Holocene shifts in marine mammal distributions around Northern Greenland revealed by sedimentary ancient DNA

Domain: earth_science
Published: 2025-05-15
Editorial outcome: minor_revision

Abstract
Arctic marine ecosystems have undergone notable reconfigurations in response to Holocene climate and environmental changes. Yet our understanding of how marine mammal occurrence was impacted remains limited, due to their relative scarcity in the fossil record. We reconstruct the occurrence of marine mammals across the past 12,000 years through detections based on sedimentary ancient DNA from four marine sediment cores collected around Northern Greenland, and integrate the findings with local and regional environmental proxy records. Our findings indicate a close association between marine mammals at densities detectable in marine sediments and the deglaciation of high Arctic marine environments at the onset of the Holocene. Further, we identify air temperature and changes in sea ice cover as significant drivers of community change across time. Several marine mammals are detected in the sediments earlier than in the fossil record, for some species by several thousand years. During the Early-to-Mid Holocene, a period of warmer climate, we record northward distribution shifts of temperate and low-arctic marine mammal species. Our findings provide unique, long-term baseline data on the occurrence of marine mammals around Northern Greenland, enabling insights into past community dynamics and the effects of Holocene climatic shifts on the region’s marine ecosystems.

Introduction
Ongoing anthropogenic climate change is transforming the Arctic. The region is warming four times faster than the global average1 and the extent of summer sea ice has already declined by as much as 50% over the past 40 years2. Temporarily ice-free conditions in the Arctic Ocean, defined as the first occurrence of a total sea ice area <1 million km2, may already emerge during summer by the end of this decade3. In response to these shifting environmental conditions, the spatial distribution of marine species across the Arctic is changing4–7. Species endemic to the Arctic region are expected to face a drastic reduction in suitable habitats8,9, while temperate species may benefit from the reconfiguration of oceanic currents and increased availability of ice-free habitats10,11.

Arctic marine mammals are sensitive to climate change, especially due to their dependence on sea ice12,13. Seven species are found around Northern Greenland year-round, including the three Arctic cetacean species [beluga whale (Delphinapterus leucas), narwhal (Monodon monoceros), and bowhead whale (Balaena mysticetus)], three pinniped species [ringed seal (Pusa hispida), bearded seal (Erignathus barbatus), walrus (Odobenus rosmarus)], and polar bear (Ursus maritimus). In addition, harp seal (Phoca groenlandica) and hooded seal (Cystophora cristata) seasonally migrate northwards along the east and west coasts of Greenland, and depend on the presence of sea ice for reproduction14,15. At least 12 temperate cetacean species with distribution ranges not confined to the Arctic have been recorded in Greenland, with species such as fin whale (Balaenoptera physalus) and minke whale (Balaenoptera acutorostrata) seasonally migrating in large numbers to ice-free feeding grounds along the central and northern coasts of Greenland16,17. The observed impacts of ongoing climate change on marine mammals found around Greenland are not uniform18. For example, the extended open-water season may boost the availability of prey (e.g., krill, copepods) for species such as bowhead whales19,20, but the associated increase in the presence of orcas (Orcinus orca) also poses higher risks of predation21.

Monitoring efforts provide crucial data on population dynamics, distribution shifts, and behavioral changes in response to changing environmental conditions13,22,23. However, we lack an understanding of the longer-term dynamics of Arctic marine ecosystems. Integrating knowledge on the shorter-term response of species to anthropogenic climate change24 with longer-term perspectives on how species distributions have shifted in response to past environmental changes may enhance our understanding of their resilience to global warming25. Population genetic studies of marine mammals in the Arctic document the impacts of the environmental changes of the Holocene (past 11.7 thousand years [ka]) on present-day population structure26–28. Holocene paleoclimate records reveal periods with regional air temperatures up to 6°C warmer than the pre-industrial average29, which may be used as near-future climate analogs. Specifically, a period in the Early-to-Mid Holocene was characterized by elevated air and ocean temperatures, as a consequence of higher boreal summer insolation, known as the Holocene Thermal Maximum (here broadly used to refer to the period of peak Holocene warmth ~10−5.5 ka BP)30. As a result, marine outlet glaciers along the coasts of Greenland retreated dramatically31–33, sea ice extent and thickness decreased as indicated by driftwood deposition along the northern coast of Ellesmere Island and Greenland34,35, and oceanic currents such as the West Greenland Current (Fig. 1a) intensified36.

