experiments.

One of the emergency huts where people can find refuge during bad weather conditions. In one of our field works to the Alpine National Park, we spent a night in a similar hut to shelter from the wind and freezing temperatures.

Next steps. A crucial next step would be to disentangle the contributions of plasticity versus adaptation to the ecophysiological changes across elevation in the Garden skinks. To do that, a common garden experiment would be necessary. This would provide a more powerful inference about the fundamental niche and its role in shaping the distribution of these ectothermic animals.

If you could study any organism on Earth, what would it be? It would have to be the Maned Wolf (Chrysocyon brachyurus), or Lobo-Guará in Portuguese, because this extraordinary animal is perhaps the most beautiful mammal in the world, but is sadly a near threatened species. The savannah-like Cerrado in Brazil, where the Maned Wolf lives, is also endangered and deserves more attention from the general public and scientific community.

Pseudocongruent phylogeographic patterns in forest-living herpetofauna

Similar phylogeographic patterns do not necessarily imply similar evolutionary histories. Instead, environmental factors like the formation of rivers, ancient climatic cycles and climatic gradients could collectively interact with the unique life histories species to strengthen dispersal barriers at different times and generate complex biogeographic patterns.

Above: Isolated forest fragment in the Eastern Cape Province of South Africa.

Climatic and geological changes play important roles in shaping species distributions over evolutionary time. Ancient climatic fluctuations have particularly impacted habitat structure and composition, resulting in numerous contractions and expansion events that often led to extinction or diversification of organisms associated with these habitats. Understanding how past environmental changes impacted individual species or regional patterns of diversity is important for developing effective conservation strategies for the future.

Editors’ choice article: (Free to read online for two years.)
Busschau, T., Jordaan, A., Conradie, W., & Daniels, S. R. (2022). Pseudocongruent phylogeography reflects unique responses to environmental perturbations in a biodiversity hotspot. Journal of Biogeography, 49, 445–459. 

In my masters (MSc) research I wanted to understand more about the population structure and genetic diversity of three codistributed forest-living reptile species, two snakes and a gecko, considering the fragmented nature of forest habitats in South Africa (Busschau, Conradie, & Daniels, 2019; Busschau, 2019; Busschau, Conradie, & Daniels, 2021). I generally found a high degree of genetic diversity and some populations were isolated long enough that they can be regarded as separate species, suggesting forests may hold a higher degree of biodiversity than previously recognized. In the meantime, other studies uncovered high levels of genetic diversity in a forest associated frog (Kushata, Conradie, Cherry, & Daniels, 2021; Tolley, Conradie, Harvey, Measey, & Blackburn, 2018) and a lizard (Zhao et al., 2019). Comparisons among these studies revealed that the five species share congruent phylogeographic patterns along the east coast of South Africa, i.e., the genetic breaks between populations were similar. The most obvious pattern was a phylogeographic break between populations in the northern region and those in the south. This raised two intriguing questions – do similar phylogeographic patterns mean these species with different life histories responded similarly to past environmental changes, and what environmental factors shaped the genetic diversity we see today? Notably, most of the east coast of South Africa falls within a biodiversity hotspot. So, answering these questions could provide clues to the factors generating and maintaining diversity in the region.

Map of the study region, Maputoland-Pondoland-Albany biodiversity hotspot along the eastern escarpment of South Africa. Shading depicts the northern and southern phylogeographic regions deduced from previous phylogeographic studies. The three rivers coinciding with the transitional zone between regions are shown.

To answer these questions, we used a comparative phylogeographic approach that makes statistical comparisons among the five species groups and then correlates the genetic patterns with a set of environmental factors that could be driving these patterns. First, we confirmed that the observed patterns were generally comparable among species and statistically supported. The next important step was to test whether the observed patterns of genetic divergence happened at the same time. This was not so straightforward. Genetic data can be used to estimate the time populations or species diverged, but to do this we need either reliable fossil calibration points or know the gene mutation rates, neither of which were available for the study species. So, we searched the literature for mutation rates of other snakes, lizards, frogs, etc., and realized that even within each of these groups the mutation rates can sometimes be very different. Basing our mutation rates on other studies could therefore introduce errors in our analyses. To overcome this issue, we decided to take a reasonably conservative approach and estimate our gene mutation rates with a broad range of possible values deduced from other studies. This resulted in large confidence intervals around the times populations diverged in each species, yet there was still no overlap among some species. This provided evidence that although the study species show similar genetic patterns, they do not necessarily share the same evolutionary histories.

