Adaptation to elevation in Brassicaceae species of the central Alps

by Alessio Maccagni
Supervisors: Prof. Yvonne Willi, PD Dr. Günter Hoch, Prof. Jake Alexander

Species are restricted in their spatial distribution, but the reasons behind this phenomenon are still not entirely known. Temperature has been considered to play an important role for a long time, for example because of the commonly observed overlap between isoclines and distribution limits, or for the direct impact that temperature has on the physiology of organisms. From an evolutionary point of view however, it is unclear why the climate niche of species does not seem to evolve such that species ranges can extend unlimitedly.
To shed light on the evolutionary constraints limiting species distribution, I studied patterns of adaptation along an elevational gradient, which is essentially a thermal gradient. I chose a macro-evolutionary approach and included in my analyses 100 Brassicaceae species covering a high diversity of restricted elevational ranges in the European Alps. Species were compared in their thermal responses and thermal adaptation based on a climate chamber experiment and a transplant experiment on a mountain slope, with 5 transplant sites from 600 to 2000 m of elevation. Climate chamber experiments revealed that low- and high-elevation species mainly differed in the response of growth to temperature, with high-elevation species being better at growing when daily temperatures reached a high maximum, but worse at growing to large size when night frosts occurred. Therefore, results indicated a trade-off between fast growth under warm conditions and frost tolerance. Analyses on an association between elevational range size and phenotypic plasticity revealed no support for a positive link. However, I found that increased thermal heterogeneity selected for stronger thermal specialisation, countering the hypothesis that temporal environmental variability selects for increased plasticity. The transplant experiment demonstrated that species were indeed adapted to their optimal elevation of occurrence; lifetime performance declined if the transplant site was at a different elevation than the typical elevation of occurrence of a species. Patterns established not via temperature-dependent mortality, but because reproduction declined with increasing difference in elevation relative to the typical elevation. The probability of fruit set decreased with increasing distance. Furthermore, I found that reproduction negatively affected survival to the next year, suggesting an allocation trade-off between reproduction and longevity that may be also important in constraining the climate niche and its evolution.
Overall, this body of work supported that elevational range limits generally reflect niche limits, and that species seem to have been selected for thermal specialisation. Evolutionary constraints in the widening of the climate niche seem to include genetic trade-offs in growing fast under warm conditions and being frost tolerant, and an allocation trade-off between reproduction and longevity. It is these two axes of trade-offs or four axes of life-history aspects that future micro evolutionary studies should focus on to confirm their role in constraining the evolution of the climate niche within species.

Genetic and environmental constraints causing species’ range limits

by Antoine Perrier
Supervisors: Prof. Yvonne Willi, Dr. Kay Lucek, PD Dr. Lukas Schärer, Dr. Joëlle Ronfort

Human-caused global change has led to shifts in the geographic distribution of many wild species. This has renewed the interest of understanding the factors that shape species’ contemporary range limits from both an ecological and evolutionary perspective. Recent evolutionary theory particularly emphasized the role of past demographic processes and neutral evolution in contributing to range limits. The aim of my thesis was to study these factors and their interaction with the environment experienced at range edges in an empirical system, the North American plant Arabidopsis lyrata. By crossing populations of varying range position and demographic history, and raising their offspring in gardens distributed across and beyond the species range, I found that populations with a history of small size due to past range expansion or rear-edge isolation suffered from increased expression of mutational load driven by genetic drift. This latter effect was even stronger under environmental stress, particularly under a warmer climate. Furthermore, populations at range edges with heightened past exposure to genetic drift had a reduced signature of climate adaptation. Finally, I compared A. lyrata and a novel species it gave rise to, A. arenicola, with a more northern distribution, in a climate chamber experiment. This new taxon diverged from A. lyrata in coping with a cool climate and strong reproductive isolation, most likely allowing it to colonize subarctic regions and escape maladaptive gene flow. Results generally support the newer evolutionary theory about a predominant role of neutral evolution in contributing to geographic range limits, via genetic drift opposing purifying and directional selection. The study of sister taxa however shows that these constraints to evolution at range limits are not absolute, and can be broken.


