Examining Natural History through the Lens of Palaeogenomics

Mitchell, Kieren J.; Rawlence, Nicolas J.

doi:10.1016/j.tree.2020.10.005

Cited by 33 publications

(28 citation statements)

References 96 publications

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“…Continuous human activities and a changing climate have influenced terrestrial and marine ecosystems for millennia (Venter et al, 2016;Rodrigues et al, 2019;Mitchell and Rawlence, 2021), impacting the evolutionary potential and population demography of a range of species (Seersholm et al, 2018). Ancient mitochondrial DNA (mtDNA) has been widely used to understand long-term genomic consequences of such impacts (Shapiro et al, 2004;Nyström et al, 2006;Stiller et al, 2010;Paijmans et al, 2013;Fortes and Paijmans, 2015;Casas-Marce et al, 2017).…”

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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Section: Introductionmentioning

confidence: 99%

Historical Demographic Processes Dominate Genetic Variation in Ancient Atlantic Cod Mitogenomes

et al. 2021

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“…The major significance of this distinction is that optimal methods for sampling, isolating, bioinformatic processing, and analyzing hDNA and aDNA, differ due to their contrasting DNA degradation history. These differences are produced because of the natural versus archival preservation conditions, and the different ages of the DNA [11,12].…”

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confidence: 99%

Mining museums for historical DNA: advances and challenges in museomics

Raxworthy

Smith

2021

Trends in Ecology & Evolution

134

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“…With the application of shotgun metagenomics and target enrichment approaches, it is now possible to recover haplotypic and genomic information directly from sedaDNA [43][44][45][47][48][49], which enables the exploration of populationlevel changes and has the potential to detect the arrival or disappearance of alleles and lineages in a region, as recently showcased for Neanderthals from a cave in Spain [48]. This expansion of sedaDNA into environmental palaeogenomics, together with the integration of sedaDNA and traditional palaeogenomic data derived from body fossils [55], will open up new approaches to understanding past biodiversity changes that are inaccessible with other palaeoecological proxies.…”

Section: Sedimentary Ancient Dna Adds Another Dimensionmentioning

confidence: 99%

Integrating multi-taxon palaeogenomes and sedimentary ancient DNA to study past ecosystem dynamics

et al. 2021

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Ancient DNA (aDNA) has played a major role in our understanding of the past. Important advances in the sequencing and analysis of aDNA from a range of organisms have enabled a detailed understanding of processes such as past demography, introgression, domestication, adaptation and speciation. However, to date and with the notable exception of microbiomes and sediments, most aDNA studies have focused on single taxa or taxonomic groups, making the study of changes at the community level challenging. This is rather surprising because current sequencing and analytical approaches allow us to obtain and analyse aDNA from multiple source materials. When combined, these data can enable the simultaneous study of multiple taxa through space and time, and could thus provide a more comprehensive understanding of ecosystem-wide changes. It is therefore timely to develop an integrative approach to aDNA studies by combining data from multiple taxa and substrates. In this review, we discuss the various applications, associated challenges and future prospects of such an approach.

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Examining Natural History through the Lens of Palaeogenomics

Abstract: Under ideal conditions, it is possible to retrieve genomic data from the remains of organisms hundreds of thousands of years old. These 'palaeogenomic' data can be used to test hypotheses about past biological change with a level of resolution that is not possible using other methods.

Cited by 33 publications

References 96 publications

Historical Demographic Processes Dominate Genetic Variation in Ancient Atlantic Cod Mitogenomes

Historical Demographic Processes Dominate Genetic Variation in Ancient Atlantic Cod Mitogenomes

Mining museums for historical DNA: advances and challenges in museomics

Integrating multi-taxon palaeogenomes and sedimentary ancient DNA to study past ecosystem dynamics

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