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1. Mitochondrial genomes of Pleistocene megafauna retrieved from recent sediment layers of two Siberian lakes.

Author

Seeber, Peter, Batke, Laura, Dvornikov, Yury, Schmidt, Alexandra, Wang, Yi, Stoof-Leichsenring, Kathleen, Moon, Katie, Vohr, Samuel, Epp, Laura, and Shapiro, Beth

Subjects
genetics, genomics, mammal, mammoth, woolly rhinoceros, Humans, Genome, Mitochondrial, Lakes, Ecosystem, DNA, Sequence Analysis, DNA, DNA, Ancient
Abstract

Ancient environmental DNA (aeDNA) from lake sediments has yielded remarkable insights for the reconstruction of past ecosystems, including suggestions of late survival of extinct species. However, translocation and lateral inflow of DNA in sediments can potentially distort the stratigraphic signal of the DNA. Using three different approaches on two short lake sediment cores of the Yamal peninsula, West Siberia, with ages spanning only the past hundreds of years, we detect DNA and identified mitochondrial genomes of multiple mammoth and woolly rhinoceros individuals-both species that have been extinct for thousands of years on the mainland. The occurrence of clearly identifiable aeDNA of extinct Pleistocene megafauna (e.g. >400 K reads in one core) throughout these two short subsurface cores, along with specificities of sedimentology and dating, confirm that processes acting on regional scales, such as extensive permafrost thawing, can influence the aeDNA record and should be accounted for in aeDNA paleoecology.

