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Numerous insertions of mitochondrial DNA in the genome of the northern mole vole, Ellobius talpinus
(2024)
Background
Ellobius talpinus is a subterranean rodent representing an attractive model in population ecology studies due to its highly special lifestyle and sociality. In such studies, mitochondrial DNA (mtDNA) is widely used. However, if nuclear copies of mtDNA, aka NUMTs, are present, they may co-amplify with the target mtDNA fragment, generating misleading results. The aim of this study was to determine whether NUMTs are present in E. talpinus.
Methods and results
PCR amplification of the putative mtDNA CytB-D-loop fragment using ‘universal’ primers from 56 E. talpinus samples produced multiple double peaks in 90% of the sequencing chromatograms. To reveal NUMTs, molecular cloning and sequencing of PCR products of three specimens was conducted, followed by phylogenetic analysis. The pseudogene nature of three out of the seven detected haplotypes was confirmed by their basal positions in relation to other Ellobius haplotypes in the phylogenetic tree. Additionally, ‘haplotype B’ was basal in relation to other E. talpinus haplotypes and found present in very distant sampling sites. BLASTN search revealed 195 NUMTs in the E. talpinus nuclear genome, including fragments of all four PCR amplified pseudogenes. Although the majority of the NUMTs studied were short, the entire mtDNA had copies in the nuclear genome. The most numerous NUMTs were found for rrnL, COXI, and D-loop.
Conclusions
Numerous NUMTs are present in E. talpinus and can be difficult to discriminate against mtDNA sequences. Thus, in future population or phylogenetic studies in E. talpinus, the possibility of cryptic NUMTs amplification should always be taken into account.
Biological invasions pose global threats to biodiversity and ecosystem functions. Invasive species often display a high degree of phenotypic plasticity, enabling them to adapt to new environments. This study examines plasticity to water stress in native and invasive Opuntia ficus-indica populations, a prevalent invader in arid and semi-arid ecosystems. Through controlled greenhouse experiments, we evaluated three native and nine invasive populations. While all plants survived the dry treatment, natives exhibited lower plasticity to high water availability with only a 36% aboveground biomass increase compared to the invasives with a greater increase of 94%. In terms of belowground biomass, there was no significant response to increased water availability for native populations, but plants from the invasive populations showed a 75% increase from the dry to the wet treatment. Enhanced phenotypic plasticity observed in invasive populations of O. ficus-indica is likely a significant driver of their success and invasiveness across different regions, particularly with a clear environmental preference towards less arid conditions. Climate change is expected to amplify the invasion success due to the expansion of arid areas and desertification. Opuntia ficus-indica adapts to diverse environments, survives dry spells, and grows rapidly in times of high-water supply, making it a candidate for increased invasion potential with climate change.
Plant roots influence many ecological and biogeochemical processes, such as carbon, water and nutrient cycling. Because of difficult accessibility, knowledge on plant root growth dynamics in field conditions, however, is fragmentary at best. Minirhizotrons, i.e. transparent tubes placed in the substrate into which specialized cameras or circular scanners are inserted, facilitate the capture of high-resolution images of root dynamics at the soil-tube interface with little to no disturbance after the initial installation. Their use, especially in field studies with multiple species and heterogeneous substrates, though, is limited by the amount of work that subsequent manual tracing of roots in the images requires. Furthermore, the reproducibility and objectivity of manual root detection is questionable. Here, we use a Convolutional Neural Network (CNN) for the automatic detection of roots in minirhizotron images and compare the performance of our RootDetector with human analysts with different levels of expertise. Our minirhizotron data come from various wetlands on organic soils, i.e. highly heterogeneous substrates consisting of dead plant material, often times mainly roots, in various degrees of decomposition. This may be seen as one of the most challenging soil types for root segmentation in minirhizotron images. RootDetector showed a high capability to correctly segment root pixels in minirhizotron images from field observations (F1 = 0.6044; r2 compared to a human expert = 0.99). Reproducibility among humans, however, depended strongly on expertise level, with novices showing drastic variation among individual analysts and annotating on average more than 13-times higher root length/cm2 per image compared to expert analysts. CNNs such as RootDetector provide a reliable and efficient method for the detection of roots and root length in minirhizotron images even from challenging field conditions. Analyses with RootDetector thus save resources, are reproducible and objective, and are as accurate as manual analyses performed by human experts.