Information on the past occurrence of species can be retrieved from the fossil record. However, discoveries of marine mammal fossils are rare, as most species live and die at sea. Archeological sites are rich sources of faunal remains, but are limited to the species harvested by humans37 and for Greenland extend back only 4.5 ka38. Although individual, older remains of e.g., bowhead whale, narwhal, ringed seal, walrus, and polar bear, have been recovered from paleontological contexts39–42, a detailed, long-term reconstruction of these species´ histories is limited by the scarcity of fossils.

Sediment archives provide an alternative substrate to document the occurrence of species through time43. In the terrestrial realm, sediment archives have been used to broaden our understanding of spatiotemporal patterns of species occurrence. For example, DNA retrieved from permafrost sediments has indicated the presence of species in the landscape for millennia after they were presumed extinct based on their last appearance dates in the fossil record44,45. Marine sediments have long been used for paleoenvironmental reconstruction46, but their full potential for detecting species occurrence using DNA remains underexplored47,48. So far, most research on marine sediments has been based on traditional micropalaeontological methods and has focused on obtaining time-series data from organisms at the base of the food web49–53. However, the retrieval of sedimentary ancient DNA from higher trophic level organisms provides the opportunity to improve our understanding of the dynamics of marine ecosystems through time54,55.

In this work, we characterize the occurrence of marine mammal species across the Holocene, using sedimentary ancient DNA retrieved from four marine sediment cores collected around the northern coast of Greenland that span the past ca. 12 ka (Fig. 1). We applied two complementary molecular approaches (metagenomic shotgun sequencing and hybridization capture enrichment of mitochondrial genomes) for marine mammal detection, and integrated our findings with paleoceanographic proxy data derived from the same or nearby sediment cores that provide information on primary productivity, sea ice cover, and the influence of Atlantic-derived (warmer) water masses. Specifically, we investigated (i) the occurrence through time of the seven marine mammals that at present inhabit the Atlantic sector of the Arctic year-round; (ii) the occurrence through time of marine mammal species that at present only inhabit the Arctic seasonally; and (iii) spatiotemporal associations between marine mammal occurrence and Holocene paleoenvironmental proxy data. Our findings indicate environmental changes as significant drivers of community shifts across time; we identify the presence of marine mammals at densities detectable in marine environments coincident with Arctic marine deglaciation at the onset of the Holocene, and record subsequent northward distribution shifts of temperate and low-arctic marine mammal species during the warmer Early-to-Mid Holocene.

Results
Overview of sequencing data and DNA damage
Using a combination of shotgun sequencing and mitochondrial genome hybridization capture, we retrieved DNA time-series data spanning the past ~12 ka from four marine sediment cores collected off the coasts of Northern Greenland, albeit with varying temporal resolution (Fig. 1); LK21-IC-st26-GC1 (75.32°N 61.91°W, 912 m water depth, 320 cm sediment recovery; hereafter Melville Bay 26G), Ryder19-24-PC1 (81.62°N 62.30°W, 520 m water depth, 525 cm sediment recovery; hereafter Hall Basin 24PC), Ryder19-12-GC1 (82.58°N 52.53°W, 867 m water depth, 273.5 cm sediment recovery; hereafter Lincoln Sea 12-GC) and DA17-NG-ST07-073G (79.07°N 11.90°W, 385 m water depth, 410 cm sediment recovery; hereafter North-East Greenland 73G). Melville Bay 26G and Lincoln Sea 12-GC comprise a complete record of the Holocene, while Hall Basin 24PC covered the past ca. 9.6 cal ka BP and North-East Greenland 73G covered the past ca. 9.5 cal ka BP (Fig. 1c).

Subsamples of 0.35-1 g of sediment were collected from each of the cores (11–42 samples per core) for DNA analysis, resulting in 116 samples, of which all were processed using hybridization capture, and a subset was subjected to additional shallow shotgun sequencing (Fig. 1c, and Supplementary Data 1). When comparing DNA concentrations of total DNA extracts across sediment cores and samples, samples <2 ka BP generally had the highest DNA concentrations (7.4±5.1 ng µL⁻¹), while older samples yielded lower concentrations (1.4±1.5 ng µL⁻¹) or remained below the detection limit of 0.05 ng µL⁻¹ (Figs. 2d, 3d, 3g, 4d).

