ECR feature: Maria Guerrina on post-glacial contraction in an Alpine endemic plant.

Maria Guerrina is a postdoc at the Università degli Studi di Genova in Italy. She is a plant biologist interested in the evolution of endemic biota. Here, Maria shares her recent work on the post-glacial contraction of an Alpine endemic species.

Maria Guerrina during fieldwork in the South-western European Alps.

Personal links. Research Gate

Institute. Dipartimento di Scienze della terra, dell’ambiente e della vita (DISTAV) – Università degli Studi di Genova.

Academic life stage. Postdoc

Major research themes. Endemic species, conservation, glacial refugia, climate change, reproductive biology, alpine flora, phylogeography.

Current study system. My study species is Berardia subacaulis Vill., the only living species belonging to a monospecific genus endemic to the South-western European Alps. This cold-adapted species is a relic of the Tertiary paleo flora (~24 mya), which almost went completely extinct during Late Quaternary climatic oscillations. Being such an “ancient” species makes it interesting and necessary to understand how past climatic changes affected the demographic history of this species. By doing so, we can make more reliable predictions on how it will respond to future pressures.

Maria out in the field collecting leaves of B. subacaulis.

Recent JBI paper. Guerrina M, Theodoridis S, Minuto L, Conti E,Casazza G (2022) First evidence of post-glacial contraction of Alpine endemics: insights from Berardia subacaulis in the European Alps. Journal of Biogeography. 49 (1): 79-93 https://doi.org/10.1111/jbi.14282

Motivation behind this paper. This study sought to understand the possible responses of plants to the Late Quaternary dynamics (i: post-glacial expansion; ii: post-glacial contraction; and iii: long-term stability). The study is located in the South-western European Alps (SW Alps). This area was less affected by the glaciations than the rest of the Alps because of the Mediterranean Sea influence. Given the proximity of the SW Alps to the Mediterranean and Alpine climates, the region is characterized by high local climatic variability and topographic heterogeneity, which promoted a variety of phylogeographical patterns in the biota. Until today, two common hypotheses have been proposed: post-glacial expansion or long-term stability (mainly by altitudinal shift). However, an interesting pattern never yet detected is the expansion of cold-adapted species during glaciation due to the limited extent of the glacial sheet in the area, followed by a population contraction after glaciation.

A blooming individual of B. subacaulis. It is possible to see the secondary presentation of pollen on the stigma in the central open flowers.

Key methodologies. Our paper relies on species distribution models (SDMs) throughout the last 28 Ky and genome-wide sequences (genotyping-by-sequencing; GBS) to estimate current spatial structure patterns from genetic diversity. Because B. subacaulis grows only on specific calcareous substrates, we added substrate information into the in SDMs to report the presence/absence of this suitable substrate, based on the global lithological map dataset (GLiM). Integrating the results of the two independent approaches (SDMs and GBS) allowed us to test several demographic models under an Approximate Bayesian Computation framework.

Unexpected challenges. One of the biggest challenges we faced was field sampling. Berardia subacaulis grows on very steep scree, and this kind of habitat did not make sampling easy! Because of it, before starting the sampling, I went shopping for comfortable boots for walking on scree – the clerk looked at me strangely! The sampling season began with two outings of about eight hours of hiking each before we managed to find the plant (I’m glad I got proper boots!). Funny thing, I was with a colleague, and none of us had ever seen the plant before. But it was really nice to find some populations following herbarium information from the end of the 19th century.

Achenes of B. subacaulis.

Major results. For the first time, we provide empirical evidence of post-glacial demographic contraction and a recent split between the two genetic groups for an endemic plant in the European Alps during the Late Quaternary. The pattern observed might be due to several factors. First, the SW Alps were characterized by greater availability of ice-free terrain during the Last Glacial Maximum (LGM) because of the Mediterranean Sea mitigation that maintained temperatures some degrees higher than in the rest of the Alps. Second, the SW Alps were characterized by relatively high precipitation, which, combined with the ice-free areas, might have allowed B. subacaulis to persist or even expand in most climatically suitable areas at high altitudes during the LGM.

Next steps for this research. Several hypotheses explaining patterns of endemism have been explicitly tested at the global scale, raising questions about the persistence of biodiversity during the present era of changing climate. However, these hypotheses have never been tested at local scales, and the SW Alps are an interesting place to test them. The next step in this research is to explore the environmental drivers promoting endemic richness distribution in the SW Alps.

Typical habitat of B. subacaulis, growing on steep calcareous scree.

If you could study any organism on Earth, what would it be? Plants, I cannot change my study organism! In particular, I would like to study any rare and endemic plants with peculiarities, such as blooming every 40 years or growing in almost inaccessible places.

It is a good day to study lichens

“There is a low mist in the woods­–It is a good day to study lichens.” Henry David Thoreau, A Year in Thoreau’s Journal: 1851.

Above: Brownish monk’s-hood lichen (Hypogymnia vittata) on a mossy rock wall in an old-growth forest, eastern Norway.

Lichens all share a common “lifestyle” – whether you call it a symbiosis, parasitism, a collective of productive fungal farmers, or teams of brilliant algal architects, this lifestyle has no doubt been a successful strategy for survival. From miniscule Arctic extremophiles growing within solid rock to conspicuous meters-long cascading strands of Methuselah’s beard (Usnea longissima) festooning a veteran conifer canopy, lichens’ beautifully sophisticated biological machinery has allowed colonization of virtually every terrestrial habitat on Earth. Over their quarter of a billion year evolutionary story, they have developed the tools to thrive on every continent: from the inter-tidal to alpine zones, and from aquatic to desert habitats.

Cover image article: (Free to read online for a year.)
Phinney, N. H., Ellis, C. J., & Asplund, J. (2022). Trait-based response of lichens to large-scale patterns of climate and forest availability in Norway. Journal of Biogeography, 49, 286–298. https://doi.org/10.1111/jbi.14297 

Unlike vascular plants, lichens are “poikilohydric,” meaning they are unable to actively regulate their water uptake and storage. To cope with a diverse range of environmental demands, these often alien-looking organisms have developed striking variation in physiology, anatomy, morphology and architecture. These “functional traits” represent direct operative links to their environment at both micro-and macroclimate scales, offering a window into each thallus’ unique survival scheme. Documenting the intimate relationship between lichen and environment is crucial in improving our understanding of how lichen communities assemble in nature and how they adapt in a changing climate.

