The preservation of ancient DNA in archaeological fish bone

Ferrari, Giada; Cuevas, Angélica; Gondek-Wyrozemska, Agata T.; Ballantyne, Rachel; Kersten, Oliver; Pálsdóttir, Albína Hulda; Jagt, Inge van der; Hufthammer, Anne Karin; Ystgaard, Ingrid; Wickler, Stephen; Bigelow, Gerald F.; Harland, Jennifer; Nicholson, Rebecca; Orton, David; Clavel, Benoît; Boessenkool, Sanne; Barrett, James H.; Star, Bastiaan

doi:10.1016/j.jas.2020.105317

Cited by 22 publications

(28 citation statements)

References 80 publications

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“…The modern reads were aligned as described above for the Heliconius butterflies. Ancient herring reads were aligned as described in Ferrari et al (2021), using BWA-aln, which is commonly held to be the most appropriate mode for aligning ancient genome sequences (Schubert et al, 2012).…”

Section: Atlantic Herringmentioning

confidence: 99%

“…Second, recent strategies targeting organelle (mitochondrial or chloroplast) reference databases increasingly use genome skimming sequencing approaches (Bohmann et al, 2020). Finally, DNA preservation in subfossil, archaeological, historical, or degraded biological material remains variable and is often context‐specific (Ferrari et al, 2021; Keighley et al, 2021; Tin et al, 2014). In order to account for such unpredictability, ancient DNA sequencing studies typically screen many specimens, from which a subset with the best DNA preservation is selected for deeper sequencing (e.g., Martínez‐García et al, 2021; Star et al, 2018; van der Valk et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

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An accurate assignment test for extremely low‐coverage whole‐genome sequence data

Ferrari

Atmore

Jentoft

et al. 2021

Molecular Ecology Resources

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Genomic assignment tests can provide important diagnostic biological characteristics, such as population of origin or ecotype. Yet, assignment tests often rely on moderate‐ to high‐coverage sequence data that can be difficult to obtain for fields such as molecular ecology and ancient DNA. We have developed a novel approach that efficiently assigns biologically relevant information (i.e., population identity or structural variants such as inversions) in extremely low‐coverage sequence data. First, we generate databases from existing reference data using a subset of diagnostic single nucleotide polymorphisms (SNPs) associated with a biological characteristic. Low‐coverage alignment files are subsequently compared to these databases to ascertain allelic state, yielding a joint probability for each association. To assess the efficacy of this approach, we assigned haplotypes and population identity in Heliconius butterflies, Atlantic herring, and Atlantic cod using chromosomal inversion sites and whole‐genome data. We scored both modern and ancient specimens, including the first whole‐genome sequence data recovered from ancient Atlantic herring bones. The method accurately assigns biological characteristics, including population membership, using extremely low‐coverage data (as low as 0.0001x) based on genome‐wide SNPs. This approach will therefore increase the number of samples in evolutionary, ecological and archaeological research for which relevant biological information can be obtained.

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Section: Atlantic Herringmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

An accurate assignment test for extremely low‐coverage whole‐genome sequence data

Ferrari

Atmore

Jentoft

et al. 2021

Molecular Ecology Resources

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“…DNA extraction and library preparation from ancient samples were performed in the aDNA laboratory at the University of Oslo under rigorous measures (Cooper and Poinar, 2000;Gilbert et al, 2005). All ancient samples were processed with the same DNA extraction and library protocols according to Ferrari et al (2021). In short, bones were UV-treated for 10 min per side and pulverized using a stainless-steel mortar (Gondek et al, 2018).…”

Section: Dna Extraction Amplification and Sequencingmentioning

confidence: 99%

“…In order to provide a long-term perspective on fishing exploitation impacts, the use of archeological evidence, such as fish bone remains, is essential for those periods for which little or no historical data are available. Recent developments in whole genome aDNA methods now allow the inference of demographic histories and the estimation of genetic fluctuations over time from fishbone samples (Oosting et al, 2019;Ferrari et al, 2021). Such combined molecular analyses of historical and modern samples can potentially provide an understanding of the association between human-environmental impact and population declines (Hofman et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

Historical Demographic Processes Dominate Genetic Variation in Ancient Atlantic Cod Mitogenomes

et al. 2021

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Ancient DNA (aDNA) approaches have been successfully used to infer the long-term impacts of climate change, domestication, and human exploitation in a range of terrestrial species. Nonetheless, studies investigating such impacts using aDNA in marine species are rare. Atlantic cod (Gadus morhua), is an economically important species that has experienced dramatic census population declines during the last century. Here, we investigated 48 ancient mitogenomes from historical specimens obtained from a range of archeological excavations in northern Europe dated up to 6,500 BCE. We compare these mitogenomes to those of 496 modern conspecifics sampled across the North Atlantic Ocean and adjacent seas. Our results confirm earlier observations of high levels of mitogenomic variation and a lack of mutation-drift equilibrium—suggestive of population expansion. Furthermore, our temporal comparison yields no evidence of measurable mitogenomic changes through time. Instead, our results indicate that mitogenomic variation in Atlantic cod reflects past demographic processes driven by major historical events (such as oscillations in sea level) and subsequent gene flow rather than contemporary fluctuations in stock abundance. Our results indicate that historical and contemporaneous anthropogenic pressures such as commercial fisheries have had little impact on mitogenomic diversity in a wide-spread marine species with high gene flow such as Atlantic cod. These observations do not contradict evidence that overfishing has had negative consequences for the abundance of Atlantic cod and the importance of genetic variation in implementing conservation strategies. Instead, these observations imply that any measures toward the demographic recovery of Atlantic cod in the eastern Atlantic, will not be constrained by recent loss of historical mitogenomic variation.

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“…However, palaeogenomic analysis is far less frequently applied to marine populations, particularly those heavily exploited by humans, both past and present (Oosting et al, 2019). In the last few years, the use of ancient marine samples has begun to increase as laboratory techniques for such samples have improved (Boessenkool et al, 2017;Der Sarkissian et al, 2020;Ferrari et al, 2021b;Martínez-García et al, 2021).…”

Section: Palaeogenomicsmentioning

confidence: 99%

Shifting Baselines to Thresholds: Reframing Exploitation in the Marine Environment

2021

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Current research on anthropogenic impacts on marine ecosystems often relies on the concept of a “baseline,” which aims to describe ecosystems prior to human contact. Recent research is increasingly showing that humans have been involved in marine ecosystems for much longer than previously understood. We propose a theoretical framework oriented around a system of “thresholds” referring to system-wide changes in human culture, ecosystem dynamics, and molecular evolution. The concept of the threshold allows conceptual space to account for the fluid nature of ecosystems throughout time while providing a critical framework for understanding drivers of ecosystem change. We highlight practical research approaches for exploring thresholds in the past and provide key insights for future adaptation to a changing world. To ensure ecological and societal goals for the future are met, it is critical that research efforts are contextualized into a framework that incorporates human society as integral to ecology and evolution.

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The preservation of ancient DNA in archaeological fish bone

Cited by 22 publications

References 80 publications

An accurate assignment test for extremely low‐coverage whole‐genome sequence data

An accurate assignment test for extremely low‐coverage whole‐genome sequence data

Historical Demographic Processes Dominate Genetic Variation in Ancient Atlantic Cod Mitogenomes

Shifting Baselines to Thresholds: Reframing Exploitation in the Marine Environment

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