Two codistributed species that revealed pseudocongruent phylogeographic patterns along the east coast of South Africa. Left Afroedura pondolia. Right Macrelaps microlepidotus.

How is it possible for multiple species to share the same phylogeographic patterns if they do not share the same history in response to past events such as climate change and/or forest fragmentation? In an attempt to answer this question, we tested how well rivers, past climatic changes or climatic gradients could explain the patterns we see. Although we detected some genetic variation explained by the rivers, they do not correlate with genetic patterns across all species. Niche modeling revealed that only one species had a fragmented distribution in past climates, and one species had a significantly reduced distribution while the rest remained relatively stable. Lastly, current climatic variables explained the genetic patterns across all species reasonably well. Multiple climatic variables were significantly different among populations in each species group and significantly correlated with latitude. While this list of environmental factors is certainly not exhaustive, these results indicate that latitudinal climatic gradients may have been persistent drivers of genetic diversity throughout the unique evolutionary histories of species along the east coast of South Africa. We ultimately conclude that additional factors like the formation of rivers or ancient climatic cycles, would collectively have interacted with climatic gradients and the unique life histories of the study species to strengthen dispersal barriers at different times and generate complex biogeographic patterns in the region.

Our study highlights the utility of comparative phylogeographic studies to uncover drivers of biodiversity. Interestingly, our niche modeling also identified a small region that was climatically stable for all species throughout past climatic changes, emphasizing the importance of this region for forest conservation in the face of climate change. This is the first study of its kind in South Africa and we believe similar studies in the future could uncover even higher levels of hidden diversity and previously unrecognized biogeographical processes.

Written by:
Theo Busschau
Current: PhD student in Biology at New York University Abu Dhabi
This study stems from my MSc work at Stellenbosch University, South Africa

Additional information:

I would like to thank my MSc supervisors, Prof. Savel Daniels and Werner Conradie, for their support and guidance throughout my research career, and of course their patience, and thank you to my friend and mega niche modeler, Adriaan Jordaan, for his help and major contribution to this study.


Busschau, T., Conradie, W., & Daniels, S. R. (2019). Evidence for cryptic diversification in a rupicolous forest-dwelling gecko (Gekkonidae: Afroedura pondolia) from a biodiversity hotspot. Molecular Phylogenetics and Evolution, 139, 106549.

Busschau, T. (2019). Phylogeographic patterning of three co-distributed forest-dwelling reptile species along the east coast of South Africa. MSc Thesis, Stellenbosch Uniiversity.

Busschau, T., Conradie, W., & Daniels, S. R. (2021). One species hides many: Molecular and morphological evidence for cryptic speciation in a thread snake (Leptotyphlopidae: Leptotyphlops sylvicolus Broadley & Wallach, 1997). Journal of Zoological Systematics and Evolutionary Research, 59, 195–221.

Kushata, J. N. T., Conradie, W., Cherry, M. I., & Daniels, S. R. (2021). Comparison of the mitochondrial phylogeographical structure of a generalist and two specialist frog species reveals contrasting patterns in the Eastern and Western Cape provinces of South Africa. Biological Journal of the Linnean Society, 130, 783–799.

Tolley, K. A., Conradie, W., Harvey, J., Measey, J., & Blackburn, D. C. (2018). Molecular phylogenetics reveals a complex history underlying cryptic diversity in the bush squeaker frog (Arthroleptis wahlbergii) in Southern Africa. African Zoology, 53, 83–97.

Zhao, Z., Verdú-Ricoy, J., Mohlakoana, S., Jordaan, A., Conradie, W., & Heideman, N. (2019). Unexpected phylogenetic relationships within the world’s largest limbless skink species (Acontias plumbeus) highlight the need for a review of the taxonomic status of Acontias poecilus. Journal of Zoological Systematics and Evolutionary Research, 57, 445–460.

