Rapid global warming is severely impacting Arctic ecosystems and is predicted to transform the abundance, distribution, and genetic diversity of Arctic species, though these linkages are poorly understood. We address this gap in knowledge using palaeogenomics to examine how earlier periods of global warming influenced the genetic diversity of Atlantic walrus (Odobenus rosmarus rosmarus), a species closely associated with sea ice and shallow-water habitats. We analysed 82 ancient and historical Atlantic walrus mitochondrial genomes (mitogenomes), including now-extinct populations in Iceland and the Canadian Maritimes, to reconstruct the Atlantic walrus’ response to Arctic deglaciation. Our results demonstrate that the phylogeography and genetic diversity of Atlantic walrus populations were initially shaped by the Last Glacial Maximum (LGM), surviving in distinct glacial refugia, and subsequently expanding rapidly in multiple migration waves during the late Pleistocene and early Holocene. The timing of diversification and establishment of distinct populations corresponds closely with the chronology of the glacial retreat, pointing to a strong link between walrus phylogeography and sea ice. Our results indicate that accelerated ice loss in the modern Arctic may trigger further dispersal events, likely increasing the connectivity of northern stocks while isolating more southerly stocks putatively caught in small pockets of suitable habitat.

Conservation strategies centred around species habitat protection rely on species’ dietary information. One species at the focal point of conservation efforts is the herbivorous grouse, the western capercaillie (Tetrao urogallus), which is an indicator species for forest biodiversity conservation. Non-molecular means used to study their diet are time-consuming and at low taxonomic resolution. This delays the implementation of conservation strategies including resource protection due to uncertainty about its diet. Thus, limited knowledge on diet is hampering conservation efforts. Here we use non-invasive environmental DNA (eDNA) metabarcoding on DNA extracted from faeces to present the first large-scale molecular dietary analysis of capercaillies. Faecal samples were collected from seven populations located in Norway (Finnmark, Troms, Trøndelag, Innlandet) and France (Vosges, Jura, Pyrenees) (n=172). We detected 122 plant taxa belonging to 46 plant families of which 37.7% of the detected taxa could be identified at species level. The average dietary richness of each sample was 7 ± 5 SD taxa. The most frequently occurring plant groups with the highest relative read abundance (RRA) were trees and dwarf shrubs, in particular, Pinus and Vaccinium myrtillus, respectively. There was a difference in dietary composition (RRA) between samples collected from the different locations (adonis pseudo F5,86= 11.01, r2 = 0.17, p = 0.001) and seasons (adonis pseudo F2,03 = 0.64, r2 = 0.01, p = 0.036). Dietary composition also differed between sexes at each location (adonis pseudo F1,47 = 2.77, r2 = 0.04, p = 0.024), although not significant for all data combined. In total, 35 taxa (36.8% of taxa recorded) were new capercaillie food items compared to existing knowledge from non-molecular means. The non-invasive molecular dietary analysis applied in this study provides new ecological information of capercaillies’ diet, improving our understanding of adequate habitat required for their conservation.

Resolution of relationships at lower taxonomic levels is crucial for answering many evolutionary questions, and as such, sufficiently varied species representation is vital. This latter goal is not always achievable with relatively fresh samples. To alleviate the difficulties in procuring rarer taxa, we have seen increasing utilization of historical specimens in building molecular phylogenies using high throughput sequencing. This effort, however, has mainly focused on large-bodied or well-studied groups, with small-bodied and under-studied taxa under-prioritized. Here, we utilize both historical and contemporary specimens, to increase the resolution of phylogenetic relationships among a group of under-studied and small-bodied metazoans, namely, cheilostome bryozoans. In this study, we pioneer sequencing of air-dried cheilostomes, utilizing a recent library preparation method for low DNA input. We evaluate a de novo mitogenome assembly and two iterative methods, using the sequenced target specimen as a reference for mapping, for our sequences. In doing so, we present mitochondrial and ribosomal RNA sequences of 43 cheilostomes representing 37 species, including 14 from historical samples ranging from 50 to 149 years old. The inferred phylogenetic relationships of these samples, analyzed together with publicly available sequence data, are shown in a statistically well-supported 65 taxa and 17 genes cheilostome tree, which is also the most broadly sampled and largest to date. The robust phylogenetic placement of historical samples whose contemporary conspecifics and or congenerics have been sequenced verify the appropriateness of our workflow and give confidence in the phylogenetic placement of those historical samples for which there are no close relatives sequenced.  The success of our workflow is highlighted by the circularization of a total of 27 mitogenomes, seven from historical cheilostome samples. Our study highlights the potential of utilizing DNA from micro-invertebrate specimens stored in natural history collections for resolving phylogenetic relationships among species.