Published
2024

3. Contributors

Author

Adamovicz, Laura A., primary, Ahlstrom, Christina A., additional, Allender, Matthew C., additional, Anderson, Neil E., additional, Arnemo, Jon M., additional, Atwood, Todd C., additional, Backues, Kay A., additional, Baitchman, Eric, additional, Ballard, Jennifer R., additional, Barbon, Alberto Rodriguez, additional, Binkley, Laura E., additional, Blyde, David, additional, Brenner, Deena, additional, Brock, A. Paige, additional, Buss, Peter E., additional, Calderón-Hernández, Alejandra, additional, Carpenter, James W., additional, Catenacci, Lilian Silva, additional, Causton, Charlotte, additional, Chai, Norin, additional, Charpentier, Thomas, additional, Chinnadurai, Sathya K., additional, Clancy, Meredith M., additional, Clauss, Marcus, additional, Clifford, Deana L., additional, Conde, Dalia A., additional, Cranfield, Michael, additional, Cushing, Andrew, additional, Dadone, Liza, additional, David, Hugo, additional, Deem, Sharon L., additional, Desbiez, Arnaud L.J., additional, Dislich, Mathias, additional, Dowling, Katherine, additional, Drew, Mark L., additional, Lawrenz, Arne, additional, Duncan, Mary, additional, Edes, Ashley N., additional, Epstein, Jonathan H., additional, Reiss, Andrea Evlyn, additional, Ferrell, Shannon T., additional, Fessl, Birgit, additional, Fidgett, Andrea L., additional, Fox, Kami Z., additional, Foxworth, Steve, additional, Gamble, Kathryn C., additional, Gebreyes, Wondwossen A., additional, Georges, Jean-Yves, additional, Goe, Alexandra, additional, Goeritz, Frank, additional, González-Barrientos, Rocío, additional, de Graaff, Nicolas, additional, Greenwood, Alex D., additional, Greenwood, Andrew, additional, Grimaldi, Wray, additional, Hadfield, Catherine, additional, Hampton, Jordan O., additional, Hanley, Christopher S., additional, Harms, Craig A., additional, Harrison, Tara M., additional, Hernández-Mora, Gabriela, additional, Hermes, Robert, additional, Heatley, J. Jill, additional, Hernández, Benjamín E. Alcántar, additional, Hildebrandt, Thomas Bernd, additional, Hilsenroth, Robert, additional, Hilton, Clayton D., additional, Hoang, Thuy Thi Thu, additional, Holliday, Dawn K., additional, Hyndman, Timothy H., additional, Jakob-Hoff, Richard, additional, Janssen, Donald L., additional, Jennings, Jonathan, additional, Jensen, Trine Hammer, additional, Johnson, Gary, additional, Kalogeropoulu, Szilvia Kalliopi, additional, Kasielke, Susie, additional, Kemp, Lucy, additional, Kertesz, Peter, additional, Kinney, Matthew E., additional, Kluyber, Danilo, additional, Koeppel, Katja N., additional, Krol, Lana, additional, Kuiken, Thijs, additional, Lamberski, Nadine, additional, Langan, Jennifer N., additional, Latimer, Erin E., additional, Leach, Kathryn S., additional, Leclerc, Antoine, additional, Ling, Paul, additional, Lung, Nancy P., additional, Lécu, Alexis, additional, Marinkovich, Matt, additional, Marschang, Rachel E., additional, Masters, Nic, additional, Masuda, Bryce, additional, Mathur, Vibhu Prakash, additional, McLellan, William A., additional, McLelland, David J., additional, Meegan, Jennifer M., additional, Mendoza, Ana Patricia, additional, Meyerson, Randi, additional, Miller, Michael W., additional, Miller, Michele A., additional, Milnes, Ellie L., additional, Moore, Michael J., additional, Moriarty, Megan E., additional, Murphy, Lisa, additional, Murray, Michael J., additional, Mutlow, Adrian, additional, Myers, Debbie, additional, Myers, Gwen, additional, Nevitt, Benjamin, additional, Di Nucci, Dante L., additional, Orozco, María Marcela, additional, Padilla, Luis R., additional, Painer-Gigler, Johanna, additional, Pas, An, additional, Pelton, Craig A., additional, Pereira, Nuno M., additional, Petit, Thierry, additional, Pinter, Adriano, additional, Plangsangmas, Tithipong, additional, Prittie, Jennifer, additional, Quintard, Benoit, additional, Raath, Jacobus P., additional, Ramer, Jan, additional, Ramey, Andrew M., additional, Raphael, Bonnie L., additional, Ratanakorn, Parntep, additional, Rivera, Sam, additional, Rodriguez, Carlos, additional, Rooney, Tess, additional, Rousselet, Estelle, additional, S, Ilayaraja., additional, Sailler, Anaïs, additional, Sanderson, Stephanie, additional, Schiffmann, Christian, additional, Seeber, Peter A., additional, Semjonov, Aleksandr, additional, Sha, Arun A., additional, Sharp, Sarah, additional, Shaw, Michelle E., additional, Sheldon, Julie D., additional, Shopland, Sara, additional, Sleeman, Jonathan M., additional, Smith, Cynthia R., additional, Smith, Joseph A., additional, Soares-Neto, Lauro L., additional, Sripiboon, Supaphen, additional, Stratton, Karin, additional, Swanson, William F., additional, Sós-Koroknai, Viktória, additional, Sós, Endre, additional, Taylor-Cousar, Jennifer L., additional, Teare, J. Andrew, additional, Terio, Karen A., additional, Terrell, Scott P., additional, Thompson, Steve B., additional, Thongthip, Nikorn, additional, Torres, Rodrigo S. Garcés, additional, Tubbs, Christopher W., additional, Vicino, Greg A., additional, Vilchez-Delgado, Fernando Javier, additional, Wack, Raymund F., additional, Wahltinez, Sarah, additional, Walsh, Michael T., additional, Walzer, Chris, additional, Wenker, Christian John, additional, Wiedner, Ellen, additional, Wolfe, Barbara A., additional, Wolfe, Lisa L., additional, Wolfe, Tammy Culpepper, additional, Wyatt, Jeff, additional, Xie, Shangzhe, additional, Yanong, Roy, additional, and Yarto-Jaramillo, Enrique, additional

Published
2023
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10. Physiological costs of infection: herpesvirus replication is linked to blood oxidative stress in equids

Author

Costantini, David, Seeber, Peter A., Soilemetzidou, Sanatana-Eirini, Azab, Walid, Bohner, Julia, Buuveibaatar, Bayarbaatar, Czirják, Gábor Á., East, Marion L., Greunz, Eva Maria, Kaczensky, Petra, Lamglait, Benjamin, Melzheimer, Jörg, Uiseb, Kenneth, Ortega, Alix, Osterrieder, Nikolaus, Sandgreen, Ditte-Mari, Simon, Marie, Walzer, Chris, and Greenwood, Alex D.