Ecological Impacts and Phenotypic Plasticity of a Global Invasive Cactus, Opuntia ficus-indica
(2023)
Biological invasions by non-native species pose one of the major threats to biodiversity, the way ecosystems function, and the well-being of humans. These invasions can occur through various means, including accidental or intentional introductions by humans, natural dispersal, and climate change. Non-native species can harm the native species and ecosystems, by homogenizing plant communities, competing for resources, changing how the ecosystem operates, and eventually causing native species to go extinct. Even though not all non-native species become invasive, changes in climate and ecosystems can cause the successful establishment and spread of non-native species. Despite the advancements in our understanding of biological invasions in recent years, research has been biased towards temperate regions, whereas arid and semi-arid regions that are highly impacted by climate change are underrepresented. Thus, particularly focusing on the impacts of biological invasions in subtropical arid and semi-arid regions, the goal of this PhD project was to explore the effects of an invasive cactus on the local native communities and investigate the mechanisms of its successful invasion. Certain species are found to take advantage of the ever-drying climates in the arid/ semi-arid regions of the world. Opuntia ficus-indica, native to Mexico, is an exceptionally successful drought-tolerant invasive cactus that successfully grows in these regions. O. ficus-indica, a most widespread invasive cactus, is considered an ecosystem engineer as it modifies the habitats of indigenous plant species and dependent animals. This project aimed to identify the ecological impacts of O. ficus-indica in the highlands of Eritrea, the competitive potential of O. ficus-indica and the plastic changes that enabled its spread and invasion (Chapters I-III). For this purpose, field observations and common garden experiments were carried out throughout the project.
We investigated the effects of Opuntia ficus-indica on the spatial diversity of native plant communities (Chapter I), its competitive ability against native species (Chapter II) and the phenotypic plasticity of O. ficus-indica (Chapter III). To investigate the main ecological effects of O. ficus-indica on the native community, field data was collected from the highlands of Eritrea and comparisons were made between O. ficus-indica invaded and noninvaded areas (Chapter I). The study aimed to understand the effects of O. ficus-indica by examining species composition, richness, and diversity across vegetation layers and revealed that O. ficus-indica homogenises the species composition of the native ecosystem. This provides evidence that the presence of O. ficus-indica reduces landscape-level heterogeneity or spatial diversity. However, O. ficus-indica did not influence the species richness and diversity of the local communities. The mechanisms of the successful homogenisation of the local communities by O. ficus-indica were attributed to the potential competitive abilities of O. ficus-indica against the native species, and the plastic and adaptive traits it developed in the non-native ranges. The first assumption was tested by setting up a common garden competition experiment between two native Eritrean species, Ricinus communis and Solanum marginatum (Chapter II). The experiment used two water availability treatments, wet and dry, and categorized plants into intraspecific (native or invasive only) and interspecific (native and invasive) competition. The study evaluated the impacts by comparing the growth of O. ficus-indica alone to the growth alongside native species which revealed the weak competitive potential of O. ficus-indica. However, O. ficus-indica was observed to outgrow the native species in several folds which can be attributed to its successful invasion. The second assumption of the successful spread of O. ficus-indica was attributed to the phenotypic plastic traits adapted by O. ficus-indica in the non-native ranges (Chapter III). The phenotypic plasticity of O. ficus-indica was assessed by exposing it to water stress across dry and wet environments. The species were cultivated from a diverse set of 12 populations, encompassing its native range in Mexico with three cultivars and nonnative ranges in Africa (Algeria, Eritrea, Ethiopia), the island of Madeira off the coast of Africa, and in Europe, Italy with two cultivars and in Portugal from three sites. In Mexico and Italy, we collected various cultivars to ensure a wide representation of genotypes. We found that the species originating from the native range of O. ficus-indica exhibited lower plasticity to conditions of elevated water availability. Furthermore, a trial gradient experiment on O. ficus-indica was conducted to determine the appropriate watering levels for the species and the experiment revealed not only the species' capacity to endure a lack of water for nine months but also its ability to withstand prolonged waterlogged conditions.
