Examining the causes of large mammal extinction in the Alaskan interior since the Late Quaternary using lake sediment geochemistry

The cause of Late Quaternary mammalian extinctions in North America is debated and it remains unclear whether climate (Stewart et al., 2021) or human hunting (Fordham et al., 2021) is the primary mechanism for driving this loss. Continuous connected records of human occupation, mammal population and climate are essential to advance our understanding of the causes of these late Pleistocene and Holocene extinctions. Lakes and their sediments – located at the nexus of past human occupation and migratory pathways and/or grazing in the landscape – present an ideal opportunity to develop such records. Lake sediments accumulate over time and incorporate signals from within the lake and its catchment, and they represent an integrated archive of human and mammal activity, as well as climate (e.g. D’Anjou et al., 2012). There are now a selection of proxies in our toolbox to track humans and mammals in the environment and to reconstruct past environmental change from lake sediments, such as lipid biomarkers (e.g., Castañeda and Schouten, 2011; Prost et al., 2017), stable isotopes (Leng et al., 2006) and sedimentary ancient DNA (sedaDNA) (Capo et al. 2021).

This PhD project aims to identify the causes of large mammal extinctions since the late Pleistocene in the Alaskan interior by developing lake geochemical records of human and mammal populations, and climate change.

The Tanana River Valley in central Alaska presents an ideal location to examine drivers of past changes in mammalian populations since there is a well characterised Late Quaternary archaeological record that contains clear evidence for several changes in mammalian populations and shifts in hunting technologies since first occupation c. 14,000 cal. yr BP. New records of human and mammal activity and climate change will be developed from naturally accumulating lake sedimentary archives that will be independently dated. Lipid biomarkers (sterols, bile acids) and sedaDNA analyses will generate continuous records of human and mammal population changes, against which the climate, vegetation and archaeological record will be compared.

The specific objectives of the PhD are to:
• Characterise the taphonomy and representability of mammal biomarker signatures in modern lake sediments by comparing them to modern herd populations and lake catchment processes in the Alaskan interior.
• Reconstruct changes in mammal species since the Late Pleistocene in the Tanana River Valley, Alaska, using geochemical analysis of lake sediments.
• Characterise the climate-human-mammal relationship by comparing the lake-sediment record of mammal activity with existing palaeoenvironmental reconstructions and archaeology.

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Image Captions

Winter fieldwork view of Arctic lakes,Examples of the lipid biomarker extracts that will be analysed as part of this project


The project focuses on using organic geochemical analyses of lake sediments. During fieldwork in Alaska, the student will survey lake study sites, analyse water column physiochemistry and recover Late Pleistocene to Holocene sediment cores from the lake centre. These sediments, and existing sediment cores, will undergo lithostratigraphic analysis using loss-on-ignition (LOI), mineral magnetics and XRF scanning. To assess changes in the timings and intensities of human and mammalian activities, the student will date the lake sediments using radiocarbon and use lipid biomarkers (sterols, bile acids) and nitrogen isotopes to track faecal input into the lake. The student will use sedaDNA analyses to refine characterisation of the mammalian community and population structure. Carbon isotopes and leaf wax n-alkanes will be used to reconstruct vegetation changes and hydrogen isotopes to reconstruct past hydroclimate. Depending on how the project develops there will be opportunities to explore other lipid biomarker analyses to complement the proposed palaeoenvironmental analyses. For example, analyses of GDGTs could be included to reconstruct changes in temperature. There is scope for the successful candidate to shape the direction of the laboratory analyses based on their interests (e.g. the project lends itself well to sedimentary palaeoecological analyses).

Full training will be provided in all analytical and fieldwork methods by the supervisory team. The project benefits from working closely with project partners, Prof. Mary Edwards (University of Southampton) and Dr. Nancy Bigelow (University of Alaska, Fairbanks), who specialise in Alaskan environmental change and will advise on the field campaign. There is an opportunity for the successful candidate to undertake a training placement in sedaDNA analysis at the Centre for Palaeogenetics and Stockholm University, with project partner Dr. Peter Heintzman.