With a diverse and dramatic landscape and climate – from boreal rainforests to alpine heathland and arctic tundra – Norway is an impeccable biogeographic laboratory for such investigations. Here, we were encouraged to ask questions about why certain lichen groups occur where they do. We used likely drivers, such as precipitation, temperature, and forest cover to predict current distributions of traits. In doing so, we found that some traits, such as types of photobionts (photosynthetic lichen components, i.e., green algae, cyanobacteria, or both), appear to respond well to broadscale environmental filtering, making their distributions reasonably predicable. Lichens with cyanobacterial photobionts (cyanolichens) and those with green algal partners (chlorolichens) have unique physiological tolerances that restrict them to a certain climate space. For example, the majority of cyanolichens are found in oceanic habitats in Norway but become scarce in the high Arctic. Why? Unsurprisingly, because this group requires liquid water for photosynthesis, so their affinity for the rainy, western coast makes sense. On the other hand, many chlorolichens are connoisseurs of non-rain water sources, such as fog or high humidity – a secret Thoreau seemed privy to. Some chlorolichens (i.e., trebouxioid) can even maintain activity in temperatures well below 0° C and, lo and behold, they are liberally scattered throughout a seemingly inhospitable Arctic “wasteland”.

But are some trait distributions more predictive than others? Growth form, for instance, while being intimately coupled to environmental stressors, shows relatively weaker relationships to climate at the macroscale. Perhaps these categories – although widely applied – are actually too broadly-defined to consistently represent meaningful functional relationships to their environment: growth forms contain a massive amount of physiologically relevant variation, which cannot be adequately captured in such a sweeping generalisation. Even within single tree canopies, hair or beard lichen thalli, for example, can show considerable variability in their morphology, despite being in the same growth form category. Trait categories can also be nested within or interact with each other so that their unique effect may be masked as part of a complex mosaic of traits. In future studies, we hope to discover how combinations of traits might contribute to an ecological response, as any given combination might dictate an organism’s fitness and, ultimately, explains how they distribute across space and time.

Although often overlooked, lichens are clearly key players in the ecosystems around us. They modify climate, provide food and habitat for both micro- and macrofauna and are informative environmental and bioclimatic indicators (not to mention they are exquisite champions of evolution). By better understanding the mechanisms by which lichens operate at the thallus level and how large-scale climate patterns drive their growth and distribution, we can more accurately predict how lichen communities will change in a drastically warmer northern climate.

Written by:
Nathan H. Phinney: Postdoctoral researcher, Dept. of Biological Sciences, University of Bergen, Norway

Acknowledgements:
Many thanks to the coauthors, Christopher Ellis and Johan Asplund for the comments on the above text and for joining me on this fun lichen ride.

Are bluebells too slow for climate change?

Slow demography and colonization rates 17,500 times lower than the current velocity of climate change make range shifts virtually impossible in the emblematic forest plant Bluebell.

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

Climate change causes many species to shift their distributions towards higher elevations and latitudes to track their optimal climatic conditions. The current rate of change in the climate system, however, is high. Possibly too high for many species, such that the optimal climate conditions are moving faster than the rate at which a species can disperse. If you know that the distribution limits of many plant species native to temperature forests of Europe are still singed by dispersal limitation since last glacial maximum c. 11,7000 year ago, can we actually expect these species to be able to keep pace with the current rate of climate change?

Cover image article: (Free to read online for a year.)
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, xxx–xxx. https://doi.org/10.1111/jbi.14325 

To answer this question, I revisited, to my knowledge, one of the longest running transplant experiments in the world: It was 1960 when the pioneer in Belgian forest ecology, Jules Register, decided to transplant bluebells (Hyacinthoides non-scripta) from a natural population within its range to several forest sites beyond its range in Belgium. Bluebell is an emblematic species growing in deciduous forests of Europe, and probably among the most famous forest herb in Europe for laymen. The species has its emblematic status due to its pale-blue flowers: in optimal conditions, bluebells form continuous carpets covering the understorey layer, resulting in magnificent views in Spring. For this reason, the Hallerbos in Belgium is nicknamed ‘the blue forest’ and attracts yearly more than 100,000 visitors during its flowering time. However, as it is true for many understorey plant species, bluebell has long life cycles and seed dispersal is extremely limited in space. It can take 5 to 10 year for bluebell seedlings to reach a reproductive state, and previous estimates of annual colonization rates in natural populations are low, varying between 100 cm to only 0.6 cm per year. With such slow colonization rates, it is highly questionable if bluebell will be able to track the 21st century climate change.

It was only 45 years after the installation of the transplant experiment that a first evaluation was conducted. The performance of the source (within bluebell’s natural range) and transplanted (beyond bluebell’s natural range) populations was measured to understand the main limiting factors of the species’ distribution. Recently, I revisited the experiment. I asked “couldn’t we gain new insights if we combine present-day modelling techniques with data from this extremely old experiment?”

Hence, in Spring 2020, I relocated all populations and performed the same measurements. Unfortunately, when pairing my data to the previous data, I found clear signals that the population performance has decreased: in both the source and transplanted populations, individual plant performance and also the population growth rates were lower in 2020 compared to the previous survey in 2005. To interpret these negative trends within a larger spatial context, I built species distribution models. These models indeed confirmed a gradual decrease of the habitat suitability within large parts of the species distribution under climate change. Thus, the decrease predicted by the models has likely already started in the study populations.


Two of the transplanted populations in 2020. Several traits were measured on 10 flowering individuals within each population. (© Pieter Sanczuk)

Moreover, based on the colonization distance of the main dense population front since 1960, I estimated that the average colonization rate is only 0.02 m per year. Currently, this is 17,500 times lower than the velocity of climate change (the isotherms in temperate broadleaf and mixed forests are shifting at a rate of 350 m per year). Especially in the highly fragmented landscape of north-west Europe, such low colonization rates make range shifts that are fast enough to track the shifting climate, virtually impossible. In essence, bluebell’s climatic envelope is currently running away from its natural distribution.