Published
2018
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13. Long-term funguseplant covariation from multi-site sedimentary ancient DNA metabarcoding

Author

von Hippel, Barbara, Stoof-Leichsenring, Kathleen R., Schulte, Luise, Seeber, Peter, Epp, Laura S., Biskaborn, Boris K., Diekmann, Bernhard, Melles, Martin, Pestryakova, Luidmila, Herzschuh, Ulrike, von Hippel, Barbara, Stoof-Leichsenring, Kathleen R., Schulte, Luise, Seeber, Peter, Epp, Laura S., Biskaborn, Boris K., Diekmann, Bernhard, Melles, Martin, Pestryakova, Luidmila, and Herzschuh, Ulrike

Abstract

Climate change has a major impact on arctic and boreal terrestrial ecosystems as warming leads to northward treeline shifts, inducing consequences for heterotrophic organisms associated with the plant taxa. To unravel ecological dependencies, we address how long-term climatic changes have shaped the co-occurrence of plants and fungi across selected sites in Siberia. We investigated sedimentary ancient DNA from five lakes spanning the last 47,000 years, using the ITS1 marker for fungi and the chloroplast P6 loop marker for vegetation metabarcoding. We obtained 706 unique fungal operational taxonomic units (OTUs) and 243 taxa for the plants. We show higher OTU numbers in dry forest tundra as well as boreal forests compared to wet southern tundra. The most abundant fungal taxa in our dataset are Pseudeurotiaceae, Mortierella, Sordariomyceta, Exophiala, Oidiodendron, Protoventuria, Candida vartiovaarae, Pseudeurotium, Gryganskiella fimbricystis, and Tricho-sporiella cerebriformis. The overall fungal composition is explained by the plant composition as revealed by redundancy analysis. The fungal functional groups show antagonistic relationships in their climate susceptibility. The advance of woody taxa in response to past warming led to an increase in the abun-dance of mycorrhizae, lichens, and parasites, while yeast and saprotroph distribution declined. We also show co-occurrences between Salicaceae, Larix, and Alnus and their associated pathogens and detect higher mycorrhizal fungus diversity with the presence of Pinaceae. Under future warming, we can expect feedbacks between fungus composition and plant diversity changes which will affect forest advance, species diversity, and ecosystem stability in arctic regions. (c) 2022 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

Published
2022

15. Seasonal host and ecological drivers may promote restricted water as a viral vector

Author

Dayaram, Anisha, primary, Seeber, Peter, additional, Courtiol, Alexandre, additional, Soilemetzidou, Sanatana, additional, Tsangaras, Kyriakos, additional, Franz, Mathias, additional, McEwen, Gayle K., additional, Azab, Walid, additional, Kaczensky, Petra, additional, Melzheimer, Jörg, additional, East, Marion L., additional, Ganbaatar, Oyunsaikhan, additional, Walzer, Christian, additional, Osterrieder, Nikolaus, additional, and Greenwood, Alex D., additional

Published
2021
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20. Equid herpesvirus infections in zebras (Equus sp.): host physiology and non-invasive detection of virus shedding