We used shotgun sequencing to characterize the most abundant eukaryotic taxa and hybridization capture to specifically enrich the genetic traces of marine mammals endemic to the Arctic and of relevant marine mammals, whose present-day distribution is not confined only to the Arctic. We investigated the association of the combined dataset with paleoceanographic proxy data to identify potential drivers of change through time. All genetic detections are reported per taxon and sample, in unique sequence abundances (defined as the number of unique DNA sequences) and in relative sequence abundances (defined as the number of unique sequences divided by the number of quality-filtered sequences). Both metrics are interpreted as confidence of the genetic signal underlying the detection of a taxon; high unique sequence abundance and high relative sequence abundance translate into a detection with higher confidence, and low unique sequence abundance and low relative sequence abundance into a detection with lower confidence.

The analysis of nucleotide deamination rates (DNA damage) in the shotgun sequencing and hybridization capture data enabled us to identify the accumulation of nucleotide deaminations for older samples typical of ancient DNA, and thus provided an authentication of our species detections. We visualized mean nucleotide deamination rates across the last three bases of sequences assigned to eukaryotes for the shotgun sequencing dataset, and sequences assigned to marine mammals in the hybridization capture dataset for each core assigned to Phocidae across time bins of 3000 years for each core (Supplementary Figs. 2–5), we observed higher nucleotide deamination rates for DNA sequences corresponding to older samples and overall low DNA fragment lengths (≤125 bp).

Age-depth models of the studied marine sediment cores
We established age-depth models for the Melville Bay 26G and Hall Basin 24PC cores. Age-depth models are available for Lincoln Sea 12-GC (Supplementary Fig. 6)56 and North-East Greenland 73G (Supplementary Fig. 7)57.

For Melville Bay 26G, we constructed an age-depth model using 14C radiocarbon dates of three mixed planktonic (2.7±0.3 cal ka BP; 4.2±0.3 cal ka BP; 5.3±0.4 cal ka BP) and three mixed benthic (7.3±0.7 cal ka BP; 8.8±0.7 cal ka BP; 10.1±0.8 cal ka BP) foraminifera samples (Supplementary Data 2), 210Pb excess activity from the uppermost part of the sediment core (Supplementary Data 3), and an upper age constraint for the surface of the sediment core corresponding to the year of retrieval (2021 CE) (Supplementary Fig. 8). The lower part of Melville Bay 26G (320-213 cm) was laminated with high magnetic susceptibility and we did not find sufficient microfossils for 14C dating in this part of the core (Supplementary Fig. 8). At 213 cm core depth, we noted a shift in the sedimentology from laminated to homogenous and a pronounced increase in the magnetic susceptibility, followed by a gradual decrease towards the surface of the core. Due to the observed shift in sedimentology and the absence of datable material in the lower part of the core, we extrapolated the age-depth model only up to the depth where the sedimentology changes (213 cm depth; 12.3±1.4 cal ka BP). The upper section of Melville Bay 26G (213–0 cm) was homogeneous with larger drop stones deposited throughout. Due to lower sedimentation rates in the uppermost part of the sediment core (14–0 cm), the temporal resolution of the past two thousand years is limited to two samples (Fig. 1). The age-depth model was constrained in the top of the sediment core to the year of retrieval (2021 CE). A modern age for the surface of the core is supported by the presence of detectable 210Pb excess activity in the uppermost centimeter of the core (Supplementary Data 3). Raw and calibrated 14C dates are listed in Supplementary Data 2 and Supplementary Fig. 8 shows an overview of the final chronology.