Knowledge of the range and chronology of historic trade and long-distance transport of natural resources is essential for determining the impacts of past human activities on marine environments. However, the specific biological sources of imported fauna are often difficult to identify, in particular if species have a wide spatial distribution and lack clear osteological or isotopic differentiation between populations. Here, we report that ancient fish-bone remains, despite being porous, brittle, and light, provide an excellent source of endogenous DNA (15–46%) of sufficient quality for whole-genome reconstruction. By comparing ancient sequence data to that of modern specimens, we determine the biological origin of 15 Viking Age (800–1066 CE) and subsequent medieval (1066–1280 CE) Atlantic cod (Gadus morhua) specimens from excavation sites in Germany, Norway, and the United Kingdom. Archaeological context indicates that one of these sites was a fishing settlement for the procurement of local catches, whereas the other localities were centers of trade. Fish from the trade sites show a mixed ancestry and are statistically differentiated from local fish populations. Moreover, Viking Age samples from Haithabu, Germany, are traced back to the North East Arctic Atlantic cod population that has supported the Lofoten fisheries of Norway for centuries. Our results resolve a long-standing controversial hypothesis and indicate that the marine resources of the North Atlantic Ocean were used to sustain an international demand for protein as far back as the Viking Age.

Human population expansion and associated degradation of the habitat of many wildlife species cause loss of biodiversity and species extinctions. The small Simen Mountains National Park in Ethiopia is one of the last strongholds for the preservation of a number of afro-alpine mammals, plants and birds, and it is home to the rare endemic Walia ibex, Capra walie. The narrow distribution range of this species as well as potential competition for resources with livestock, especially with domestic goat, Capra hircus, may compromise its future survival. Based on a curated afro-alpine taxonomic reference library constructed for plant taxon identification, we investigated the diet of the Walia ibex and addressed the dietary overlap with domestic goat using DNA metabarcoding of faecal samples. Faeces of both species were collected from different localities in the National Park. We show that both species are browsers, with forbs, shrubs and trees comprising the largest proportion of their diet, supplemented by grasses. There was a considerable overlap in dietary preferences. Several of the preferred diet items of the Walia ibex (Alchemilla sp., Hypericum revolutum, Erica arborea and Rumex sp.) were also among the most preferred diet items of the domestic goat. These results indicate that there is potential for competition between the two species, especially during the dry season, when resources are limited. Our findings, in combination with the expected increase in domestic herbivores, suggest that management plans should consider the potential threat posed by domestic goats to ensure future survival of the endangered Walia ibex.

High Arctic environments are particularly sensitive to climate changes, but retrieval of paleoecological data is challenging due to low productivity and biomass. At the same time, Arctic soils and sediments have proven exceptional for long-term DNA preservation due to their constantly low temperatures. Lake sediments contain DNA paleorecords of the surrounding ecosystems and can be used to retrieve a variety of organismal groups from a single sample. In this study, we analyzed vascular plant, bryophyte, algal (in particular diatom) and copepod DNA retrieved from a sediment core spanning the Holocene, taken from Bliss Lake on the northernmost coast of Greenland. A previous multi-proxy study including microscopic diatom analyses showed that this lake experienced changes between marine and lacustrine conditions. We inferred the same environmental changes from algal DNA preserved in the sediment core. Our DNA record was stratigraphically coherent, with no indication of leaching between layers, and our cross-taxon comparisons were in accordance with previously inferred local ecosystem changes. Authentic ancient plant DNA was retrieved from nearly all layers, both from the marine and the limnic phases, and distinct temporal changes in plant presence were recovered. The plant DNA was mostly in agreement with expected vegetation history, but very early occurrences of vascular plants, including the woody Empetrum nigrum, document terrestrial vegetation very shortly after glacial retreat. Our study shows that multi-taxon metabarcoding of sedimentary ancient DNA from lake cores is a valuable tool both for terrestrial and aquatic paleoecology, even in low-productivity ecosystems such as the High Arctic.

Although it is generally agreed that the arctic flora is among the youngest and least diverse on Earth, the processes that shaped it are poorly understood. Here we present 50 thousand years (kyr) of arctic vegetation history, derived from the first large-scale ancient DNA metabarcoding study of circumpolar plant diversity. For this interval we additionally explore nematode diversity as a proxy for modelling vegetation cover and soil quality, and diets of herbivorous megafaunal mammals, many of which became extinct around 10 kyr BP (before present). For much of the period investigated, arctic vegetation consisted of dry steppe tundra dominated by forbs (non-graminoid herbaceous vascular plants). During the Last Glacial Maximum (25–15 kyr BP), diversity declined markedly, although forbs remained dominant. Much changed after 10 kyr BP, with the appearance of moist tundra dominated by woody plants and graminoids. Our analyses indicate that both graminoids and forbs would have featured in megafaunal diets. As such our findings question the predominance of a late Quaternary graminoid-dominated arctic “mammoth steppe”.

