@phdthesis{Hempel2024, author = {Hempel, Elisabeth}, title = {Resolving the evolutionary history of two hippotragin antelopes using archival and ancient DNA}, doi = {10.25932/publishup-64771}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-647718}, school = {Universit{\"a}t Potsdam}, pages = {xii, 224}, year = {2024}, abstract = {African antelopes are iconic but surprisingly understudied in terms of their genetics, especially when it comes to their evolutionary history and genetic diversity. The age of genomics provides an opportunity to investigate evolution using whole nuclear genomes. Decreasing sequencing costs enable the recovery of multiple loci per genome, giving more power to single specimen analyses and providing higher resolution insights into species and populations that can help guide conservation efforts. This age of genomics has only recently begun for African antelopes. Many African bovids have a declining population trend and hence, are often endangered. Consequently, contemporary samples from the wild are often hard to collect. In these cases, ex situ samples from contemporary captive populations or in the form of archival or ancient DNA (aDNA) from historical museum or archaeological/paleontological specimens present a great research opportunity with the latter two even offering a window to information about the past. However, the recovery of aDNA is still considered challenging from regions with prevailing climatic conditions that are deemed adverse for DNA preservation like the African continent. This raises the question if DNA recovery from fossils as old as the early Holocene from these regions is possible. This thesis focuses on investigating the evolutionary history and genetic diversity of two species: the addax (Addax nasomaculatus) and the blue antelope (Hippotragus leucophaeus). The addax is critically endangered and might even already be extinct in the wild, while the blue antelope became extinct ~1800 AD, becoming the first extinct large African mammal species in historical times. Together, the addax and the blue antelope can inform us about current and past extinction events and the knowledge gained can help guide conservation efforts of threatened species. The three studies used ex situ samples and present the first nuclear whole genome data for both species. The addax study used historical museum specimens and a contemporary sample from a captive population. The two studies on the blue antelope used mainly historical museum specimens but also fossils, and resulted in the recovery of the oldest paleogenome from Africa at that time. The aim of the first study was to assess the genetic diversity and the evolutionary history of the addax. It found that the historical wild addax population showed only limited phylogeographic structuring, indicating that the addax was a highly mobile and panmictic population and suggesting that the current European captive population might be missing the majority of the historical mitochondrial diversity. It also found the nuclear and mitochondrial diversity in the addax to be rather low compared to other wild ungulate species. Suggestions on how to best save the remaining genetic diversity are presented. The European zoo population was shown to exhibit no or only minor levels of inbreeding, indicating good prospects for the restoration of the species in the wild. The trajectory of the addax's effective population size indicated a major bottleneck in the late Pleistocene and a low effective population size well before recent human impact led to the species being critically endangered today. The second study set out to investigate the identities of historical blue antelope specimens using aDNA techniques. Results showed that six out of ten investigated specimens were misidentified, demonstrating the blue antelope to be one of the scarcest mammal species in historical natural history collections, with almost no bone reference material. The preliminary analysis of the mitochondrial genomes suggested a low diversity and hence low population size at the time of the European colonization of southern Africa. Study three presents the results of the analyses of two blue antelope nuclear genomes, one ~200 years old and another dating to the early Holocene, 9,800-9,300 cal years BP. A fossil-calibrated phylogeny dated the divergence time of the three historically extant Hippotragus species to ~2.86 Ma and demonstrated the blue and the sable antelope (H. niger) to be sister species. In addition, ancient gene flow from the roan (H. equinus) into the blue antelope was detected. A comparison with the roan and the sable antelope indicated that the blue antelope had a much lower nuclear diversity, suggesting a low population size since at least