Author

Seeber, Peter Andreas

Subjects
reactivation, recrudescence, virus transmission, EHV
Abstract

The equid herpesviruses (EHV) are highly prevalent pathogens in all global equid populations, with infection prevalence rates of up to 100%. They are responsible for considerable economic losses in the equine industry, and can also readily adapt to infecting new (non-equid) host species. In these novel hosts, EHV infections are typically more severe than in equids and often fatal. Herpesviruses typically remain in their hosts as a latent, lifelong infection in the host’s neural tissue and lymphoid cells and can reactivate during times of acute stress or reduced immunocompetence. So far, the triggers causing EHV reactivation in equids are not comprehensively understood. Following viral recrudescence and viraemia, EHVs are typically shed in nasal discharge and transmitted via a naso-nasal infection route. Therefore, EHV monitoring in wildlife has mostly been performed employing invasive methods, including capture and immobilization. These approaches, however, involve various risks for the target animal and for the people involved in the procedures. Furthermore, due to intense time and financial effort, invasive measures are usually limited to very few individuals. In contrast, non-invasive sampling relies on collecting sample material which is shed from the target organism into its environment, thereby circumventing the need for direct contact with the animal. In chapter 2 I established a non-invasive, indirect sampling method to collect nasal discharge and saliva of captive zebras. This method was tested on three different zebra species, and I successful isolated DNA of sporadically reactivated EHVs as well as host DNA from an enrichment toy which was provided to the study animals for certain periods of time. A similar approach might be tested on wild equids in their natural habitats to facilitate non-invasive EHV screening in situ with a time- and cost-efficient approach. In chapter 3 I used non-invasive sampling methods to screen EHV shedding in captive zebras in order to investigate the effect of presumed environmental stressors on the probability of EHV reactivation and transmission. In addition, I measured faecal glucocorticoid metabolite (fGCM) concentrations to assess a potential physiological stress response to a translocation event and subsequent social group re-structuring. Both fGCM concentrations and EHV shedding frequencies increased significantly after the translocation event and group re-structuring, compared to control periods, in the 108 translocated and in the non-translocated animals. This indicates that environmental stressors, including potential social conflict, may play a crucial role for reactivation and transmission of EHV infections in wild equids. In chapter 4 I examined whether ex situ captivity and its inherent deviations from natural living conditions of zebras (e.g. differences in climate, diet, movement space, social structure, and infection pressure) and acute EHV infections would had an effect on selected markers of the innate and adaptive immune system. Moreover, I also examined the effect of lactation on these markers, as it is known from other species that energy re- allocation may lead to a down-regulation of certain immune functions, while other immune markers are up-regulated for passive immunisation of nursing offspring. I found that constitutive innate markers were significantly higher in the natural, than in the captive environment, whereas induced immune markers were significantly higher in the wild. Lactating zebras also showed significantly higher constitutive immune functions than non-lactating mares, which may be a result of passive immunization of the offspring, but also of increased activity of this branch of immunity. Acute EHV infections, however, did not affect the measured immune markers. In chapter 5 I aimed to identify the factors which contribute to an increase of the allostatic load of free-ranging plains zebras in the Serengeti ecosystem. For this, I measured fGCM concentrations of zebras at different life history stages and under different (socio-)ecological conditions. I found significantly higher fGCM levels in zebras during times of large aggregations, compared to medium-sized and small aggregations. Furthermore, family group stallions produced higher fGCM concentrations than bachelors. Lactation and season, however, had no effect on fGCM concentrations. This indicates that EHV recrudescence is most likely when zebras are in large aggregations, and is presumably more frequent in family group stallions than in bachelors. Taken together, my results indicate that social cues seem to be important factors contributing to perceived stress, and thereby, to the probability of EHV reactivation, in zebras. Non-invasive methods for VH screening should be evaluated in the future to facilitate large-scale screening of free-ranging equid populations, in order to identify the factors which promote reactivation and transmission of latent infections such as EHV.

Published
2019

25. Non-invasive detection of equid herpesviruses in fecal samples.

Author

Seeber, Peter A., Dayaram, Anisha, Sicks, Florian, Osterrieder, Nikolaus, Franz, Mathias, and Greenwood, Alex D.

Subjects
*HERPESVIRUSES, *FECAL analysis, *PATHOGENIC microorganisms, *WILDLIFE diseases, *POLYMERASE chain reaction
Abstract

Equid Herpesviruses (EHV) are pathogens of equid and non-equid hosts that can cause disease and fatalities in captivity and in the wild. EHVs establish latent infections but can reactivate, and most EHVs are shed via the nasal passage. Therefore, nasal swabs are generally used for EHV monitoring. However, invasive sampling of wild equids is difficult. While feces is a commonly used substrate for detecting other pathogens, to our knowledge EHVs have never been detected in feces of naturally infected equids. We systematically tested zebra feces for EHV presence by A) establishing nested PCR conditions for fecal DNA extracts, B) controlling for environmental EHV contamination, and C) large-scale testing on a free ranging zebra population. A dilution minimizing inhibition while maximizing viral DNA concentration was determined in captive Grévys zebra (Equus grevyi) fecal samples from individuals shedding EHV nasally. Sixteen of 42 fecal samples (38%) were EHV-positive. To demonstrate that the EHV positivity was not a result of environmental contamination, rectal swabs of wild zebras were screened (N = 18; E. quagga and E. zebra), and 50% were EHV-positive, indicating that the source of EHV in feces is likely the intestinal mucosa, and not post-defecation contamination. Out of 270 fecal samples of wild zebras 26% were EHV-positive. Quantitative PCRs showed that the amount of virus DNA in feces was not significantly lower than in other samples. In summary, fecal sampling facilitates large scale screening and may be useful to non-invasively investigate phylogenetic EHV diversity in wild and domestic equids. [ABSTRACT FROM AUTHOR]

