@phdthesis{Kiemel2023, author = {Kiemel, Katrin}, title = {Zooplankton adaptations and community dynamics in space and time}, school = {Universit{\"a}t Potsdam}, year = {2023}, abstract = {In times of ongoing biodiversity loss, understanding how communities are structured and what mechanisms and local adaptations underlie the patterns we observe in nature is crucial for predicting how future ecological and anthropogenic changes might affect local and regional biodiversity. Aquatic zooplankton are a group of primary consumers that represent a critical link in the food chain, providing nutrients for the entire food web. Thus, understanding the adaptability and structure of zooplankton communities is essential. In this work, the genetic basis for the different temperature adaptations of two seasonally shifted (i.e., temperature-dependent) occurring freshwater rotifers of a formerly cryptic species complex (Brachionus calyciflorus) was investigated to understand the overall genetic diversity and evolutionary scenario for putative adaptations to different temperature regimes. Furthermore, this work aimed to clarify to what extent the different temperature adaptations may represent a niche partitioning process thus enabling co-existence. The findings were then embedded in a metacommunity context to understand how zooplankton communities assemble in a kettle hole metacommunity located in the northeastern German "Uckermark" and which underlying processes contribute to the biodiversity patterns we observe. Using a combined approach of newly generated mitochondrial resources (genomes/cds) and the analysis of a candidate gene (Heat Shock Protein 40kDa) for temperature adaptation, I showed that the global representatives of B. calyciflorus s.s.. are genetically more similar than B. fernandoi (average pairwise nucleotide diversity: 0.079 intraspecific vs. 0.257 interspecific) indicating that both species carry different standing genetic variation. In addition to differential expression in the thermotolerant B. calyciflorus s.s. and thermosensitive B. fernandoi, the HSP 40kDa also showed structural variation with eleven fixed and six positively selected sites, some of which are located in functional areas of the protein. The estimated divergence time of ~ 25-29 Myr combined with the fixed sites and a prevalence of ancestral amino acids in B. calyciflorus s.s. indicate that B. calyciflorus s.s. remained in the ancestral niche, while B. fernandoi partitioned into a new niche. The comparison of mitochondrial and nuclear markers (HPS 40kDa, ITS1, COI) revealed a hybridisation event between the two species. However, as hybridisation between the two species is rare, it can be concluded that the temporally isolated niches (i.e., seasonal-shifted occurrence) they inhabit based on their different temperature preferences most likely represent a pre-zygotic isolation mechanism that allows sympatric occurrence while maintaining species boundaries. To determine the processes underlying zooplankton community assembly, a zooplankton metacommunity comprising 24 kettle holes was sampled over a two-year period. Active (i.e., water samples) and dormant communities (i.e., dormant eggs hatched from sediment) were identified using a two-fragment DNA metabarcoding approach (COI and 18S). Species richness and diversity as well as community composition were analysed considering spatial, temporal and environmental parameters. The analysis revealed that environmental filtering based on parameters such as pH, size and location of the habitat patch (i.e., kettle hole) and surrounding field crops largely determined zooplankton community composition (explained variance: Bray-Curtis dissimilarities: 10.5\%; Jaccard dissimilarities: 12.9\%), indicating that adaptation to a particular habitat is a key feature of zooplankton species in this system. While the spatial configuration of the kettle holes played a minor role (explained variance: Bray-Curtis dissimilarities: 2.8\% and Jaccard dissimilarities: 5.5\%), the individual kettle hole sites had a significant influence on the community composition. This suggests monopolisation/priority effects (i.e., dormant communities) of certain species in individual kettle holes. As environmental filtering is the dominating process structuring zooplankton communities, this system could be significantly influenced by future land-use change, pollution and climate change.}, language = {en} } @article{CoramanDietzHempeletal.2019, author = {Coraman, Emrah and Dietz, Christian and Hempel, Elisabeth and Ghazaryan, Astghik and Levin, Eran and Presetnik, Primoz and Zagmajster, Maja and Mayer, Frieder}, title = {Reticulate evolutionary history of a Western Palaearctic Bat Complex explained by multiple mtDNA introgressions in secondary contacts}, series = {Journal of biogeography}, volume = {46}, journal = {Journal of biogeography}, number = {2}, publisher = {Wiley}, address = {Hoboken}, issn = {0305-0270}, doi = {10.1111/jbi.13509}, pages = {343 -- 354}, year = {2019}, abstract = {Aim There is an increasing evidence showing that species within various taxonomic groups have reticulate evolutionary histories with several cases of introgression events. Investigating the phylogeography of species complexes can provide insight into these introgressions, and when and where these hybridizations occurred. In this study, we investigate the biogeography of a widely distributed Western Palaearctic bat species complex, namely Myotis nattereri sensu lato. This complex exhibits high genetic diversity and in its western distribution range is composed of deeply diverged genetical lineages. However, little is known about the genetic structure of the eastern populations. We also infer the conservation and taxonomical implications of the identified genetic divergences. Taxon Myotis nattereri sensu lato including M. schaubi. Location Western Palaearctic. Methods We analysed 161 specimens collected from 67 locations and sequenced one mitochondrial and four nuclear DNA markers, and combined these with the available GenBank sequences. We used haplotype networks, PCA, t-SNE and Bayesian clustering algorithms to investigate the population structure and Bayesian trees to infer the phylogenetic relationship of the lineages. Results We identified deeply divergent genetical lineages. In some cases, nuclear and mitochondrial markers were discordant, which we interpret are caused by hybridization between lineages. We identified three such introgression events. These introgressions occurred when spatially separated lineages came into contact after range expansions. Based on the genetic distinction of the identified lineages, we suggest a revision in the taxonomy of this species group with two possible new species: M. hoveli and M. tschuliensis. Main conclusions Our findings suggest that the M. nattereri complex has a reticulate evolutionary history with multiple cases of hybridizations between some of the identified lineages.