This thesis illustrates the fact that invasive species are a major threat to biodiversity and ecosystem functioning worldwide, especially in rarely studied regions with dry climates and limited resources. How can invasive plants spread and cause negative impacts on native ecosystems (Chapter I), despite their weak competitive abilities (Chapter II)? This thesis explored these questions by examining the case of O. ficus-indica, an invasive species in arid/ semi-arid climates (Chapter I). It showed that O. ficus-indica has a high growth potential that allows it to overcome resource limitations, that its growth is not affected by competition from native species (Chapter II), and that it exhibits adaptive plasticity that enhances its invasion success in different environments (Chapter III). This thesis revealed the complex mechanisms and consequences of biological invasions in dry climates and contributes to the understanding of invasive species. It also suggests that more research is needed in understudied regions to assess the impacts of O. ficus-indica or invasive species in general on native biodiversity and ecosystem services and to identify the factors that influence the competitive and adaptive potentials.
Aim
Climate change challenges temperate forest trees by increasingly irregular precipitation and rising temperatures. Due to long generation cycles, trees cannot quickly adapt genetically. Hence, the persistence of tree populations in the face of ongoing climate change depends largely on phenotypic variation, that is the capability of a genotype to express variable phenotypes under different environmental conditions, known as plasticity. We aimed to quantify phenotypic variation of central Europe's naturally dominant forest tree across various intraspecific scales (individuals, mother trees (families), populations) to evaluate its potential to respond to changing climatic conditions.
Location
Europe.
Time Period
2016–2019.
Major Taxa Studied
European beech (Fagus sylvatica L.).
Methods
We conducted a fully reciprocal transplantation experiment with more than 9000 beech seeds from seven populations across a Europe-wide gradient. We compared morphological (Specific Leaf Area), phenological (leaf unfolding) and fitness-related (growth, survival) traits across various biological scales: within single mother trees, within populations and across different populations under the contrasting climates of the translocation sites.
Results
The experiment revealed significant phenotypic variation within the offspring of each mother tree, regardless of geographic origin. Initially, seedling height growth varied among mother trees and populations, likely due to maternal effects. However, the growth performance successively aligned after the first year. In summary, we observed a consistent growth response in different beech populations to diverse environments after initial maternal effects.
Main Conclusions
The study strikingly demonstrates the importance of considering intraspecific variation. Given the surprisingly broad spectrum of phenotypes each mother tree holds within its juvenile offspring, we conclude that Fagus sylvatica might have the potential for medium-term population persistence in face of climate change, provided that this pattern persists into later life stages. Hence, we also suggest further investigating the inclusion of passive adaptation and natural dynamics in the adaptive management of forests.
In micro-densitometry of wood it is standard procedure to extract resin and other soluble compounds before X-ray analysis to eliminate the influence of these extractives on wood-density. Dendrochemical studies using X-ray fluorescence analysis on the other hand are commonly conducted without previous extraction. However, it is well known that translocation processes of elements during heartwood formation in trees or (temporal) differences in sap content of wood samples can influence dendrochemical element profiles. This might bias environmental signals stored in time series of element concentrations in wood proxies. We hypothesize that metals tightly bound to cell walls show a more robust proxy potential for environmental conditions than easily translocated ones. To eliminate the noise of these soluble substances in wood elemental time series, their extraction prior to analysis might be necessary. In our study we tested the effect of different solvents (water, alcohol, and acetone) and different extraction times on elemental time series of three tree species with differing wood structure (Pinus sylvestris; Quercus robur and Populus tremula). Micro-XRF analysis was conducted on nine replicates per species using an ITRAX-Multiscanner. A set of elements commonly detected in wood (S, Cl, K, Ca, Ti, Mn, Fe, and Ni) was analysed at high resolution before and after several extraction runs. Besides lowering their levels, extraction did not significantly change the temporal trends for most elements. However, for some elements, e.g., Potassium, Chlorine or Manganese, especially the water extraction led to significant decreases in concentrations and altered temporal trends. Apparently the dipole effect of water produced the strongest extraction power of all three solvents. In addition we observed a dependency of extraction intensity from wood density which differed between wood types. Our results help in interpreting and evaluating element profiles and mark a step forward in establishing dendrochemistry as a robust proxy in dendro-environmental research.