Published
2019
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26. Grazing behaviour of the giraffe in Hwange National Park, Zimbabwe

Author

Seeber, Peter A., Ndlovu, Honestly T., Duncan, Patrick, Ganswinds, André, Department of Production Animal Studies (Faculty of Veterinary Science), University of Pretoria [South Africa], Department of Forest Resources & Wildlife Management, National University of Science and Technology [Bulawayo], Centre d'études biologiques de Chizé (CEBC), Centre National de la Recherche Scientifique (CNRS), and Department of Zoology and Entomology [Pretoria]

Subjects
[SDE]Environmental Sciences, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2012

29. Behavioural inventory of the giraffe (Giraffa camelopardalis)

Author

Seeber, Peter A., Ciofolo, Isabelle, Ganswindt, André, Seeber, Peter A., Ciofolo, Isabelle, and Ganswindt, André

Abstract

Background Numerous factors like continuous habitat reduction or fragmentation for free-ranging giraffes (Giraffa camelopardalis) as well as e.g. suboptimal housing conditions for animals in captivity might lead to behavioural alterations as part of the overall adaptation process to the changing living conditions. In order to facilitate current and future studies on giraffe behaviour, a comprehensive ethogram was compiled based on existing literature, as well as observations on giraffes in the wild (Hwange National Park, Zimbabwe; Entabeni Game Reserve, South Africa), and in captivity (National Zoological Gardens of South Africa, Pretoria). Findings The resulting ethogram lists 65 different behavioural patterns, which were described and grouped into seven categories: General activities, Abnormal repetitive behaviours, General interactions, Bull-Cow behaviour, Bull-Bull behaviour, Cow-Bull behaviour, Maternal behaviours, and Interactions by calves. The behaviours were further described regarding a presumed purpose, particularly with respect to social interactions and sexual behaviour. Contradictory descriptions from previous studies were considered and discussed in comparison with our own observations. Conclusions This ethogram provides a basis for current and future studies by suggesting a terminology which can be used for harmonizing behavioural observations, thus helping to facilitate comparability of future results. Subsequently, a better understanding of the behavioural ecology of giraffes in the wild as well as in captivity could aid future conservation efforts.

30. Behavioural inventory of the giraffe (Giraffa camelopardalis)

Author

Seeber, Peter A., Ciofolo, Isabelle, Ganswindt, André, Seeber, Peter A., Ciofolo, Isabelle, and Ganswindt, André

Abstract

Background Numerous factors like continuous habitat reduction or fragmentation for free-ranging giraffes (Giraffa camelopardalis) as well as e.g. suboptimal housing conditions for animals in captivity might lead to behavioural alterations as part of the overall adaptation process to the changing living conditions. In order to facilitate current and future studies on giraffe behaviour, a comprehensive ethogram was compiled based on existing literature, as well as observations on giraffes in the wild (Hwange National Park, Zimbabwe; Entabeni Game Reserve, South Africa), and in captivity (National Zoological Gardens of South Africa, Pretoria). Findings The resulting ethogram lists 65 different behavioural patterns, which were described and grouped into seven categories: General activities, Abnormal repetitive behaviours, General interactions, Bull-Cow behaviour, Bull-Bull behaviour, Cow-Bull behaviour, Maternal behaviours, and Interactions by calves. The behaviours were further described regarding a presumed purpose, particularly with respect to social interactions and sexual behaviour. Contradictory descriptions from previous studies were considered and discussed in comparison with our own observations. Conclusions This ethogram provides a basis for current and future studies by suggesting a terminology which can be used for harmonizing behavioural observations, thus helping to facilitate comparability of future results. Subsequently, a better understanding of the behavioural ecology of giraffes in the wild as well as in captivity could aid future conservation efforts.

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