Hall Basin 24PC was positioned to re-core a site first sampled during the Petermann 2015 expedition of I/B Oden (OD1507-18GC58; 81.63°N, 62.30°W; 4.35 m long). The two coring sites are less than 450 m apart, and an integrated stratigraphy and age model for OD1507-18GC/Ryder19-24PC has been published58. The radiocarbon dates from OD1507-18GC (four 14C dates performed on monospecific aliquots of the benthic foraminifera Cassidulina neoteretis, and a single paired date of the planktic foraminifera Neogloboquadrina pachyderma) were migrated onto the depth scale of Hall Basin 24PC (Supplementary Fig. 9, Supplementary Data 4). The age-depth model was constrained by assuming the top of the sediment core corresponded to the year of collection (2019 CE), and a further age constraint was applied at the transition into the basal diamicton. Here we assigned an age of 8910±100 BP, based on the interpreted timing of the retreat of glacial ice from the Polaris Foreland region, near to where the core was collected59,60.

Hall Basin 24PC is composed of three major lithofacies (Supplementary Fig. 9 and S10). An upper bioturbated mud with clasts (0-134.5 cm) divided into an IRD-rich bioturbated mud (BI) (0–46 cm) and IRD-poor bioturbated mud (BM) (46-134.5 cm). The bioturbated muds are separated from an underlying laminated mud (LM) by an IRD-rich layer (I) (134.5-164.5 cm). The laminated mud (164.5-525 cm) transitions sharply into a structureless diamicton (Dm) (5.25-672.5 cm) interpreted as an ice-proximal facies58 (Supplementary Fig. 9).

Shotgun sequencing data
After quality-filtering the shotgun sequencing data, a total of 478–109,137 sequences per sample (median: 4548) were taxonomically assigned (Supplementary Data 1). Of these, 64–100% (median: 96%) were assigned to prokaryotes, which were excluded from further analysis. All ten blanks as well as five sediment samples did not contain any taxonomic assignments after quality-filtering. The resulting taxonomic profile contained only six eukaryotic families (or ten, if eukaryotic families detected in less than three samples are considered), as expected from the relatively shallow sequencing depth of 1.5±0.7 M raw sequences per sample. We refrained from deeper shotgun sequencing due to the high cost of data needed to exhaustively describe samples.

Our shotgun sequencing data revealed DNA of cod fishes (Gadidae) and pinnipeds (Phocidae) in all four sediment cores, and DNA of diatoms (Chaetoceraceae) in all cores except for North-East Greenland 73G (Supplementary Data 1, Supplementary Fig. 11–S13). Across sediment cores, we detected a higher number of eukaryotic families in samples >2 cal ka BP. Additionally, the number of sequences assigned to eukaryotes decreased from past to present, and across sediment cores, all five samples that did not contain any sequences assigned to eukaryotes fall in the most recent time period (<2 cal ka BP). We recorded low numbers of sequences assigned to cod fishes in the five Melville Bay 26G samples from the lower, laminated part of the sediment core (>213 cm; Supplementary Fig. 11).

Melville Bay
Using hybridization capture, we detected a total of ten different marine mammal species in the Melville Bay 26G record (Fig. 2e and S14). No DNA was assigned to marine mammals in the six samples from the lower, laminated part of the sediment core (>213 cm). The earliest detected marine mammal DNA was assigned to ringed seals (≥11.6–11 cal ka BP). Between 11.4−7.3 cal ka BP, we detected at least three different species in samples with marine mammal DNA. In a sample with estimated age 11.4±1.2 cal ka BP, we recorded the highest number of sequences assigned to one species (670 sequences assigned to harp seal). In a sample with estimated age 7.3±0.6 cal ka BP, we recorded DNA from eight different marine mammals (Fig. 2e). After 7 cal ka BP, we detected fewer species, especially 3–0 cal ka BP. Between 8–7 cal ka BP, we recorded fin whale DNA (north of the species’ current distribution range) and DNA of harp seal, beluga whale, minke whale, and orca; all of which only occur seasonally in the region today (Fig. 2e; Supplementary Data 5).

The fossil remains of foraminifera, single-celled protists that live in either the water column or at the seafloor, can be used to reconstruct paleoceanographic conditions49–53. For our analysis of Melville Bay 26G, we grouped the following foraminifera species to indicate influx of Atlantic-derived water masses indicative of relatively warmer and saltier sub-surface waters associated with the West Greenland Current36,61: the calcareous species Cassidulina neoteretis, Cassidulina reniforme, Islandiella norcrossi, and Pullenia osloensis, as well as the agglutinated species Adercotryma glomerata, Lagenammina difflugiformis, Reophax catella, Reophax pilulifer, and Reophax fusiformis. We recorded their absence or near-absence in the oldest samples (>11 cal ka BP), high counts from 10–5 cal ka BP and low counts in the Late Holocene (<5 cal ka BP) (Fig. 2c, and Supplementary Data 6).