Where is the good news? Owing to the high structural complexity of forest canopies, temperature extremes experienced by organisms living in the shade of trees can be buffered. For instance, forest-floor maximum temperatures are on average 4.1 °C cooler compared to free-air measurements. This is a larger difference in temperature compared to the projected increase by the end of the 21st century due to climate change. Moreover, forest floor temperatures are even cooler in structurally complex forests with a closed canopy (up to 8.3 °C during warm summer days). If we optimize forest management towards cool and dark forest understorey conditions, we can make an important step forward to maintain bluebell in ancient deciduous forests across their entire range.

Written by:
Pieter Sanczuk, PhD candidate, Forest & Nature Lab, Department of Environment, Faculty of Bioscience Engineering, Ghent University, Belgium

Additional information:
google scholar: https://scholar.google.be/citations?user=IphWVxwAAAAJ&hl=nl&oi=sra
ERC project website: https://formica.ugent.be/
@PieterDeFrenne
@K_VanMeerbeek
@HaesenStef

ECR feature: Katie Nigro on disturbances impact on pine distributions

Katie Nigro is a PhD candidate at the Colorado State University in the USA. She is an ecologist interested in plant distributions and their responses to impacts. Here, Katie shares her recent work on the effects of wildfire and beetle outbreaks on the range expansion of trembling aspen.

Katie Nigro in the field, after a day of searching for aspen seedlings.

Personal links. Twitter

Institute. Colorado State University

Academic life stage. PhD (4th year)

Major research themes. Disturbance impacts on vegetation recovery and plant species range shifts.

Current study system. I work in the montane and subalpine forests of Colorado and currently am focused on two tree species – trembling aspen and ponderosa pine. This system is experiencing rapid change via the increased frequency of large, severe wildfires, bark beetle outbreaks, and drought. Studying aspen and ponderosa simultaneously is super interesting because they both exhibit different responses to disturbances and thus are likely to face very different futures. In our recently published paper, we focus on aspen, which is great at repopulating after disturbance but needs a lot of water, whereas, in an ongoing study for my PhD, we are focusing on ponderosa pine, which is not as prolific a reproducer but is extremely drought tolerant.

A spruce-fir forest in the study area (Colorado, USA) with extensive canopy mortality due to spruce beetle outbreaks.

Recent JBI paper. Nigro, K. M., Rocca, M. E., Battaglia, M. A., Coop, J. D., & Redmond, M. D. (2022). Wildfire catalyzes upward range expansion of trembling aspen in southern Rocky Mountain beetle-killed forests. Journal of Biogeography 49(1), 201– 214 https://doi.org/10.1111/jbi.14302.

Motivation behind this paper. Until a decade or so ago, it was commonly thought that trembling aspen trees almost always reproduce asexually (by resprouting from their roots) and that sexual reproduction (aspen trees growing from seed) was extremely rare, occurring only under the perfect combination of soil and climate conditions. However, researchers have recently been stumbling upon aspen seedlings (from seed) more and more, especially in burned areas. Many of these seedling sightings have been far away from adult aspen, which led us to think that disturbance could facilitate aspen’s migration to cooler areas in response to climate warming. Tree migrations are usually projected to lag behind climate change because trees are long-lived and can’t just get up and walk to cooler sites, which leaves them vulnerable. We wanted to see if disturbances like fire and bark beetle outbreaks could promote faster migrations for tree species like aspen.

A severely burned area in the West Fork Fire Complex of 2013, Colorado, USA – where the study was located.

Key methodologies. This project hinged on two key methods – the first was figuring out what the upper elevational limit of aspen was in the study area via aerial imagery, and the second was to go out and survey areas above that upper elevational limit to see if signs of upward migration were occurring in fire and bark beetle impacted sites. Figuring out the local elevational limits of aspen’s distribution was novel for our study area and highlighted the fact that species elevations are highly localized and do not follow a strict minimum and maximum elevation profile for a given latitude. In addition, focusing the surveys on just those elevations above the local maximum allowed us to uncover patterns of range expansion at the same time as documenting post-disturbance forest recovery.

Katie conducting field surveys looking for aspen and characterizing site conditions.

Unexpected challenges. One surprising thing was the rarity of aspen seedlings overall. I was amazed that we did not find any aspen seedlings in sites that were beetle-killed but not burned. I expected less in beetle-killed sites than burned sites, given the documented benefit of bare soil for aspen seedling establishment. However, due to increased light availability, I still expected to find some seedlings in the beetle-killed forests. In general, the rarity of seedlings on the landscape (even in burned areas) was definitely a mental challenge at the beginning of the field season – we surveyed 25 plots before encountering an aspen seedling. You can imagine the adrenaline rush I felt when my field technician finally yelled over, “I think I found one!” 

Major results. We found that wildfire has the capacity to accelerate migrations for trembling aspen and likely other wind-dispersed, shade-intolerant tree species, thereby allowing them to catch up with climate changes that have already occurred. Interestingly, another widespread disturbance agent, bark beetles, did not facilitate the same expansion of aspen’s upward elevational limit as fire did. This reveals that tree species migrations will be differentially impacted by the increasing frequency and severity of disturbances in the coming decades. Importantly, we found that aspen regeneration not only depended on wildfire, but was also significantly impacted by local site conditions. Therefore, range shifts are unlikely to progress uniformly upwards in elevation, but rather will occur quite heterogeneously across the landscape.  

A burned aspen tree with abundant resprouts at its base, this is an example of aspen’s asexual mode of reproduction

Next steps for this research. Now that we have documented upward elevational shifts in a shade-intolerant wind dispersed species due to wildfire, I am looking into other tree species prominent in the western United States to see how disturbances and life history traits may impact their range margins. I am also investigating the potential for certain populations of trees to be better adapted to future climates than others. In the case where a species is unable to migrate fast enough, we can use this information to reforest disturbed areas with individuals that will be more resistant to future climate changes.