the early Holocene. This concurs with findings from the fossil record that show a considerable decline in abundance after the Pleistocene-Holocene transition. Moreover, it suggests that the blue antelope persisted throughout the Holocene regardless of a low population size, indicating that human impact in the colonial era was a major factor in the blue antelope's extinction. This thesis uses aDNA analyses to provide deeper insights into the evolutionary history and genetic diversity of the addax and the blue antelope. Human impact likely was the main driver of extinction in the blue antelope, and is likely the main factor threatening the addax today. This thesis demonstrates the value of ex situ samples for science and conservation, and suggests to include genetic data for conservation assessments of species. It further demonstrates the beneficial use of aDNA for the taxonomic identification of historically important specimens in natural history collections. Finally, the successful retrieval of a paleogenome from the early Holocene of Africa using shotgun sequencing shows that DNA retrieval from samples of that age is possible from regions generally deemed unfavorable for DNA preservation, opening up new research opportunities. All three studies enhance our knowledge of African antelopes, contributing to the general understanding of African large mammal evolution and to the conservation of these and similarly threatened species.}, language = {en} } @article{SandhageHofmannLinstaedterKindermannetal.2021, author = {Sandhage-Hofmann, Alexandra and Linst{\"a}dter, Anja and Kindermann, Liana and Angombe, Simon and Amelung, Wulf}, title = {Conservation with elevated elephant densities sequesters carbon in soils despite losses of woody biomass}, series = {Global change biology}, volume = {27}, journal = {Global change biology}, number = {19}, publisher = {Blackwell Science}, address = {Oxford [u.a.]}, issn = {1354-1013}, doi = {10.1111/gcb.15779}, pages = {4601 -- 4614}, year = {2021}, abstract = {Nature conservation and restoration in terrestrial ecosystems is often focused on increasing the numbers of megafauna, expecting them to have positive impacts on ecological self-regulation processes and biodiversity. In sub-Saharan Africa, conservation efforts also aspire to protect and enhance biodiversity with particular focus on elephants. However, elephant browsing carries the risk of woody biomass losses. In this context, little is known about how increasing elephant numbers affects carbon stocks in soils, including the subsoils. We hypothesized that (1) increasing numbers of elephants reduce tree biomass, and thus the amount of C stored therein, resulting (2) in a loss of soil organic carbon (SOC). If true, a negative carbon footprint could limit the sustainability of elephant conservation from a global carbon perspective. To test these hypotheses, we selected plots of low, medium, and high elephant densities in two national parks and adjacent conservancies in the Namibian component of the Kavango Zambezi Transfrontier Area (KAZA), and quantified carbon storage in both woody vegetation and soils (1 m). Analyses were supplemented by the assessment of soil carbon isotopic composition. We found that increasing elephant densities resulted in a loss of tree carbon storage by 6.4 t ha(-1). However, and in contrast to our second hypothesis, SOC stocks increased by 4.7 t ha(-1) with increasing elephant densities. These higher SOC stocks were mainly found in the topsoil (0-30 cm) and were largely due to the formation of SOC from woody biomass. A second carbon input source into the soils was megaherbivore dung, which contributed with 0.02-0.323 t C ha(-1) year(-1) to ecosystem carbon storage in the low and high elephant density plots, respectively. Consequently, increasing elephant density does not necessarily lead to a negative C footprint, as soil carbon sequestration and transient C storage in dung almost compensate for losses in tree biomass.}, language = {en} } @article{MalchowBocediPalmeretal.2021, author = {Malchow, Anne-Kathleen and Bocedi, Greta and Palmer, Stephen C. F. and Travis, Justin M. J. and Zurell, Damaris}, title = {RangeShiftR}, series = {Ecography : pattern and diversity in ecology / Nordic Ecologic Society Oikos}, volume = {44}, journal = {Ecography : pattern and diversity in ecology / Nordic Ecologic Society Oikos}, number = {10}, publisher = {Wiley-Blackwell}, address = {Oxford [u.a.]