Hall Basin and Lincoln Sea
The earliest detected marine mammal DNA in the Hall Basin 24PC record was assigned to ringed seals (7.2±0.1 cal ka BP) (Fig. 3e and S14). We detected narwhal and ringed seal using hybridization capture in all Hall Basin 24PC samples <5 cal ka BP, albeit with decreasing sequence abundance over time (Fig. 3e). Between 5 cal ka BP and 3 cal ka BP, we also recorded harp and hooded seal DNA, two species which have only recently been recorded this far north62. In addition, we detected beluga whale DNA at 2.4±0.0 cal ka BP, which has never been recorded this far north in present-day and historic surveys (Supplementary Data 5). The first detection of marine mammals (ringed seal) in the Lincoln Sea 12-GC record using hybridization capture is 8.4±0.1 cal ka BP, and ringed seal DNA is recorded in all but one younger sample (Fig. 3h). Narwhal DNA was first identified at 7.9±0.1 cal ka BP, and was detected in all but one younger sample, again with decreasing sequence abundance over time. We also detected DNA assigned to hooded seals in three samples (7.8±0.1, 7.1±0.1 & 1.8±0.1 cal ka BP), albeit only with a low number of sequences and low relative sequence abundance.

North-East Greenland
The hybridization capture data from the North-East Greenland 73G record revealed DNA of four endemic Arctic marine mammals (Fig. 4e and S14). We also retrieved DNA of harp seal (Fig. 4), which seasonally migrates northwards along the East Greenland coast (Supplementary Data 5). Most samples of this core are characterized by low numbers of DNA sequences (3–10 sequences per species per sample). For example, ringed seal DNA was detected throughout the core (13 out of 38 samples) but samples always contained <50 sequences. In a sample with estimated age 7.9±0.2 cal ka BP, narwhal DNA was first retrieved, but only samples <4.5 cal ka BP showed a continuous genetic signal of narwhals. DNA from harp seals was detected in samples >3 cal ka BP. The highest number of sequences (145 sequences) was assigned to bearded seals in the youngest sample (0.3±0.1 cal ka BP).

DNA detections in the context of changing paleoenvironmental conditions
The statistical analysis of our DNA detections in conjunction with reconstructed air temperatures, sea-ice biomarker IP25, primary productivity biomarkers brassicasterol and dinosterol, and foraminifera assemblages, revealed correlations between DNA detections and interpolated paleoenvironmental measurements, and identified air temperature and sea-ice algae productivity (IP25) as significant drivers of community change (Supplementary Fig. 15 and S16; Supplementary Data 7). Based on the pairwise Spearman’s rank correlation analysis, we found strong positive correlations between e.g., cod fishes and pinnipeds (rs = 0.8; p < 0.01), cod fishes and ringed seals (rs = 0.7; p < 0.01), cod fishes and interpolated air temperatures (rs = 0.6; p < 0.01), and priapulids (Priapulidae) and bowhead whales (rs = 0.7; p < 0.01) (Supplementary Fig. 15; Supplementary Data 7).

The redundancy analysis (RDA) of DNA data revealed air temperature and sea-ice algae productivity (IP25) to be significant explanatory variables (air temperature: F = 2.52; Pr(>F) = 0.04; IP25: F = 3.50; Pr(>F) = 0.02) albeit explaining only ~2% (air temperature) and ~3% (IP25) of the observed variance (Supplementary Fig. 17).

Methods
Permits and permissions
In compliance with the Biological Diversity Convention, the Nagoya Protocol and the Greenland Parliament Act No. 3 of 3rd June 2016, we obtained Prior Informed Consent licenses for the collection and use of genetic resources in West Greenland (non-exclusive licence no. G21-041 and G19-009) from the Ministry of Foreign Affairs, Business, Trade and Climate of Greenland. This includes an export permit for the genetic resources. For Northeast Greenland, we obtained permits to enter the National Park and conduct biological investigations from the Ministry of Nature and Environment of Greenland and the Ministry of Industry, Labor and Trade, respectively (permits no. C-17-61 and C-19-50) as well as permits from the Mineral Licence and Safety Authority for geological investigations (permit no: VU-00125) and for the collection and export of sediments (permit no: 129/2017). Further, a research survey permit to enter the Northeast Greenland National Park was provided by the Greenlandic/Danish authorities (Permits C-19-50 and JTHAV 2019-14122) and for Canadian waters, surveys operated under permit IGR-940.