If you could study any organism on Earth, what would it be? I think I would still stick with plants – they’re generally agreeable, so resilient, and will sit still for hours on end while you measure anything and everything about them.

An aspen seedling found at a burned site, growing out from under a downed log. This is an example of sexual reproduction.

Anything else to add? I think I must shoutout once more to all the wonderful people that helped me collect field data for this project. The final data reflected in the paper is the result of steep, grueling off-trail hikes through snow, streams, and around downed logs, running from thunderstorms (more than once) and just generally sacrificing the comforts of home for the sake of science – I couldn’t have done it without the help of some seriously tough and adventurous folks.

ECR feature: Jeronymo Dalapicolla on different forest-association impacts on functional connectivity in the Amazon.

Jeronymo Dalapicolla is a postdoc at the Instituto Tecnológico Vale in Brazil. He is an evolutionary biologist interested in the impact of landscape features on evolutionary processes. Here, Jeronymo shares his recent work on the influence of different forest associations in the genetic variation of two sympatric species of spiny rats in the Western Amazon.

Jeronymo in a boat on Guamá River, Brazil.

Personal links. Twitter | Instagram | Research Gate

Institute. Instituto Tecnológico Vale (Belém, Brazil)

Academic life stage. Postdoc

Major research themes. Phylogenomics, Landscape Genetics, Conservation Genetics, and Statistical Phylogeography of Neotropical Mammals and Plants.

Current study system. Proechimys is a genus with more than 20 species of spiny rats (rodents closely related to capybaras and cavies) distributed throughout the Amazon basin. Given its distribution, this genus is an excellent model to study the evolutionary processes that generated current Amazonian biodiversity patterns. Furthermore, there is an unusual fact: the high rate of sympatry and syntopy between species of Proechimys. Usually, different species in the same Neotropical rodent genus show parapatric or allopatric distributions, with rare cases of sympatry. However, up to five species of Proechimys can be sampled in the same area, sometimes even in the same trapline! Which makes this genus more intriguing to study how species can use the landscape/habitat.

Jeronymo installing traps to collect rodent samples during fieldwork for his PhD.

Recent JBI paper. Dalapicolla, J.; Prado, J. R.; Percequillo, A. R.; Knowles, L. L. Functional connectivity in sympatric spiny rats reflects different dimensions of Amazonian forest-association. J. Biogeography, 48(12): 3196-3209 https://doi.org/10.1111/jbi.14281

Motivation behind this paper. I was greatly influenced by the work of Latin and North American mammalogists. One of these works was performed by James Patton’s group (UC Berkeley) using sympatric species of Proechimys and mitochondrial DNA (mtDNA) to test how gene flow occurs between river banks in the Amazon (Matocq et al. 2000: https://doi.org/10.1111/j.0014-3820.2000.tb00574.x). In general, their results confirmed an established premise for the species inhabiting seasonal floodplain forests where this habitat works as linear corridors to dispersal along the river. In contrast, in inland areas (non-flooded forests), species should present more restrictive dispersal patterns. However, Patton’s group also found some peculiar results, with some species not entirely fitting this premise. So, our goal using genomic data was to effectively test whether habitat preference impacts levels of gene flow and genetic diversity patterns. Also, we aimed to clarify why some of the previous results based on mtDNA did not fit in the general premise for seasonal floodplain forests.

Spiny rat (Proechimys sp.) collected on non-flooded forests close to the Madeira River, Rondônia, Brazil (Photo by J. L. Souza).

Key methodologies. Comparative studies on phylogeography and landscape genetics with mammals usually employ phylogenetically distant species living in the same area to look for similar patterns of diversification. The particularity of our study was to use closely related species (all in the same genus) living in the same area but showing differences in habitat preferences. Another key for our study was to use mixed models to analyse isolation-by-resistance. By doing it, we were able to control for spatial autocorrelation and for pairwise comparisons effect to improve the models’ explanations. Moreover, I consider that the landscape variables we generated representing characteristics of different habitats are also new insights going further than classical temperature and precipitation variables typically used in evolutionary studies in the Amazon region.

Unexpected challenges. Using genomic data may be commonplace for most researchers from the Global North. However, it is still challenging and expensive for researchers from Brazil like me (and other countries in the Global South). Studies involving genomics in Amazonian mammals are still scarce. As I mentioned above, this work was motivated by Matocq’s study, and we thought we would confirm their results and explain some results that did not fit the initial premise on habitat preferences. However, by using more data and increasing the scale, we were surprised that we didn’t corroborate the previous results. Indeed, we demonstrated that habitat preferences assumptions might sometimes oversimplify the real world and might not be the primary driver explaining genetic and diversity patterns.

Putumayo-Içá River in Amazonas, Brazil (Photo: R. Recorder).

Major results. Biologists have been highly dedicated to explaining the diversity patterns of species, especially in mega-diverse regions, such as Amazon. These explanations typically use hypotheses about major historical events (e.g., climate change, mountains uplift, river as barriers) to explain current diversity. Researchers often look for concordance of patterns in different species to indicate the existence of a unique or generalizable factor to explain the diversity. Our study shows that premises like “species from seasonal floodplain forests have low structure and high gene flow” are not completely accurate for the entire biota, which can bring important conservation implications. So, understanding the relationship between ecology and how different species use the landscape can be more important in explaining diversity patterns in some instances than historical events. In addition, in this study, we applied modern analytical methods that can be used in other studies – with all scripts, data, and examples available as supplementary material (Dryad; GitHub).

Next steps for this research. We still have lots of work to do with this rodent group and the Amazon. Our research group is focused on unravelling the patterns of diversity of small Amazonian mammals to promote a better understanding of the evolution of the Amazonian region to provide key information for the conservation of this biome. Specifically, about the Proechimys, we are working on the species delimitation for the genus and the taxonomic rearrangements using morphological data. We hope to share these results as soon as possible.

Boat on Putumayo-Içá River during a scientific expedition in Amazonas, Brazil (2015) to collect material for the Zoology Museum of Universidade de São Paulo during my PhD (Photo: I. Prates).