Conservation of biodiversity may in the future increasingly depend upon the availability of scientific information to set suitable restoration targets. In traditional paleoecology, sediment-based pollen provides a means to define preanthropogenic impact conditions, but problems in establishing the exact provenance and ecologically meaningful levels of taxonomic resolution of the evidence are limiting. We explored the extent to which the use of sedimentary ancient DNA (sedaDNA) may complement pollen data in reconstructing past alpine environments in the tropics. We constructed a record of afro-alpine plants retrieved from DNA preserved in sediment cores from 2 volcanic crater sites in the Albertine Rift, eastern Africa. The record extended well beyond the onset of substantial anthropogenic effects on tropical mountains. To ensure high-quality taxonomic inference from the sedaDNA sequences, we built an extensive DNA reference library covering the majority of the afro-alpine flora, by sequencing DNA from taxonomically verified specimens. Comparisons with pollen records from the same sediment cores showed that plant diversity recovered with sedaDNA improved vegetation reconstructions based on pollen records by revealing both additional taxa and providing increased taxonomic resolution. Furthermore, combining the 2 measures assisted in distinguishing vegetation change at different geographic scales; sedaDNA almost exclusively reflects local vegetation, whereas pollen can potentially originate from a wide area that in highlands in particular can span several ecozones. Our results suggest that sedaDNA may provide information on restoration targets and the nature and magnitude of human-induced environmental changes, including in high conservation priority, biodiversity hotspots, where understanding of preanthropogenic impact (or reference) conditions is highly limited.

Metabarcoding approaches use total and typically degraded DNA from environmental samples to analyse biotic assemblages and can potentially be carried out for any kinds of organisms in an ecosystem. These analyses rely on specific markers, here called metabarcodes, which should be optimized for taxonomic resolution, minimal bias in amplification of the target organism group and short sequence length. Using bioinformatic tools, we developed metabarcodes for several groups of organisms: fungi, bryophytes, enchytraeids, beetles and birds. The ability of these metabarcodes to amplify the target groups was systematically evaluated by (1) in silico PCRs using all standard sequences in the EMBL public database as templates, (2) in vitro PCRs of DNA extracts from surface soil samples from a site in Varanger, northern Norway, and (3) in vitro PCRs of DNA extracts from permanently frozen sediment samples of late-Pleistocene age (~ 16 000–50 000 yr BP) from two Siberian sites, Duvanny Yar and Main River. Comparison of the results from the in silico PCR with those obtained in vitro showed that the in silico approach offered a reliable estimate of the suitability of a marker. All target groups were detected in the environmental DNA, but we found large variation in the level of detection among the groups and between modern and ancient samples. Success rates for the Pleistocene samples were highest for fungal DNA, whereas bryophyte, beetle and bird sequences could also be retrieved, but to a much lesser degree. The metabarcoding approach has considerable potential for biodiversity screening of modern samples and also as a paleoecological tool.

Analyses of degraded DNA are typically hampered by contamination, especially when employing universal primers such as commonly used in environmental DNA studies. In addition to false-positive results, the amplification of contaminant DNA may cause false-negative results due to competition, or bias, during the PCR. In this study, we test the utility of human-specific blocking primers in mammal diversity analyses of ancient permafrost samples from Siberia. Using quantitative PCR (qPCR) on human and mammoth DNA we first optimised the design and concentration of blocking primer in the PCR. Subsequently, 454 pyrosequencing of ancient permafrost samples amplified with and without the addition of blocking primer revealed that DNA sequences from a diversity of mammalian representatives of the Beringian megafauna were retrieved only when the blocking primer was added to the PCR. Notably, we observe the first retrieval of woolly rhinoceros (C. antiquitatis) DNA from ancient permafrost cores. In contrast, reactions without blocking primer resulted in complete dominance by human DNA sequences. These results demonstrate that in ancient environmental analysis, the PCR can be biased towards amplification of contaminant sequences to such an extent that retrieval of the endogenous DNA is severely restricted. The application of blocking primers is a promising tool to avoid this bias and can greatly enhance the quantity and the diversity of the endogenous DNA sequences that are amplified.