}, issn = {1600-0587}, doi = {10.1111/ecog.05689}, pages = {1443 -- 1452}, year = {2021}, abstract = {Reliably modelling the demographic and distributional responses of a species to environmental changes can be crucial for successful conservation and management planning. Process-based models have the potential to achieve this goal, but so far they remain underused for predictions of species' distributions. Individual-based models offer the additional capability to model inter-individual variation and evolutionary dynamics and thus capture adaptive responses to environmental change. We present RangeShiftR, an R implementation of a flexible individual-based modelling platform which simulates eco-evolutionary dynamics in a spatially explicit way. The package provides flexible and fast simulations by making the software RangeShifter available for the widely used statistical programming platform R. The package features additional auxiliary functions to support model specification and analysis of results. We provide an outline of the package's functionality, describe the underlying model structure with its main components and present a short example. RangeShiftR offers substantial model complexity, especially for the demographic and dispersal processes. It comes with elaborate tutorials and comprehensive documentation to facilitate learning the software and provide help at all levels. As the core code is implemented in C++, the computations are fast. The complete source code is published under a public licence, making adaptations and contributions feasible. The RangeShiftR package facilitates the application of individual-based and mechanistic modelling to eco-evolutionary questions by operating a flexible and powerful simulation model from R. It allows effortless interoperation with existing packages to create streamlined workflows that can include data preparation, integrated model specification and results analysis. Moreover, the implementation in R strengthens the potential for coupling RangeShiftR with other models.}, language = {en} } @article{TaguchiGotoMatsuokaetal.2023, author = {Taguchi, Mioko and Goto, Mutsuo and Matsuoka, Koji and Tiedemann, Ralph and Pastene, Luis A.}, title = {Population genetic structure of Bryde's whales (Balaenoptera brydei) on the central and western North Pacific feeding grounds}, series = {Canadian Journal of Fisheries and Aquatic Sciences}, volume = {80}, journal = {Canadian Journal of Fisheries and Aquatic Sciences}, number = {1}, publisher = {Canadian science publishing}, address = {Ottawa}, issn = {0706-652X}, doi = {10.1139/cjfas-2022-0005}, pages = {142 -- 155}, year = {2023}, abstract = {The genetic structure of Bryde's whale (Balaenoptera brydei) on the central and western North Pacific feeding grounds was investigated using a total of 1195 mitochondrial control region sequences and 1182 microsatellite genotypes at 17 loci in specimens collected from three longitudinal areas, 1W (135 degrees E-165 degrees E), 1E (165 degrees E-180 degrees), and 2 (180 degrees-155 degrees W). Genetic diversities were similar among areas and a haplotype network did not show any geographic structure, while an analysis of molecular variance found evidence of genetic structure in this species. Pairwise FST and G'ST estimates and heterogeneity tests attributed this structure to weak but significant differentiation between areas 1W/1E and 2. A Mantel test and a high-resolution analysis of genetic diversity statistics showed a weak spatial cline of genetic differentiation. These findings could be reconciled by two possible stock structure scenarios: (1) a single population with kin-association affecting feeding ground preference and (2) two populations with feeding ground preference for either area 1W or area 2. An estimated dispersal rate between areas 1W and 2 indicates that both scenarios should be considered as a precautionary principle in stock assessments.}, language = {en} } @article{PaetzigKalettkaOnandiaetal.2020, author = {P{\"a}tzig, Marlene and Kalettka, Thomas and Onandia, Gabriela and Balla, Dagmar and Lischeid, Gunnar}, title = {How much information do we gain from multiple-year sampling in natural pond research?}, series = {Limnologica : ecology and management of inland waters}, volume = {80}, journal = {Limnologica : ecology and management of inland waters}, publisher = {Elsevier}, address = {Amsterdam [u.a.]