Colonization across oceanic islands, and how to estimate it

Colonization across oceanic islands is a central topic in island biogeography. PAICE, a new methodological tool to estimate colonization events using floristics, genetics, and accounting for sample size. PAICE is designed to perform comparisons among organisms and archipelagos, and can be used to test explicit biogeographic hypotheses such as the difference in colonization success between species with or without long-distance dispersal traits.

Above: Schematic representation of colonization events.

Because oceanic islands emerged lifeless from the bottom of the sea floor with no connection to any continent, they are ideal systems to study complex biogeographic processes. In particular, the colonization of oceanic islands has intrigued scientists for centuries given that all their land life initially arrived in them from another distant territory. Consequently, species with dispersal abilities have traditionally been assumed to be more successful colonizers.

Editors’ choice article: (Free to read online for two years.)
Coello, A. J., Fernández-Mazuecos, M., Heleno, R. H. & Vargas, P. (2022). PAICE: A new R package to estimate the number of inter-island colonizations considering haplotype data and sample size. Journal of Biogeography, 49, xxx– xxx.

However, many species challenge this assumption. For example, Cistus monspeliensis is a plant with capsules and small seeds, that is, without any long-distance dispersal specialization, but it is a good colonizer as inferred by numerous colonization events among islands of the Canarian archipelago. This result goes against the classical dispersal hypothesis and thus encouraged us to compare the number of inter-island colonization events among numerous plant and animal species. As a general assumption, a species is considered a more successful colonizer when displaying a higher number of inter-island colonization events across a given archipelago. To our surprise, in a previous study we found that the number of estimated inter-island colonization events was highly influenced by sample size, and thus it was not possible to compare among species without some degree of bias. In fact, although there are several methods available to reconstruct inter-island colonization events, none of them considers sampling size.

In this study we propose PAICE (Phylogeographic Analysis of Island Colonization Events), a new approach implemented in an R package that not only uses floristics and haplotype sharing among islands (like previous studies) but also sample sizes in the estimation of the number of inter-island colonization events for any species within an archipelago. Based on haplotype diversity of uniparental inherited DNA regions, PAICE calculates the number of inter-island colonization events considering haplotype sharing, haplotype networks and rarefaction curves at both sampling levels (field and genetic). As a result, this approach estimates the number of inter-island colonization events accounting for sample size.

Cistus monspeliensis.

After developing PAICE, we applied it to 10 animal and plant species with data taken from the literature and noticed some problems when trying to compare their numbers of inter-island colonization events. In particular, a considerable number of case studies showed a sample size that was too small to estimate a reliable number of colonization events (birds like Buteo galapagoensis or Setophaga petechia aureola, plants like Canarina canariensis, Croton scouleri or Juniperus cedrus). Despite this challenge, a comparative estimation of colonization events suggests a higher colonization ability for species that were previously considered poor colonizers. Interestingly, animals with high flying capacity such as the carpenter bee (Xylocopa darwini) and the bird S. petechia aureola of the Galápagos Islands were considered poor colonizers in previous studies. However, the estimated number of inter-island colonization events provided by PAICE revealed that many colonization events were hidden in those previous studies because a very frequent haplotype was distributed across many islands. This increase in the estimate of colonization events was possible due to the application of rarefaction curves, which had not been use before for this purpose. In contrast, both Cistus monspeliensis and Olea europaea subsp. guanchica had similar numbers of inter-island colonization events (c. 20 – 45), although O. europaea subsp. guanchica is an endozoochorous plant while C. monspeliensis does not have dispersal specializations. Two additional plants were suggested to have a high number of inter-island colonization events, specifically Juniperus brevifolia (> 100 colonizations) and Picconia azorica (> 75 colonizations), but more studies are needed to refine these estimates.

We believe that PAICE paves the road for future studies aiming to compare colonization success among species in insular systems. In fact, this approach can also be applied to study movements among territories in other island-like systems such as lakes and mountain tops.