If you could study any organism on Earth, what would it be? It’s funny how our expectations change, right? When I was an undergrad student, I dreamed about studying Marine Biology, especially turtles and cetaceans. Today I don’t see myself studying any marine organisms – I’m not a good swimmer! Although I love living close to the ocean, it was another expectation that didn’t work! Considering terrestrial organisms, I have a fascination for big cats and would love to study them, preferably in the field.

Anything else to add? Although I like working in the molecular biology laboratory, I have three passions in Biology. The first is fieldwork, data collection, and contact with nature, which always brings insights and important research questions. My second passion is museums and scientific collections. I spent a good part of my academic life managing regional mammal collections in Brazil and a lot of my Ph.D. time in collections gathering data. My research wouldn’t be possible without these institutions, so I have to thank them so much! My third passion is teaching. I started teaching in elementary and high school more than ten years ago, and now I teach graduate courses at the Vale Institute of Technology. I love to share what I’ve learned with other people – it’s a rewarding job! I’m known among my colleagues and friends for the tutorials and “how-to-do” scripts that I like to create, explaining in detail all the steps of analyses or software’s use. I always get emails asking if I have a tutorial or material about some analysis and if I could help solve some issues. I understand that the knowledge I gained from my professors is my heritage, and using it to help others is wonderful. Sharing knowledge is probably my most precious legacy for future generations.

Sunset in Solimões River during the scientific expedition to Putumayo-Içá River, Amazonas, Brazil (2015) (Photo: R. Recoder).

ECR Feature: Yun Liu on the influence of elevation on bioregionalisation

Yun Liu is a PhD student at the Chinese Academy of Science’s Institute of Botany. She has a keen interest in phylogeography, specifically in plants. Yun shares her recent work on the incorporation of elevation into bioregionalisation classifications of the Sino-Himalaya flora.

Yun Liu

Name. Yun Liu

Personal links. ResearchGate

Institute. Institute of Botany, Chinese Academy of Sciences

Academic life stage. PhD student

Major research themes. Phylogeny, bioregionalisation, phylofloristics, biogeography

Current study system. Currently, my major research focus is on the spatial and temporal evolution of the Sino-Himalayan flora. The Sino-Himalaya is one of the most biodiverse mountain regions on Earth, harbouring a complex diversity of floristic elements and various endemic and endangered species. The biodiversity of the Sino-Himalaya bears the signature of deep-time evolutionary and ecological processes, a history well worth preserving, especially against habitat destruction and climate change. However, the origin and evolution of the unique biota is poorly understood, even though this information is crucial to enhance our understanding of the evolution of mountain biodiversity. Exploring the evolutionary history of the Sino-Himalayan flora is a cool but challenging task.

Representative plant groups in the Sino-Himalayan flora. (A) Allium yuanum (B) Pedicularis mussoti (C) Meconopsis speciosa (D) Saussurea obvallata (E) Aconitum flavum (F) Saussurea inversa (G) Primula sinensis (H) Rhododendron chamaethomsonii (I) Gentiana arethusae var. delicatula. The photos of A, B, C, G, H, and I were taken by Jianfei Ye; the photos of D, E, F were taken by Ze Wei.

Recent publication in JBI. Liu, Y., Ye, J. F., Hu, H. H., Peng, D. X., Zhao, L. N., Lu, L. M., … & Chen, Z. D. Influence of elevation on bioregionalisation: A case study of the Sino-Himalayan flora. Journal of Biogeography. (Link here)

Motivation behind this work. Our work on the Sino-Himalayan flora focuses on its bioregionalisation, that is the classification of biota into hierarchical biogeographical areas (e.g. kingdoms, regions, subregions) according to the spatial distribution of taxa (e.g. families, genera, species). In recent years, significant progress has been made in the field of bioregionalisation by incorporating evolutionary information from phylogenetic trees, instead of solely emphasising the importance of endemic taxa or using taxonomic dissimilarity. However, only a few studies have considered the effect of vertical gradients (elevation) on the bioregionalisation of montane regions. The complex topography and large elevational gradients in the Sino-Himalayan area provide an ideal system to test the influence of elevation on bioregionalisation.

The Hengduan Mountains with a broad elevational range and Faxon fir, Abies fargesii var. faxoniana (Rehder & E. H. Wilson) Tang S. Liu, forest in the Kangding county, western Sichuan, China. Photograph by Jianfei Ye.

Methods. We compiled distribution data and elevation ranges of angiosperms in the Sino-Himalaya and adjacent areas and reconstructed a species-level phylogenetic tree of 19,313 angiosperm species. The area was divided into 398 grid cells, each 1×1°. Nine datasets of different elevation ranges were then used to delineate the flora of the Sino-Himalaya and adjacent areas using the phylogenetic dissimilarity approach.
Although several studies have considered the effect of elevation on the bioregionalisation of montane regions, no study has provided adequate methodological detail to incorporate elevation data into the bioregionalisation of areas with broad elevational gradients. In this study, we built a regionalisation scheme of the Sino-Himalayan flora by combining phylogenetic and elevation data.

Major results. Our study of bioregionalisation in montane regions has moved from a two-dimensional (latitude and longitude) to a three-dimensional (latitude, longitude, and elevation) perspective. It provides novel insights into the regionalisation of the Sino-Himalayan flora and highlights the importance of incorporating elevation data in the bioregionalisation of mountainous areas. The integration of elevation helped to identify boundaries of finer biogeographical units (regions and/or subregions) within the flora. By incorporating both elevational and phylogenetic information, we were able to identify eight distinct subregions nested within the Yunnan Plateau, Hengduan Mountains, and East Himalaya regions in the Sino-Himalaya area. The bioregionalisation scheme helps us to understand the origin and evolution of the Sino-Himalayan flora and explore the spatial and temporal distribution patterns of biodiversity. It provides basic units for broad-scale ecological and evolutionary studies and spatially explicit frameworks for making conservation planning.

Complex topography of the giant Galongla Mountain in Bomê County, Xizang. Photograph by Jianfei Ye.