Lack of a shared vision has been identified as a major obstacle in transdisciplinary research involving both scientists and other stakeholders. Without a shared vision, the implementation of scientific findings is difficult. The diverse partners of collaborative research, however, imply a plurality in the valuation of nature and a need for deliberative mechanisms. If visioning processes are to do justice to local contexts, research must apply deliberative mechanisms to cover the plurality in the valuation of nature. This paper proposes a visioning approach for local communities, based on prior transdisciplinary research. This participatory workshop method invites stakeholders to approach nature conservation and livelihoods via a deliberation of desirable futures, barriers for achieving them and associated responsibilities for taking action. The paper explores this method via a case study of visioning workshops on sacred swamps in the Western Ghats (India), and their role for both freshwater swamp protection and livelihoods. The visioning exercise offered discussion opportunities facilitating conscientization, conciliation and collaboration in local bottom-up nature conservation. For conserving the tropical freshwater swamps, the results show the need for a more participatory forest governance, providing space for shared value creation. They also point to the need for further research on inter-faith nature conservation possibilities, along with innovations on value addition and value chain development for livelihood promotion and protection.
The cultivation of common reed (Phragmites australis) is one of the most promising practices of paludiculture on fen peatlands. This highly productive grass has a high adaptation capacity via high levels of genetic diversity and phenotypic plasticity. In this study, a reed experimental site established on a degraded fen in 1996/97 with a mixture of monoclonally (meristematically propagated plantlets) and polyclonally (pre-grown seedlings) planted plots was investigated by microsatellite genotyping. All nine genotypes of the monoclonal planted plots were recovered and could be genetically characterized; invasion by other genotypes was negligible. Similarly, the polyclonal plots sustained high clonal diversity with no prevalence of a single genotype. The growth characteristics of the five quantitatively investigated genotypes significantly differed from each other (α = 0.05): dry biomass per stem 5–18 g, panicles per m2 20–60, average stem diameter 3.5–6 mm, height 170–250 cm. Similarly, the persistence of genotypes at the planted plots and their invasiveness (ability to invade neighboured plots) varied. These results show that common reed stands are extremely persistent even if established with genotypes that are likely not to be locally adapted. Their genetic structure remained stable for at least 24 years regardless of the planting density (1, 4, and 10 plants per m2). Our results indicate that farmers may be able to maintain favourable genotypes for many years, thus the selection and breeding of common reed as a versatile crop for rewetted peatlands is a promising objective for paludiculture research.
Forests are ecologically important ecosystems, for example, they absorb CO2 from the
atmosphere, mitigate climate change, and constitute habitats for the majority of terrestrial
flora and fauna. Currently, due to increasing human pressure, forest ecosystems are
increasingly subjected to changing environmental conditions, which may alter forest growth
to varying degrees. However, how exactly different tree species will respond to climate
change remains uncertain and requires further comprehensive studies performed at different
spatial scales and using various tree-ring parameters.
This dissertation aims to advance the knowledge about tree-ring densitometry and
tree responses to climate variability and extremes at different spatial scales, using various
tree species. More specifically, the following aims are pursued: (i) to obtain and compare
wood density data using different techniques, and to assess variability among laboratories
(Chapter I). (ii) To investigate microsite effects on local and regional Scots pine (Pinus
sylvestris L.) responses to climate variability (Chapter II) and extremes (Chapter III),
using ring width (RW) and latewood blue intensity (LBI) parameters. (iii) To give a general
site- and regional-scales overview of Scots pine, pedunculate oak (Quercus robur L.), and
European beach (Fagus sylvatica L.) RW responses to climate variability (Chapter IV). (iv)
To discuss the challenges which may result from compiling tree ring records from different
(micro)sites into large-scale networks. The study area comprises nine coastal dune sites, each
represented by two contrasting microsites: dune ridge and bottom (Chapters II and III), and
310 different sites within the south Baltic Sea lowlands (Chapter IV).