We hope that future island biogeographic studies will benefit from PAICE to evaluate species colonization success, as well as the relative importance of dispersal and establishment in the colonization process. In particular, classical hypotheses in island biogeography, such as the higher colonization success of species with long-distance dispersal abilities, can be addressed using PAICE. Although PAICE provides user-friendly R functions, the corresponding authors offer to guide any phylogeographical studies aiming to estimate numbers of colonization events and thus colonization success across islands and island-like system.

The carpenter bee (Xylocopa darwini)

Written by:
Alberto J. Coello (1), Mario Fernández-Mazuecos (2), Ruben H. Heleno (3) & Pablo Vargas (4)
(1) PhD candidate, Department of Biodiversity and Conservation, Real Jardín Botánico (RJB-CSIC)
(2) Lecturer, Department of Biology (Botany), Facultad de Ciencias, Universidad Autónoma de Madrid
(3) Assistant Professor, Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra
(4) Professor, Department of Biodiversity and Conservation, Real Jardín Botánico (RJB-CSIC)

Additional information:
Alberto J. Coello: @albertojcoello (Twitter)
Mario Fernández-Mazuecos: @mfmazuecos (Twitter), (website)
Ruben H. Heleno: @ruben_heleno (Twitter),
Pablo Vargas: @pablovargas1111 (Twitter)

ECR Feature: Rowan Schley on the diversification of pantropical trees

Rowan J. Schley is a postdoc at the University of Exeter and the University of Edinburgh. He is particularly interested in using genomic approaches to study diversity in tropical ecosystems. Rowan shares his recent work on the diversification of the pantropical tree genus, Pterocarpus, and the relative roles of biome-switching and long-distance dispersal.

Rowan with Wallace’s Flying Frog (Rhacophorus nigropalmatus).

Personal links. ResearchGate | Twitter | Website | ORCID | GoogleScholar

Institute. University of Exeter & University of Edinburgh

Academic life stage. Postdoc

Major research themes. I am particularly interested in asking questions about speciation, hybridisation, diversification, biogeography and genome evolution to understand the superlative diversity of the tropics.

Current study system. I work on tropical trees, which as a whole are relatively understudied despite their incredible diversity. As an example, one hectare of the Ecuadorian Amazon may contain more tree species than the entirety of Europe (>600 species). It is critically important to understand how this diversity was assembled, both to further our understanding of how species diversify and because tree species are the basis of many tropical ecosystems. In particular, the genus, Pterocarpus (Fabaceae/Leguminosae), is an excellent study system for understanding tropical tree diversification and biogeography because it is ecologically diverse, exhibits multiple dispersal phenotypes and is found across the tropics.

Recent paper in JBI. Schley R. J., Qin, M., Vatanparast, M., Malakasi, P., de la Estrella, M., Lewis G. P., Klitgård, B. (2022) ‘Pantropical diversification of padauk trees and relatives was influenced by biome-switching and long-distance dispersal’. Journal of Biogeography.

(left) Pterocarpus rohrii sensu lato; (right) Pterocarpus angolensis © Gwilym P. Lewis

Main motivation. Many plant groups are found pantropically, and there has been much debate about how such distributions arise. The prevailing narrative was that of vicariance, where the splitting of continental landmasses led to isolation of populations on different continents, and therefore, different evolutionary trajectories. However, time-calibrated molecular phylogenies have shifted this paradigm for many groups, and now, dispersal is believed to have led to the pantropical distributions of many tropical tree species. This is because the estimated divergences between many plant groups post-date continental splitting, and because long-distance dispersal is well known in plants. The macroevolutionary consequences of dispersal can be influenced by phenotypes which promote dispersal at ecological scales, as shown by work on the Podocarpaceae (Klaus & Matzke, 2020) and Annonaceae (Onstein et al., 2019). This work showed that dispersal traits influenced the distribution, diversity and ecology of these plant groups, inspiring us to ask similar questions in Pterocarpus.