Unexpected challenges. One challenge was the reconstruction of a species-level phylogenetic tree of 19,313 angiosperm species. We had to align sequences and then manually adjust them to fit homology criteria. This process was very time consuming and required a lot of patience. To study the effects of elevation on bioregionalisation, we used segmentation analysis to obtain sub-datasets of different elevation gradients. We divided the elevation range of species, extracted species from each elevation range, and then compared regionalisation results based on datasets of different elevation ranges to reveal the influence of elevation on bioregionalisation.

Next steps. Our regionalisation scheme of the Sino-Himalayan flora revealed the distribution patterns of biodiversity and provided us a spatially explicit framework for the future research. Therefore, the next step is to focus on the evolutionary history of the Sino-Himalayan flora. The Sino-Himalayan flora is composed of complex floristic elements from various floras and harbours many endemic and endangered species. It is fascinating for us to explore when and how the exceptionally species-rich and unique flora formed over geological time.

Yun (pictured in center) out in the field with her colleagues in the Gansu province, China.

If you could study any organism on Earth, what would it be? Plants are my passion. Plants make our living world colourful and form the backbone of terrestrial ecosystems and the base of food chains. They also serve as the material basis for human survival by providing oxygen, food, medicines, biofuels, building materials and other products. We can’t live without plants. But aside from their importance to ecosystem function, I find plants so incredibly beautiful, and they harbour so much diversity that I could spend a lifetime studying.

Anything else to share? Fieldwork is an interesting thing. When you are not in a state to write your paper or come up with a new idea to study, take a walk in the wild and enjoy the beauty and mystery of nature.

RFP: Journal of Biogeography Innovation (JBI) Awards, 2022

The Journal of Biogeography invites submissions of manuscript proposals (brief outlines of manuscripts yet to be prepared) by Early Career Researchers for consideration for publication and awards for innovation.  

Proposals will be considered in three categories of article:
     – Perspectives and Syntheses
     – Original research
     – Methods

(For more information, see https://onlinelibrary.wiley.com/page/journal/13652699/homepage/forauthors.html)

Proposals on any subject in biogeography are welcome. 

Proposals should be composed of the following and submitted as a single PDF:
     – Title
     – Targeted article type (see above)
     – ≤600 word proposal organized under the following headings:
          .. The gap in knowledge/understanding to be addressed 
          .. The context (incl. a brief review of the relevant literature)
          .. Goal or expected outcomes 
          .. Significance
     – List of authors (indicate the eligible ECR, who must be lead and corresponding author)
     – Contact information for the eligible ECR
     – Date the eligible ECR’s degree was conferred

Early Career Researchers are graduate students and postdocs (and equivalent positions) up to 5-years post award of the PhD (exclusive of career breaks). 

All proposals will be reviewed by an ad hoc committee of JBI academy, associate and chief editors on the following criteria:

  1. Novelty / originality of the idea (30%)
  2. Accuracy of identified problem and context (30%)
  3. Significance / impact (20%)
  4. Quality of preparation (20%)

Up to a dozen proposals in each category will be invited for submission as full articles, which should be submitted within 3 months of receiving the invitation.

Full articles will enter the standard editorial and review procedure of the journal and will be assessed for receipt of the award on the following criteria:

  1. Novelty / originality of the idea
  2. Accuracy of identified problem and context 
  3. Significance / impact of findings
  4. Quality of preparation of the manuscript

Journal of Biogeography will publish all invited articles freely under “full access” (i.e. downloadable from the journal website for one year from the date of publication).  In addition, the lead ECR authors of the three papers ranked most highly by the editorial team will receive a monetary award of $750 each.  

Timeline:
Proposal submission: 01 March 2022
Invite full manuscripts: 01 April 2022
Manuscript submission: 01 September 2022

Upload *proposals* as a single PDF with the filename “LASTNAME_FIRSTNAME_ECRproposal.pdf” only to: https://www.dropbox.com/request/kcjoSxpDrzb569JF2B27 *upload only*

Address enquiries (Subject line: “Enquiry: ECR Innovation Award”) to the Editor-in-Chief at mdawson@ucmerced.edu

JBI aims to foster inclusive science that reflects the disciplinary, human, and geographic diversity of biogeography and biogeographers. Submissions are welcomed from applicants of all ethnicities, races, colors, religions, sexes, sexual orientations, gender identities, national origins, disabilities, ages, or other individual status.

RFP: Small grants for global colloquia in biogeography, 2022

The Journal of Biogeography invites applications for funding to facilitate one or more global colloquia.  The event may be stand-alone, or may be staged in association with a larger meeting, it may be in-person or virtual. The topic may be on any aspect of biogeography.  A goal of the colloquium should be to publish a synthesis paper and/or a series of papers that represent the range of topics discussed.

The Journal wishes these colloquia to become a regular activity that helps biogeographers develop, exchange, and explore ideas globally that advance biogeography through consolidation of fragmentary knowledge, synthesis across disciplines, and innovation.  Thus, the funds up to $4000 are offered by the journal primarily with the intention of facilitating involvement of people who might not otherwise be able to participate, or to stage an event that, because of its nature, draws in people of diverse backgrounds and with varied perspectives.   

The awardees will take care of all organization and are responsible to the journal only in terms of meeting any prior agreement on publication, promotion, and staging the proposed event.  The journal is responsible to the local committee only in terms of promoting the event via journal social media and providing the funding agreed. 

Proposals should take the following format (as a single PDF):

1. Title and description of the topical focus (e.g., early career conference, a regional focus, or a disciplinary focus). ≤0.5 page.

2. Relevance, context, and how the colloquium and publications therefrom will advance the discipline of biogeography. ≤0.5 page.

3. The target number of attendees, and distribution across career stages, countries of origin/habitation, gender. ≤0.5 page.

4. The proposed format: general organization (e.g. number of keynote speakers in plenary sessions, number of concurrent sessions, talks, posters). ≤0.5 page.

5. The actual dates and details of the colloquium: a) in-person/virtual, b) facilities/technology, c) list of organizers, d) list of committed participants. ≤0.5 page.

6. The uses of and substantial difference that will be made by the support from Journal of Biogeography. ≤0.5 page.

7. Outline of the proposed publications, which will first be submitted for consideration at Journal of Biogeography. ≤0.5 page.