The dissertation confirms that sample processing and wood density measuring are
very important steps, which, if not performed carefully, may result in biases in growth trends,
climate-growth responses, and climate reconstructions. The performed experiment proved
that the mean levels of different wood density-related parameters are never comparable due
to different measurement resolutions between various techniques and laboratories. Further,
the study revealed substantial biases using data measured from rings of varying width due
to resolution issues, where resolution itself and wood density are lowered for narrow rings
compared to wide rings (Chapter I).
The (micro)site-specific investigation showed that, depending on the species,
different climate variables (temperature, precipitation, or drought) constitute important
factors driving tree growth across investigated locations (Chapters II and IV). However,
there is evidence that the strength and/or direction of climate-growth responses differ(s)
between microsite types (Chapter II) and across sites (Chapter IV). Moreover, climategrowth
responses are non-stationary over time regardless of the tree species and tree-ring
parameter used in the analysis (Chapters II and IV). There are also differences in RW and
LBI responses to extreme events at dune ridge and bottom microsites (Chapter III).
The regional-scale investigations revealed that climate-growth responses (strength
and non-stationarity) are quite similar to those observed at the local scale. However,
compiling RW or LBI measurements into regional networks to study tree responses to
extreme events led to weakened signals (Chapter III).
The findings presented in Chapters II and IV suggest that the strength, direction,
and non-stationary responses are very likely caused by several climatic and non-climatic
factors. The mild climate in the south Baltic Sea region presumably does not constitute a
leading limiting growth factor, especially for Scots pine, whose distribution extends from
southern to northern Europe. Thus, the observed climate-growth responses are usually of
weak to moderate strength. In contrast, for other species reaching their distribution limit at
the Baltic coast, the climatic signal can be very strong. However, the observed findings also
result from the effects of microsite conditions, and potentially other factors (e.g.,
management, stand dynamic), which all together alter the physiological response of the tree
at a local scale. Although climate at the south Baltic Sea coast is mild, extreme climate events
may occur and affect tree growth. As demonstrated (Chapter III), extreme climate events
affected tree growth across dune sites, however, to varying degrees. The prominent
differences in tree responses to extreme climate events were significant at the local scale but
averaged out at the regional scale. This is very likely associated with observed microsite
differences, where each microsite experiences different drivers and dynamics of extreme
growth reductions.
This dissertation helped to demonstrate that integrating local tree-ring records into
regional networks involves a series of challenges, which arise at different stages of research.
In fact, not all possible challenges have been discussed in this dissertation. However, it can
be summarized that several steps performed first at the local scale are very important for the
quality and certainty of climate-growth responses, tracking tree recovery after extreme
events, and potential climate reconstructions at the larger scale. Among them, identification
of microsite conditions, sample preparation, and measurement, examination of growth
patterns and trends, and identification of a common limiting growth factor are very
important. Otherwise, the compilation of various tree-ring data into a single dataset could
lead to over- or underestimation of the results and biased interpretations.
Myxomycetes or Myxogastria (supergroup Amoebozoa) are one of several Protistean groups dispersing via airborne spores. The model organism for the group, so far exclusively studied in a laboratory environment, is Physarum polycephalum. Here, molecular evolution, distribution and the ecology of spores dispersal was investigated for the non-model species Physarum albescens. This nivicolous myxomycete fruits with snow melt in most mountain ranges of the northern hemisphere and disperses via spherical, dark-colored and melanin-rich spores. Fruit body development and subsequent spore dispersal occurs within a short time window of a few days. At this time, the fruiting plasmodium is fully exposed to the harsh environment if the protecting snow melts away. The spores, with a diameter of 10–13 µm of the typical size for myxomycetes, can potentially reach all suitable habitats worldwide, which led to the assumption that not only Ph. albescens but most myxomycete species should be ubiquitously distributed over the world.