Key methodologies. To test how seed dispersal phenotypes influenced Pterocarpus’ biogeographical history we first inferred a ‘dated’ phylogenetic tree. This helped us understand the evolutionary relationships between Pterocarpus species in a temporal context. We built this tree based on DNA sequence datacollected from RBG Kew’s herbarium, and used fossils to calibrate the tree to understand when speciation events happened within Pterocarpus. We then performed biogeographical analyses to test whether the dispersal phenotypes of Pterocarpus species influenced the evolutionary history and geographical distribution of the group. For example, dispersal phenotypes which facilitate long-distance dispersal by water (e.g., floating fruits) may lead to very broad species distributions, whereas other phenotypes may restrict species distributions. We tested the influence of these traits on geographical range evolution as well as on adaptation to different biomes, and we assessed how many shifts between biomes occurred across Pterocarpus’ evolutionary history.

Challenges. A major challenge was to find a method which allowed us to ‘date’ our phylogenetic tree from the vast amount of next-generation sequencing data we collected. This was pretty hard because most of the methods which we can use to date phylogenetic trees were designed to use much smaller datasets (e.g., only one or a few genes), but we used more than 300 genes in our phylogenetic analyses. Because of this, we decided to use a method which was designed for dating phylogenetic trees built with entire genomes (i.e., even more data than we used in this study) called ‘MCMCtree’ (Yang et al., 2007). We were also particularly fortunate in the case of Pterocarpus, because there has been much genetic work done on closely related groups, and so we could leverage existing, smaller datasets to do a corroborative analysis using older methods, and ensure that our MCMCtree analyses were accurate.

Major results. We found that there were two evolutionary lineages within Pterocarpus – one of which diversified in the Neotropics, and the other in the Palaeotropics. These groups diverged during the Miocene (~12 Ma), and most of the species diversification in Pterocarpus occurred during this epoch. Interestingly, we found that seed dispersal phenotypes had little significant effect on contemporary distributions, but that dispersal did have a significant effect. This suggests that random, rare ‘sweepstakes dispersal’ influenced Pterocarpus’ distribution. It was also apparent that biome-switching mostly occurred into rainforests and savannas. These environments are prone to disturbance and so experience high turnover of plant species, facilitating colonisation from other biomes. Biome switching was also likely promoted by Miocene climate change, such as the aridification of Africa. Overall, our results suggest that rare long-distance dispersal, coupled with climate change and speciation in different biomes, likely explain the wide distributions of many pantropical tree genera.

Next steps. I’d love to investigate the ‘weirdest’ Pterocarpus of all – P. dubius. This looks very different to other Pterocarpus species, its phylogenetic position is different when inferred with plastid vs nuclear genes, and it was previously circumscribed in a separate genus as Etaballia dubia. It would be great to unpick these peculiarities using plastid genomes and by investigating phylogenetic incongruence, because it seems that this odd placement may result from chloroplast capture following ancient hybridisation. In addition, Klitgård et al. will be circumscribing new taxa within the P. rohrii species complex and publishing IUCN red list assessments for threatened Pterocarpus species.

Rio Tiputini in Yasuní National park, Ecuador.

If you could study any organism on Earth, what would it be? To study the extraordinary diversity of any tropical taxon is a dream come true. I have a particular love for working on tropical trees and understanding the evolution of diversity through that lens. That said, as a naturalist I am interested in a broad range of questions across the tree of life, and I have also been lucky enough to work on orchids and cichlid fishes. I would love the opportunity to further understand speciation in diverse coral reef taxa (e.g., Acanthurid fishes, Scarid fishes, Scleractinian corals), phenotypically diverse and strange plant groups (e.g., mangroves and Nepenthes pitcher plants) or in an island radiation like Scalesia. That’s the great thing about the tropics – there is so much to study, not to mention so much to conserve!

Anything else you would like to share? Pterocarpus species are valuable timber trees under immense pressure from logging. They are known as ‘rosewoods’ and ‘bloodwoods’, among many other common names. These names refer to the sought-after red colour of their wood, and to the red sap that is exuded when their trunks are cut. There is a short BBC film called ‘Trees that bleed’ that documents the poaching of rosewoodtrees in West Africa – it is really worth a watch!