8. Other budgetary considerations, partners, and obligations therein.

We aim to fund 1-2 symposia during the coming year.  Proposals on any subject in biogeography are welcome; in 2022, we encourage, but do not limit responses to this request for proposals, to colloquia exploring the following areas: Functional biogeography; Cross-scale biogeography & biodiversity (considering biological, spatial, and/or temporal hierarchies); Marine-terrestrial comparisons and contrasts (also with aerial, freshwater, and subterranean realms); Biogeography in the Anthropocene.

Submit proposals to: https://www.dropbox.com/request/RqqNgMxBZjb4uy6wRbUK *upload only*

The deadline for submissions is: 01 March 2022.  

Address enquiries (Subject line: “Enquiry: Journal of Biogeography Colloquia sponsorship”) to the Editor-in-Chief at mdawson@ucmerced.edu.

JBI aims to foster inclusive science that reflects the disciplinary, human, and geographic diversity of biogeography and biogeographers. Submissions are welcomed from applicants of all ethnicities, races, colors, religions, sexes, sexual orientations, gender identities, national origins, disabilities, ages, or other individual status.

Island birds

Bird diversity on shelf islands does not benefit from recent land-bridge connections.

Above: Brown-throated Sunbird Anthreptes malacensis, a species very commonly found on islands in Sundaland.

When studying biogeography, I make a constant effort to tell myself that what I am witnessing today is just a mere snapshot in time. I’m still in my 20s, while the planet is quite a number of times older than me. Seemingly strange observations hence make much more sense once I consider various historical influences of Earth’s climatic variations and land movements. When I first started this project, I fully expected the data to tell such a story: that species distribution and composition of birds on islands in Sundaland are primarily determined by historical factors too.

Cover image article: (Free to read online for a year.)
Sin, Y. C. K., Kristensen, N. P., Gwee, C. Y., Chisholm, R. A., & Rheindt, F. E. (2022). Bird diversity on shelf islands does not benefit from recent land-bridge connections. Journal of Biogeography, 49, 189-200. https://doi.org/10.1111/jbi.14293 

Satellite images of Sundaic Southeast Asia show that the region comprises many islands today – roughly 17,000 of varying shapes and sizes. Had such technology (and us) existed half a million years ago, we would have witnessed a completely different landscape: no islands scattered across the region, and the whole of Sundaland completely exposed as land instead. It was only ~400,000 years ago that consistent subsidence of the entire shelf led to its partial drowning, and since then, sea level fluctuations have been constantly changing the land configuration. During interglacials, high sea level causes land to be broken up into islands, while during glacial periods, the sea level is ~120 metres lower than it is today and Sundaland gets “reunited” by land-bridges. While we live in a period of interglacial, the last glacial maximum occurred only as recently as ~20,000 years ago. Furthermore, during the Holocene sea level peak ~7,000 years ago, the sea level was 3-5 metres higher than it is today. This rise causing low-lying islands to be completely submerged before they re-emerged again when the sea level returned to its current form. The configuration of Sundaland we see is truly ephemeral: a majority of the islands are shelf islands that get connected to the mainland by land-bridges during glacial periods, while a small subset are deep-sea islands that have no historic connection to the mainland.

As a consequence of the Sundaland’s complex geologic chronicles, we would expect biodiversity patterns on its islands to be heavily influenced by the past: an island that enjoyed more land-bridge connection to the mainland and used to be bigger throughout evolutionary history should harbour more species. This phenomenon where species richness in an area exceeds the expected value given its size is called supersaturation and is observed in lizard diversity on land-bridge islands in Baja California and birds on some satellite islands of New Guinea. In addition to supersaturation, recently submerged islands that just had terrestrial biodiversity obliterated should be expected to have species composition differing from similar-sized islands that did not drown.


Map of Sundaland delineated by the Sunda shelf in light blue. Study islands (n=94) are highlighted, with deep-sea islands in yellow and shelf islands in red. Many small islands are not visible at this scale and circle sizes indicate the number of study islands within a 50 km radius. The number of endemic species-level bird taxa, if any, is indicated adjacent to islands following the same colour scheme (only one shelf island—Kangean, in the extreme southeast of the shelf— has an endemic species-level taxon). In the case of the Mentawai islands (dotted yellow ellipse), three taxa are endemic to the whole island group which forms one connected paleo-island.

We investigated these hypotheses by analysing the effects of various past and present geographical variables on diversity patterns of birds on islands distributed across Sundaland. We found evidence that bird endemicity was mainly restricted to deep-sea islands. The lack of any historical land-bridge precluded gene flow between the bird populations and gave rise to endemic species. This initial result provided a strong clue that historical processes shaped diversity. However, contrary to our expectation, neither the duration of mainland connection in the past 20,000 years nor the average change in island area in recent geologic history was shown to influence the number of species breeding on the shelf-islands. Instead, the classic Island Biogeography parameters of island area and distance from mainland predominantly explained species richness. Our unexpected results suggest that once a landmass is disconnected from the mainland due to rising sea levels – effectively becoming an island – extinction kicks in rapidly, leaving no room for “excess” species as the island shrinks. We also found that in addition to island area and distance from mainland, the proportion of landmass surrounding an island played an important role in maintaining species richness. For example, a solitary island that is 50 kilometres from the mainland would have lower species richness than a similar sized island, also 50 kilometres away, but clustered together with a group of other islands. In Sundaland, avian species richness of an island equilibrates quickly based on extinction-immigration processes, which are in turn influenced by the island’s present-day geographical parameters.

We additionally discovered that species composition on similar-sized islands did not differ across recently submerged and unsubmerged islands. On recently submerged islands, the bird population present today could only have arisen from entirely new colonisers since the island was wiped clean when it drowned. These birds, by their capability of occupying brand-new islands, can be said to have high dispersal and colonising ability. On the contrary, islands that were never submerged should technically be able to host both colonisers and surviving populations from before the islands shrank. Yet our results showed that the two island classes had species composition unaffected by their history of submergence. This observation implies that only a subset of species is capable of persisting on the tiniest islands in Sundaland: the strongly dispersive birds. Our result makes sense when we think about the biology of these animals – their population density is generally low, hence, once an island shrinks below a certain size, an isolated island population is unable to sustain itself. Resultantly, small islands become home only to the most dispersive species as these birds are able to fly around and find partners in nearby islands. Having said that, a majority of these species were intriguingly not island specialists – they were also birds that do well on the mainland too, but all on edge habitats; forest dependent species are the first to disappear once an island shrinks.