In the first part of this study (article 1), the question was, if spore dispersal can realize a gene flow sufficient to meet the above-mentioned assumption. A total of 324 accessions of Ph. albescens, collected all over the northern hemisphere, was sequenced for 1-3 genetic markers (SSU, EF1A, COI), and 98 specimens were further analyzed using the genotyping by sequencing technique. As a result, at least 18 reproductively isolated units, which can be seen as cryptic biological species, emerged as phylogroups in a three-gene phylogeny, but as well in a SNP-based phylogeny and were confirmed by a recombination analysis between the three markers. However, this evolutive radiation is not simply caused by geographic fragmentation due to low dispersal capability: within a certain region, multiple phylogroups coexisted next to each other, although some appeared to be regional endemics. Most likely, mutations in mating-type genes, as shown to exist for the cultivable Ph. polycephalum, are the main drivers of speciation. This challenges the hypothesis of ubiquitous distribution of Ph. albescens and corroborates the results of the few available studies for other myxomycete species. In addition, groups of clonal specimens, mostly but not always restricted to a certain slope or valley indicated that sexual and asexual reproduction coexists in the natural populations of Ph. albescens.
In the second part (articles 2), the fundamental niche for Ph. albescens was described using all available records for the species. The resulting set of 537 unique occurrence points was subjected to a correlative spatial approach using the software MaxEnt. In dependence on the predictor variables three species distribution models emerged which differed only in details. The first consisted of only 19 bioclimatic variables and an elevation map from the WorldClim dataset. The second was corrected for pseudo-absences resulting from missing survey activities, and the third was expanded with an additional categorical environment variable on snow cover. High mean AUC (area under the curve) values above 0.97 could be reached with all three models. Variables for snow cover, precipitation of the coldest quarter (of the year), and elevation correlated highly to predict the distribution of Ph. albescens. Only in mid-northern latitudes, elevation alone was a good predictor, but it would cause false-positive predictions in arid mountain ranges and failed to explain occurrence in lowland sites at higher latitudes. Mountains in humid climates showed the highest incidences, confirming recent studies that long-lasting snow covers combined with mild summers are crucial for the ecological guild of nivicolous myxomycetes, with Ph. albescens as a typical species.
Spore size is crucial for dispersal ability and should thus be a character under strong selection. In addition, spores carrying two nuclei with opposite mating types should have a colonization advantage. This was the hypothesis for the last part of this study (articles 3 and 4), which investigated this trait in a quantitative manner. This required a method to analyze thousands of spores automatically (article 3) and with high precision for size and the number of nuclei enclosed. Human errors should be excluded, to reveal even subtle differences in the resulting spore size distributions. Two challenges had to be met for this approach. First, a preparation technique was developed to reduce false segmentations due to overlaying spores by aligning spores on one common plane with a high-frequency vibration device. Second, the segmentation process was automated to allow separating spores that are densely packed in the respective images. A machine learning algorithm was set up and trained to reliable identify and measure dark-colored spores. The technique produced consistent results with high accuracy, and the large number of spores allowed to compile spore size distributions, to check for the constancy of this character, which is impossible with manual measurements limited to low numbers.
The resulting spore size distributions, obtained from over 80 specimens (article 4), were mostly narrow, which is in accordance with our hypothesis. Spore size was as well fairly constant within fructifications from one colony. However, mean spore size within different accessions of Ph. albescens showed large variation (ca. 10%, a range often indicated to key out different morphospecies of myxomycetes), and this was explained only by a minor part with differences between biospecies. Not much smaller (8%) was the variation within a group of clonal specimens collected within 25 m distance. This points to a strong influence of environmental factors even at a micro spatial scale, perhaps caused by microclimatic differences and high phenotypic plasticity for spore size. The influence of large-scale covariates like altitude or latitude was negligible. However, spore size correlated with the variance in this trait, indicating that oversized spores may be caused by detrimental environmental conditions. Two aberrations in spore development were found: First, a few specimens showed a multimodal distribution for spore size with two or even three discernible spore populations. The estimated volumes of those populations correspond to a multiple of the first and most abundant conspicuous spore size population. Second, not all spores were uninucleate as to be expected for meiotic products. This was revealed by fluorescence signals from staining the same spores with DAPI, with a second machine learning algorithm trained to identify the nuclei in a spore. A few specimens showed a significant proportion of binucleated spores in the size range of normal-sized ones, and these specimens were not the ones with multimodal spore size distributions. This indicates that the negative impacts (inbreeding) of multinucleate spores should outweigh a possible colonization advantage and is in accordance with the high genetic diversity found in the worldwide population of Ph. albescens, indicating predominantly sexual reproduction in wild populations of myxomycetes.