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

Strengthening global-change science by integrating aeDNA with paleoecoinformatics

Ancient environmental DNA (aeDNA) data are close to enabling insights into past global-scale biodiversity dynamics at unprecedented taxonomic extent and resolution. However, achieving this potential requires solutions that bridge bioinformatics and paleoecoinformatics. Essential needs include support for dynamic taxonomic inferences, dynamic age inferences, and precise stratigraphic depth. Moreover, aeDNA data are complex and heterogeneous, generated by dispersed researcher networks, with methods advancing rapidly. Hence, expert community governance and curation are essential to building high-value data resources. Immediate recommendations include uploading metabarcoding-based taxonomic inventories into paleoecoinformatic resources, building linkages among open bioinformatic and paleoecoinformatic data resources, harmonizing aeDNA processing workflows, and expanding community data governance. These advances will enable transformative insights into global-scale biodiversity dynamics during large environmental and anthropogenic changes.

MetaDamage tool: Examining post-mortem damage in sedaDNA on a metagenomic scale

The use of metagenomic datasets to support ancient sedimentary DNA (sedaDNA) for paleoecological reconstruction has been demonstrated to be a powerful tool to understand multi-organism responses to climatic shifts and events. Authentication remains integral to the ancient DNA discipline, and this extends to sedaDNA analysis. Furthermore, distinguishing authentic sedaDNA from contamination or modern material also allows for a better understanding of broader questions in sedaDNA research, such as formation processes, source and catchment, and post-depositional processes. Existing tools for the detection of damage signals are designed for single-taxon input, require a priori organism specification, and require a significant number of input sequences to establish a signal. It is therefore often difficult to identify an established cytosine deamination rate consistent with ancient DNA across a sediment sample. In this study, we present MetaDamage, a tool that examines cytosine deamination on a metagenomic (all organisms) scale for multiple previously undetermined taxa and can produce a damage profile based on a few hundred reads. We outline the development and testing of the MetaDamage tool using both authentic sedaDNA sequences and simulated data to demonstrate the resolution in which MetaDamage can identify deamination levels consistent with the presence of ancient DNA. The MetaDamage tool offers a method for the initial assessment of the presence of sedaDNA and a better understanding of key questions of preservation for paleoecological reconstruction.

The untapped potential of macrofossils in ancient plant DNA research

The rapid development of ancient DNA analysis in the last decades has induced a paradigm shift in ecology and evolution. Driven by a combination of breakthroughs in DNA isolation techniques, high-throughput sequencing, and bioinformatics, ancient genome-scale data for a rapidly growing variety of taxa are now available, allowing researchers to directly observe demographic and evolutionary processes over time. However, the vast majority of paleogenomic studies still focus on human or animal remains. In this article, we make the case for a vast untapped resource of ancient plant material that is ideally suited for paleogenomic analyses: plant remains, such as needles, leaves, wood, seeds, or fruits, that are deposited in natural archives, such as lake sediments, permafrost, or even ice caves. Such plant remains are commonly found in large numbers and in stratigraphic sequence through time and have so far been used primarily to reconstruct past local species presences and abundances. However, they are also unique repositories of genetic information with the potential to revolutionize the fields of ecology and evolution by directly studying microevolutionary processes over time. Here, we give an overview of the current state-of-the-art, address important challenges, and highlight new research avenues to inspire future research.

Landscape modification by Last Interglacial Neanderthals

Little is known about the antiquity, nature, and scale of Pleistocene hunter-gatherer impact on their ecosystems, despite the importance for studies of conservation and human evolution. Such impact is likely to be limited, mainly because of low population densities, and challenging to detect and interpret in terms of cause-effect dynamics. We present high-resolution paleoenvironmental and archaeological data from the Last Interglacial locality of Neumark-Nord (Germany). Among the factors that shaped vegetation structure and succession in this lake landscape, we identify a distinct ecological footprint of hominin activities, including fire use. We compare these data with evidence from archaeological and baseline sites from the same region. At Neumark-Nord, notably open vegetation coincides with a virtually continuous c. 2000-year-long hominin presence, and the comparative data strongly suggest that hominins were a contributing factor. With an age of c. 125,000 years, Neumark-Nord provides an early example of a hominin role in vegetation transformation.

The Contribution of Kurī (Polynesian Dog) to the Ecological Impacts of the Human Settlement of Aotearoa New Zealand

The pre-human Aotearoa New Zealand fauna was dominated by avian and reptilian species. Prior to first human settlement by East Polynesian colonists, the top predators were two giant raptorial birds. Aside from humans themselves, colonisation also resulted in the simultaneous introduction of two novel mammalian predators into this naive ecosystem, the kiore (Pacific rat) and kurī (Polynesian dog). While the ecological impacts of kiore are relatively well understood, those of kurī are difficult to assess, and as such kurī have frequently been disregarded as having any meaningful impact on New Zealand’s biodiversity. Here we use the archaeological and palaeoecological record to reassess the potential impacts of kurī on this ecosystem. We argue that far from being confined to villages, kurī could have had a significant widespread but relatively localised impact on New Zealand’s avian, reptilian and marine mammal (seals and sea lions) fauna as a novel predator of medium-sized species. In this way, kurī potentially amplified the already significant impacts of Polynesian colonists and their descendants on New Zealand’s ecosystem, prior to European arrival. As such, kurī should be included in models of human impact in addition to over-hunting, environmental modification and predation by kiore.