Climate mal-adaptation and biotic interactions at species’ range limits

by Darío Sánchez Castro
Supervisors: Prof. Yvonne Will, PD Dr. Günter Hoch, Prof. Joan Edwards

Why species have restricted geographic distributions or why species do not occur everywhere is still an open question in ecology and evolutionary biology. It is assumed that the species range limits normally reflect the ecological conditions where the species stop occurring because of a lack of habitat suitability. Moreover, these populations at the margins are known to suffer from a history of small population size and the accumulation of genetic drift. Additionally, biotic interactions have been recently proposed to act negatively at the range edges. Among them, pollination services are particularly important as reproduction and population dynamics of the majority of the flowering plant species rely upon them. However, pollinator services are not constant, varying across different temporal and spatial scales.
Here I tested whether a history of small population size, enhanced genetic drift, and the accumulation of deleterious mutations in range-edge populations was linked with reduced adaptation in the North American Arabidopsis lyrata. I performed a transplant experiment with sites across and beyond the species distribution with source plant populations from the centre and the periphery, these last ones with a history of range expansion or long-term isolation. Additionally, I monitored pollination interactions in natural populations over a transect spanning from the southern to the northern range limit and over different temporal and spatial scales using time-lapse cameras.
The results from the transplant experiment shown that plant multiplicative performance declined toward the southern range limit and beyond, but not in the northern range.  Furthermore, populations shown evidence of climate adaptation to two suggested niche variables, temperature in spring, and precipitation of the wettest quarter. However, the signature of adaptation was reduced in populations with a history of small population size, and additionally, the heterosis effect was increased in populations with heightened genomic estimates of load, longer expansion distance or long-term isolation, and a selfing mating system. Genetic drift and mutation accumulation due to past range expansion and long-term isolation of small populations at the range margins is therefore a strong determinant of population-mean performance.
In the pollinators project, I found that the plant-pollinator network for A. lyrata is a generalist system, and southern populations had lower pollination services compared to center and northern populations. The diurnal activity of the pollinators was mostly explained by air temperature conditions, occurring the majority of the visits during the mid-day. The density of flowers in a patch explained partially the spatial variation, but the signature was specific for each taxonomic group. Even though no evidence of niche partitioning was found, the different taxonomic groups of pollinators differed in their activity window where some taxa were more tolerant under certain temperatures or intervals of the day.

Controlling "Fusarium" species and their mycotoxins in cereals

by Jennifer Mark
Supervisors: Dr. Helge Sierotzki, Prof. Yvonne Willi

Fusarium head blight (FHB) is a severe fungal disease on cereals like wheat, corn and barley. It is caused by a complex of several Fusarium species producing mycotoxins. Besides having a toxigenic effect on humans and animals, mycotoxins have a high impact on grain yield and quality. Securing yield quantity and quality is important for the farmers and the control of FHB remains strategic including appropriate agricultural practices, genetic and biological measures but the predominance of monoculture still requires the application of fungicides to save the harvest. Demethylation inhibitor (DMI) fungicides and quinone inhibitor (Qol) fungicides were reported to decrease FHB. However, decreased fungicide sensitivity or full fungicide resistance has been reported to these two fungicide classes. Therefore, the new class of SDHI (succinate dehydrogenase inhibitors) fungicides has gained attractiveness, particularly those with novel chemical structures like pydiflumetofen. Aim of this study was to investigate the interaction of fungicide action and FHB disease complex in order to provide insights helping the control of the FHB complex and its mycotoxins in wheat and corn. To perform, in-vitro assays were conducted in order to test the sensitivity of more than 500 isolates representing 13 Fusarium species to different fungicide class, DMI fungicides, quinone outside inhibitor fungicides (QoI), benzimidazole fungicides (MBC), SDHIs. SDH subunits of the Fusarium panel were analyzed and greenhouse and field assays were performed to investigate the activity of fungicides in realistic conditions. Results indicate a superior efficacy of pydiflumetofen compared to all tested fungicides. The advantage was shown for all species, all isolates and all mycotoxins.

Genetic diversity and climate adaption in Arabidopsis lyrata

by Marco Fracassetti
Supervisors: Prof. Yvonne Willi, Luca Ferretti

Applied fields of research such as the one on global climate change has heightened the interest to understand the adaptive evolution process and limits to adaptive evolution. Progress in the field depends on knowing of the traits under selection and their genetic variation. The goal of this PhD thesis was to generally assess genome-wide single nucleotide polymorphism (SNP) diversity across an entire species geographic distribution and to detect SNPs and genes linked to adaptation to climatic variables and substrate type within the herbaceous plant Arabidopsis lyrata subsp. lyrata (A. lyrata). For this work, DNA of 52 populations covering the whole geographic range of A. lyrata were analyzed by pooling DNA of multiple individuals of each population, sequencing the pools (Pool-seq) and revealing population SNP frequencies. In the first chapter the wet-lab protocol of Pool-seq and the bioinformatics pipeline were tested. In the second chapter the genetic diversity of different genomic regions was analyzed to trace the history of the populations of A. lyrata. In the third chapter, the climatic variables that determine the ecological niche limits of the species distribution were defined. And, in the fourth chapter the SNP frequencies were associated with climatic variables and substrate type to detect the genomic regions involved in adaptation to climate and edaphic conditions, highlighting potentially relevant genes and pathways.