Project Timeline

Year 1

Review existing literature on mammalian population dynamics, climate-human-mammal interactions, and long-term environmental change in the Alaskan interior. Plan and conduct fieldwork in Alaska to take lake sediment cores. Start laboratory analysis on sediment cores, which will include sediment descriptions, physical properties analysis (elemental chemistry (XRF) and LOI) and sub-sampling the core for lipid biomarker and sedaDNA analyses. Conduct initial radiocarbon dating of the cores. Complete first year progression paper to detail the project overview, research questions and methodology.

Year 2

Continue laboratory analysis (lipid biomarkers, sedaDNA and stable isotopes). Complete radiocarbon analysis and produce core chronologies. Present initial results at a national conference (e.g., BOGS/QRA). Submission of review chapter for publication. Write up of methods chapter.

Year 3

Finalise laboratory work with an opportunity for further analytical training at Stockholm University. Data analysis and interpretation. Present results as an international conference (e.g., EGU/AGU/IMOG). Write up of results chapters and begin overall thesis writeup.

Year 3.5

Preparation and completion of final chapters of the thesis and submission of papers for publication.

& Skills

This project will develop cross-disciplinary, transferable skills in problem solving, project management, experimental design, data analysis and visualisation, and report writing.

High-levels skills will be developed in:
• Field techniques with training in lake surveying and coring.
• Laboratory analyses with full training provided on sediment core logging, radiocarbon dating, XRF scanning, stable isotope analysis and lipid biomarker and sedaDNA extraction, processing and analysis. The analyses can be shaped to the interest of the successful candidate (e.g. to include palaeoecology) and there is scope to design an international placement at the Centre for Palaeogenetics and Stockholm University to be trained in state-of-the-art ancient DNA analysis.
• Computational/statistical analyses with training on computer programming in R for data visualisation and statistical analyses provided at Durham and Newcastle Universities.

The candidate will also benefit from broad skills training provided in-house at Durham (e.g. science communication, thesis writing, writing for grants and publications, presentation skills) via the Geography Department and the award winning Career and Research Development (CAROD) group. Furthermore, a broad range of environmental science training is provided within the IAPETUS Doctoral Training Partnership. Training requirements of the individual will be identified and met through the development of a personal training plan.

The presence of international collaborators ensures that the student has excellent opportunities to develop a strong multidisciplinary research network. Research skills and awareness of on-going research will be developed through regular participation in Durham’s Physical Geography weekly research group meetings and seminar series, DurhamARCTIC institute meetings and events, and external national and international conferences to support development as an independent researcher.

References & further reading

Capo, E. et al. 2021. Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations Quaternary. DOI: 10.3390/quat4010006.

Castañeda, I.S. and Schouten, S. 2011. A review of molecular organic proxies for examining modern and ancient lacustrine environments, Quaternary Science Reviews, 30, 21-22, 2851-2891.

D’Anjou, R.M., Bradley, R.S., Balascio, N.L. and Finkelstein, D.B. 2012. Climate impacts on human settlement and agricultural activities in northern Norway revealed through sediment biogeochemistry. PNAS, 109 (50), DOI:10.1073/pnas.1212730109.

Fordham, D.A. et al. 2021. Humans hastened the range collapse and extinction of woolly mammoth. bioRxi, DOI:10.1101/2021.02.17.431706
Leng, M.J. et al. 2006. Isotopes in lake sediments. In: Leng, M.J. (eds) Isotopes in Palaeoenvironmental Research. Developments in Paleoenvironmental Research, vol 10. Springer, Dordrecht. https://doi.org/10.1007/1-4020-2504-1_04.

Prost, K., Birk, J. J., Lehndorff, E., Gerlach, R., and Amelung, W. 2017. Steroid Biomarkers Revisited – Improved Source Identification of Faecal Remains in Archaeological Soil Material. PLOS ONE, 12, e0164882-e0164882.

Stewart, M. et al. 2021. Climate change, not human population growth, correlates with Late Quaternary megafauna declines in North America. Nat. Comms. 12, 965

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