Examples of non-island specialists that are commonly found on small Sundaic islands: top left – Collared Kingfisher Todiramphus chloris; top right – Olive-winged Bulbul Pycnonotus plumosus; bottom left – Ashy Tailorbird Orthotomus ruficeps; bottom right – Pink-necked Green Pigeon Treron vernans. Example of an island specialist that is found across islands in Sundaland: middle – Pied Imperial Pigeon Ducula bicolor.

Birds are known for their flight ability, and it might be a counterintuitive idea that endemicity and species composition is shaped due to their reluctance to fly to other islands. However, flying across water is actually a behaviour that many tropical birds generally avoid due to the high risks involved, and this is why only the most adventurous of species do well on tiny islands.

Our work shows that species richness of birds on shelf islands in Sundaland is predominantly determined by present-day geographical parameters. It turns out that, at least for birds, Sundaic islands themselves are also only witnessing a snapshot in time.

Written by:
Yong Chee Keita Sin
Research Assistant, Avian Evolution Lab, National University of Singapore

Additional information:
Instagram @okamoto_keita_sin

Acknowledgements:
I am greatly indebted to the co-authors of our manuscript Nadiah (Twitter @NadiahKrist; nadiah.org) , Chyi Yin, Ryan (ryanchisholm.com) and Frank (Twitter @avianevo; avianevonus.com) for the support and mentorship offered throughout the work. I would also like to thank everyone who helped out in the fieldwork and analyses of our manuscript and Geraldine Lee for comments on this blog post.

Towering trees and flying dragons

Canopy physiognomy governs the distribution of peninsular Indian flying lizards in regions of climatic suitability.

Above: Silhouette of an Indian Flying Lizard in its arboreal habitat.

I have always been intrigued by organismal distributions. Why do certain species occur in certain regions? Why do they stop, sometimes abruptly, at certain latitudes where there aren’t any physical barriers to dispersal? So, when I decided to work on peninsular Indian Flying dragons (Draco dussumieri) for my PhD, it was quite natural to ask why Dracos do not cross the Goa gap (15.8° N) in the Western Ghats mountains of peninsular India.

The Western Ghats is a great laboratory to study various aspects of organismal biology. Life here comprises of organisms with remarkably distinct evolutionary histories that have colonized these mountains at different periods in geological time. The distribution of a species in the Western Ghats is largely a factor of when its ancestor first colonized these mountains and its ecological ability to disperse and adapt to a constantly changing environment.

Cover image article: (Free to read online for two years.)
Chaitanya, R, & Meiri, S. (2021). Can’t see the wood for the trees? Canopy physiognomy influences the distribution of peninsular Indian flying lizards. Journal of Biogeography, 49, 1– 13. https://doi.org/10.1111/jbi.14298 

This mountain range is characterized by three prominent biogeographic breaks, the Shencottah pass, the Palghat gap and the Goa gap. While the former two are physical barriers – deep valleys that cut across the mountains horizontally, the Goa gap is not a physical barrier but an invisible boundary that certain organisms have failed to span. Naturally, biogeographers have long been flummoxed by the absence of certain organisms north of this ‘hypothetical’ barrier. What exactly is going on north of the Goa gap that has prevented otherwise vagile organisms such as Flying dragons from crossing over?

Studies in the past have suggested that the Goa gap may be a boundary that demarcates two different climatic regimes in the Western Ghats, the northern region being warmer and drier. While this is true, certain organisms that are dependent on high rainfall such as the Roux’s lizard (Monilesaurus rouxii) have successfully crossed the gap and colonized regions north of it, but not certain others like Draco that could easily persist in dry forests. So, why have the wet-adapted, arboreal Roux’s lizards been able to colonize the drier regions north of the Goa gap when the more climatically pliant Dracos have not?


.

To solve this riddle, Shai and I compared the ecological niches of the Roux’s lizard and Draco to try and decode the environmental variables that govern their distributions. We expected a complex concoction of reasons for Draco absence, but to our surprise we received a very simple answer: tree heights! Draco could not traverse the Goa gap because trees north of this barrier were not tall enough to support them. Simple statistical analyses of canopy physiognomy in regions of Draco presence (south of the gap) versus absence (north of the gap) revealed great disparity in canopy height and coverage. Further, niche models built based only on climatic variables revealed vast expanses of suitable habitats for Draco north of the Goa gap. This indicated that in regions of climatic suitability, the height of canopies influences the presence of these exclusively arboreal lizards.

During fieldwork, my colleagues and I have noticed that Draco occupy the upper reaches of trees closer to the canopy and only descend about midway through the tree trunk during courtship or to forage for ants. The females come down to the ground only once, when they have to lay eggs. The males never do! Roux’s lizards on the other hand, are often found mid-trunk, often even lower near the base of the tree. They are regularly seen sleeping on low shrubs too. So, despite requiring more rainfall for their persistence, Roux’s lizards have been able to disperse across the Goa gap chiefly because they are not dependent on tall canopies.

Our study belabours the point that in the absence of topographic barriers to dispersal, the environmental regime an organism occupies governs its spatial boundaries. It proposes a new, canopy physiognomy based biogeographic hypothesis for the Western Ghats region that can be tested against other model organisms.

Curiously, King Cobras, Slender Lorises and Hump nosed pit-vipers reach the Goa gap from the south but do not pass over. So, what stops these animals from spanning the Goa gap?


The Peninsular Indian Flying lizard, Draco dussumieri, takes flight. Location: Agumbe, India.
Photographed by Vinod Venugopal.

Written by:
R. Chaitanya; School of Zoology, Tel Aviv University, Tel Aviv, Israel