}, issn = {0075-9511}, doi = {10.1016/j.limno.2019.125728}, pages = {10}, year = {2020}, abstract = {Natural ponds are perceived as spatially and temporally highly variable ecosystems. This perception is in contrast to the often-applied sampling design with high spatial but low temporal replication. Based on a data set covering a period of six years and 20 permanently to periodically inundated ponds, we investigated whether this widely applied sampling design is sufficient to identify differences between single ponds or single years with regard to water quality and macrophyte community composition as measures of ecosystem integrity. In our study, the factor "pond", which describes differences between individual ponds, explained 56 \% and 63 \%, respectively, of the variance in water quality and macrophyte composition. In contrast, the factor "year" that refers to changes between individual years, contributed less to understand the observed variability in water quality and macrophyte composition (10 \% and 7 \% respectively, of the variance explained). The low explanation of variance for "year" and the low year-to-year correlation for the single water quality parameter or macrophyte coverage values, respectively, indicated high but non-consistent temporal variability affecting individual pond patterns. In general, the results largely supported the ability of the widely applied sampling strategy with about one sampling date per year to capture differences in water quality and macrophyte community composition between ponds. Hence, future research can be rest upon sampling designs that give more weight to the number of ponds than the number of years in dependence on the research question and the available resources. Nonetheless, pond research would miss a substantial amount of information (7 to 10 \% of the variance explained), when the sampling would generally be restricted to one year. Moreover, we expect that the importance of multiple-year sampling will likely increase in periods and regions of higher hydrological variability compared to the average hydrological conditions encountered in the studied period.}, language = {en} } @misc{vanReesWaylenSchmidtKloiberetal.2020, author = {van Rees, Charles B. and Waylen, Kerry A. and Schmidt-Kloiber, Astrid and Thackeray, Stephen J. and Kalinkat, Gregor and Martens, Koen and Domisch, Sami and Lillebo, Ana and Hermoso, Virgilio and Grossart, Hans-Peter and Schinegger, Rafaela and Decleer, Kris and Adriaens, Tim and Denys, Luc and Jaric, Ivan and Janse, Jan H. and Monaghan, Michael T. and De Wever, Aaike and Geijzendorffer, Ilse and Adamescu, Mihai C. and J{\"a}hnig, Sonja C.}, title = {Safeguarding freshwater life beyond 2020}, series = {Conservation letters}, volume = {14}, journal = {Conservation letters}, number = {1}, publisher = {Wiley}, address = {Hoboken}, issn = {1755-263X}, doi = {10.1111/conl.12771}, pages = {17}, year = {2020}, abstract = {Plans are currently being drafted for the next decade of action on biodiversity-both the post-2020 Global Biodiversity Framework of the Convention on Biological Diversity (CBD) and Biodiversity Strategy of the European Union (EU). Freshwater biodiversity is disproportionately threatened and underprioritized relative to the marine and terrestrial biota, despite supporting a richness of species and ecosystems with their own intrinsic value and providing multiple essential ecosystem services. Future policies and strategies must have a greater focus on the unique ecology of freshwater life and its multiple threats, and now is a critical time to reflect on how this may be achieved. We identify priority topics including environmental flows, water quality, invasive species, integrated water resources management, strategic conservation planning, and emerging technologies for freshwater ecosystem monitoring. We synthesize these topics with decades of first-hand experience and recent literature into 14 special recommendations for global freshwater biodiversity conservation based on the successes and setbacks of European policy, management, and research. Applying and following these recommendations will inform and enhance the ability of global and European post-2020 biodiversity agreements to halt and reverse the rapid global decline of freshwater biodiversity.}, language = {en} } @article{MalchowBocediPalmeretal.2021, author = {Malchow, Anne-Kathleen and Bocedi, Greta and Palmer, Stephen C. F. and Travis, Justin M. J. and Zurell, Damaris}, title = {RangeShiftR: an R package for individual-based simulation of spatial eco-evolutionary dynamics and speciesu0027 responses to environmental changes}, series = {Ecography}, volume = {44}, journal = {Ecography}, number = {10}, publisher = {John Wiley \& Sons, Inc.