}, language = {en} } @article{ZancolliBakerBarlowetal.2016, author = {Zancolli, Giulia and Baker, Timothy G. and Barlow, Axel and Bradley, Rebecca K. and Calvete, Juan J. and Carter, Kimberley C. and de Jager, Kaylah and Owens, John Benjamin and Price, Jenny Forrester and Sanz, Libia and Scholes-Higham, Amy and Shier, Liam and Wood, Liam and W{\"u}ster, Catharine E. and W{\"u}ster, Wolfgang}, title = {Is Hybridization a Source of Adaptive Venom Variation in Rattlesnakes? A Test, Using a Crotalus scutulatus x viridis Hybrid Zone in Southwestern New Mexico}, series = {Toxins}, volume = {8}, journal = {Toxins}, publisher = {MDPI}, address = {Basel}, issn = {2072-6651}, doi = {10.3390/toxins8060188}, pages = {16}, year = {2016}, abstract = {Venomous snakes often display extensive variation in venom composition both between and within species. However, the mechanisms underlying the distribution of different toxins and venom types among populations and taxa remain insufficiently known. Rattlesnakes (Crotalus, Sistrurus) display extreme inter-and intraspecific variation in venom composition, centered particularly on the presence or absence of presynaptically neurotoxic phospholipases A2 such as Mojave toxin (MTX). Interspecific hybridization has been invoked as a mechanism to explain the distribution of these toxins across rattlesnakes, with the implicit assumption that they are adaptively advantageous. Here, we test the potential of adaptive hybridization as a mechanism for venom evolution by assessing the distribution of genes encoding the acidic and basic subunits of Mojave toxin across a hybrid zone between MTX-positive Crotalus scutulatus and MTX-negative C. viridis in southwestern New Mexico, USA. Analyses of morphology, mitochondrial and single copy-nuclear genes document extensive admixture within a narrow hybrid zone. The genes encoding the two MTX subunits are strictly linked, and found in most hybrids and backcrossed individuals, but not in C. viridis away from the hybrid zone. Presence of the genes is invariably associated with presence of the corresponding toxin in the venom. We conclude that introgression of highly lethal neurotoxins through hybridization is not necessarily favored by natural selection in rattlesnakes, and that even extensive hybridization may not lead to introgression of these genes into another species.}, language = {en} } @article{MartinsSchmidtLenzetal.2018, author = {Martins, Renata F. and Schmidt, Anke and Lenz, Dorina and Wilting, Andreas and Fickel, J{\"o}rns}, title = {Historical biogeography of Rusa unicolor and R-timorensis}, series = {Ecology and evolution}, volume = {8}, journal = {Ecology and evolution}, number = {3}, publisher = {Wiley}, address = {Hoboken}, issn = {2045-7758}, doi = {10.1002/ece3.3754}, pages = {1465 -- 1479}, year = {2018}, abstract = {In this study we compared the phylogeographic patterns of two Rusa species, Rusa unicolor and Rusa timorensis, in order to understand what drove and maintained differentiation between these two geographically and genetically close species and investigated the route of introduction of individuals to the islands outside of the Sunda Shelf. We analyzed full mitogenomes from 56 archival samples from the distribution areas of the two species and 18 microsatellite loci in a subset of 16 individuals to generate the phylogeographic patterns of both species. Bayesian inference with fossil calibration was used to estimate the age of each species and major divergence events. Our results indicated that the split between the two species took place during the Pleistocene, similar to 1.8Mya, possibly driven by adaptations of R. timorensis to the drier climate found on Java compared to the other islands of Sundaland. Although both markers identified two well-differentiated clades, there was a largely discrepant pattern between mitochondrial and nuclear markers. While nDNA separated the individuals into the two species, largely in agreement with their museum label, mtDNA revealed that all R. timorensis sampled to the east of the Sunda shelf carried haplotypes from R. unicolor and one Rusa unicolor from South Sumatra carried a R. timorensis haplotype. Our results show that hybridization occurred between these two sister species in Sundaland during the Late Pleistocene and resulted in human-mediated introduction of hybrid descendants in all islands outside Sundaland.}, language = {en} } @article{ChoiSchmidtTinnefeldetal.2019, author = {Choi, Youngeun and Schmidt, Carsten and Tinnefeld, Philip and Bald, Ilko and R{\"o}diger, Stefan}, title = {A new reporter design based on DNA origami nanostructures for quantification of short oligonucleotides using microbeads}, series = {Scientific Reports}, journal = {Scientific Reports}, number = {9}, publisher = {Macmillan Publishers Limited}, address = {London}, issn = {2045-2322}, doi = {10.1038/s41598-019-41136-x}, pages = {8}, year = {2019}, abstract = {The DNA origami technique has great potential for the development of brighter and more sensitive reporters for fluorescence based detection schemes such as a microbead-based assay in diagnostic applications. The nanostructures can be programmed to include multiple dye molecules to enhance the measured signal as well as multiple probe strands to increase the binding strength of the target oligonucleotide to these nanostructures. Here we present a proof-of-concept study to quantify short oligonucleotides by developing a novel DNA origami based reporter system, combined with planar microbead assays. Analysis of the assays using the VideoScan digital imaging platform showed DNA origami to be a more suitable reporter candidate for quantification of the target oligonucleotides at lower concentrations than a conventional reporter that consists of one dye molecule attached to a single stranded DNA. Efforts have been made to conduct multiplexed analysis of different targets as well as to enhance fluorescence signals obtained from the reporters. We therefore believe that the quantification of short oligonucleotides that exist in low copy numbers is achieved in a better way with the DNA origami nanostructures as reporters.}, language = {en} }