}, address = {New Jersey}, issn = {1600-0587}, doi = {10.1111/ecog.05689}, pages = {10}, year = {2021}, abstract = {Reliably modelling the demographic and distributional responses of a species to environmental changes can be crucial for successful conservation and management planning. Process-based models have the potential to achieve this goal, but so far they remain underused for predictions of species' distributions. Individual-based models offer the additional capability to model inter-individual variation and evolutionary dynamics and thus capture adaptive responses to environmental change. We present RangeShiftR, an R implementation of a flexible individual-based modelling platform which simulates eco-evolutionary dynamics in a spatially explicit way. The package provides flexible and fast simulations by making the software RangeShifter available for the widely used statistical programming platform R. The package features additional auxiliary functions to support model specification and analysis of results. We provide an outline of the package's functionality, describe the underlying model structure with its main components and present a short example. RangeShiftR offers substantial model complexity, especially for the demographic and dispersal processes. It comes with elaborate tutorials and comprehensive documentation to facilitate learning the software and provide help at all levels. As the core code is implemented in C++, the computations are fast. The complete source code is published under a public licence, making adaptations and contributions feasible. The RangeShiftR package facilitates the application of individual-based and mechanistic modelling to eco-evolutionary questions by operating a flexible and powerful simulation model from R. It allows effortless interoperation with existing packages to create streamlined workflows that can include data preparation, integrated model specification and results analysis. Moreover, the implementation in R strengthens the potential for coupling RangeShiftR with other models.}, language = {en} } @misc{MalchowBocediPalmeretal.2021, author = {Malchow, Anne-Kathleen and Bocedi, Greta and Palmer, Stephen C. F. and Travis, Justin M. J. and Zurell, Damaris}, title = {RangeShiftR: an R package for individual-based simulation of spatial eco-evolutionary dynamics and speciesu0027 responses to environmental changes}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {10}, issn = {1866-8372}, doi = {10.25932/publishup-52397}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-523979}, pages = {12}, year = {2021}, abstract = {Reliably modelling the demographic and distributional responses of a species to environmental changes can be crucial for successful conservation and management planning. Process-based models have the potential to achieve this goal, but so far they remain underused for predictions of species' distributions. Individual-based models offer the additional capability to model inter-individual variation and evolutionary dynamics and thus capture adaptive responses to environmental change. We present RangeShiftR, an R implementation of a flexible individual-based modelling platform which simulates eco-evolutionary dynamics in a spatially explicit way. The package provides flexible and fast simulations by making the software RangeShifter available for the widely used statistical programming platform R. The package features additional auxiliary functions to support model specification and analysis of results. We provide an outline of the package's functionality, describe the underlying model structure with its main components and present a short example. RangeShiftR offers substantial model complexity, especially for the demographic and dispersal processes. It comes with elaborate tutorials and comprehensive documentation to facilitate learning the software and provide help at all levels. As the core code is implemented in C++, the computations are fast. The complete source code is published under a public licence, making adaptations and contributions feasible. The RangeShiftR package facilitates the application of individual-based and mechanistic modelling to eco-evolutionary questions by operating a flexible and powerful simulation model from R. It allows effortless interoperation with existing packages to create streamlined workflows that can include data preparation, integrated model specification and results analysis. Moreover, the implementation in R strengthens the potential for coupling RangeShiftR with other models.}, language = {en} } @phdthesis{Autenrieth2020, author = {Autenrieth, Marijke}, title = {Population genomics of two odontocetes in the North Atlantic and adjacent waters}, school = {Universit{\"a}t Potsdam}, pages = {IX, 110}, year = {2020}, abstract = {Due to continuously intensifying human usage of the marine environment worldwide ranging cetaceans face an increasing number of threats. Besides whaling, overfishing and by-catch, new technical developments increase the water and noise pollution, which can negatively affect marine species. Cetaceans are especially prone to these influences, being at the top of the food chain and therefore accumulating toxins and contaminants. Furthermore, they are extremely noise sensitive due to their highly developed hearing sense and echolocation ability. As a result, several cetacean species were brought to extinction during the last century or are now classified as critically endangered. This work focuses on two odontocetes. It applies and compares different molecular methods for inference of population status and adaptation, with implications for conservation. The worldwide distributed sperm whale (Physeter macrocephalus) shows a matrilineal population structure with predominant male dispersal. A recently stranded group of male sperm whales provided a unique opportunity to investigate male grouping for the first time. Based on the mitochondrial control region, I was able to infer that male bachelor groups comprise multiple matrilines, hence derive from different social groups, and that they represent the genetic variability of the entire North Atlantic. The harbor porpoise (Phocoena phocoena) occurs only in the northern hemisphere. By being small and occurring mostly in coastal habitats it is especially prone to human disturbance. Since some subspecies and subpopulations are critically endangered, it is important to generate and provide genetic markers with high resolution to facilitate population assignment and subsequent protection measurements. Here, I provide the first harbour porpoise whole genome, in high quality and including a draft annotation. Using it for mapping ddRAD seq data, I identify genome wide SNPs and, together with a fragment of the mitochondrial control region, inferred the population structure of its North Atlantic distribution range. The Belt Sea harbors a distinct subpopulation oppose to the North Atlantic, with a transition zone in the Kattegat. Within the North Atlantic I could detect subtle genetic differentiation between western (Canada-Iceland) and eastern (North Sea) regions, with support for a German North Sea breading ground around the Isle of Sylt. Further, I was able to detect six outlier loci which show isolation by distance across the investigated sampling areas. In employing different markers, I could show that single maker systems as well as genome wide data can unravel new information about population affinities of odontocetes. Genome wide data can facilitate investigation of adaptations and evolutionary history of the species and its populations. Moreover, they facilitate population genetic investigations, providing a high resolution, and hence allowing for detection of subtle population structuring especially important for highly mobile cetaceans.}, language = {en} } @article{MayerUllmannSundeetal.2018, author = {Mayer, Martin and Ullmann, Wiebke and Sunde, Peter and Fischer, Christina and Blaum, Niels}, title = {Habitat selection by the European hare in arable landscapes}, series = {Ecology and Evolution}, volume = {8}, journal = {Ecology and Evolution}, number = {23}, publisher = {Wiley}, address = {Hoboken}, issn = {2045-7758}, doi = {10.1002/ece3.4613}, pages = {11619 -- 11633}, year = {2018}, abstract = {Agricultural land-use practices have intensified over the last decades, leading to population declines of various farmland species, including the European hare (Lepus europaeus). In many European countries, arable fields dominate agricultural landscapes. Compared to pastures, arable land is highly variable, resulting in a large spatial variation of food and cover for wildlife over the course of the year, which potentially affects habitat selection by hares. Here, we investigated within-home-range habitat selection by hares in arable areas in Denmark and Germany to identify habitat requirements for their conservation. We hypothesized that hare habitat selection would depend on local habitat structure, that is, vegetation height, but also on agricultural field size, vegetation type, and proximity to field edges. Active hares generally selected for short vegetation (1-25 cm) and avoided higher vegetation and bare ground, especially when fields were comparatively larger. Vegetation >50 cm potentially restricts hares from entering parts of their home range and does not provide good forage, the latter also being the case on bare ground. The vegetation type was important for habitat selection by inactive hares, with fabaceae, fallow, and maize being selected for, potentially providing both cover and forage. Our results indicate that patches of shorter vegetation could improve the forage quality and habitat accessibility for hares, especially in areas with large monocultures. Thus, policymakers should aim to increase areas with short vegetation throughout the year. Further, permanent set-asides, like fallow and wildflower areas, would provide year-round cover for inactive hares. Finally, the reduction in field sizes would increase the density of field margins, and farming different crop types within small areas could improve the habitat for hares and other farmland species.}, language = {en} }