Sediment cores
We analyzed four marine sediment cores in the present study, which were collected off the coasts of Northern Greenland (Fig. 1a). All cores were cut into 1 m sections onboard the research vessels upon retrieval, and stored at 4°C until subsampling for DNA was carried out. The four cores were collected during three expeditions:

Gravity core LK21-IC-st26-GC1 (75.319°N 61.910°W, 912 m water depth, 320 cm sediment recovery; hereafter Melville Bay 26G) was retrieved from the North-West Greenland shelf during the ICAROS Expedition onboard HDMS Lauge Koch in 2021. A chronology was constructed using a combination of 210Pb and 14C dating (Supplementary Fig. 8). The upper 10 cm were tested for 210Pb activity (Supplementary Data 3) using a Canberra ultralow-background Ge-detector using the Constant Rate of Supply (CRS) model109. The radiocarbon analysis was carried out using an accelerator mass spectrometer (AMS) mini carbon dating system (MICADAS) with gas targets110 on three mixed planktonic and three mixed benthic foraminifera samples (Supplementary Data 2). The age-depth model was modeled in R111 using a Bayesian accumulation model code (BACON)112 calibrated with Marine20113 and a local reservoir correction (ΔR) of -49±59 years114.

Piston core Ryder19-24-PC1 (81.622° N 62.296° W, 520 m water depth, 525 cm sediment recovery; hereafter Hall Basin 24PC) was retrieved from the North Greenland shelf during the Ryder 2019 Expedition onboard R/V Oden. It was taken at the same station (450 m away) as OD1507-18GC, which had been collected by R/V Oden during the Petermann 2015 expedition. The motivation for re-coring the site was two-fold; 1) to recover the basal diamict at this site, and 2) to collect fresh material for organic geochemical and sedimentary ancient DNA work. The radiocarbon dates from OD1507-8GC were migrated onto the depth scale of Hall Basin 24PC, after a common depth scale was constructed through the correlation of bulk density, magnetic susceptibility, and XRF-scanning data (Supplementary Fig. 9, Supplementary Data 4). The 14C ages of OD1507-8GC58 were calibrated using the Marine20 calibration curve113. We applied reservoir corrections of 270±80 years (planktic) and 510±90 years (benthic) consistent with previous chronologies in northern Nares Strait58,59, but subtracted 150 years from these to account for the differences between the Marine13 and Marine20 calibrations113 (Supplementary Data 4). The top of the basal diamict was assigned an estimated age of 8910±100 years BP, corresponding to the inferred ice margin location just north of the core site in the Polaris Foreland region60. This age estimate was inferred by England60 based on a regional compilation of radiocarbon dates of mollusc shells, and further validated by Jakobsson et al.59 through bathymetric mapping and sub-bottom profiling of Hall Basin. We note that the published ice limit was assigned an age of 8,500 BP60, but this was after a reservoir correction of 410 years had been subtracted. The final age model (Supplementary Fig. 10) was generated using OxCal115. It displays a marked reduction in sedimentation rates after the transition from the laminated to the bioturbated mud units (BI and BM) consistent with the reduction in sedimentation rates through the Mid-to-Late Holocene in marine records from this region58. The age for the base of the bioturbated muds is consistent with other records from the Hall Basin58.

Gravity core Ryder19-12-GC1 (82.578° N 52.528° W, 867 m water depth, 273.5 cm sediment recovery; hereafter Lincoln Sea 12-GC) was also retrieved during the Ryder 2019 Expedition and an age-depth model (Supplementary Fig. 6) and a paleoceanographic reconstruction based on sterols has been published56.

Gravity core DA17-NG-ST07-073G (79.068° N 11.903° W, 385 m water depth, 410 cm sediment recovery; hereafter North-East Greenland 73G) was retrieved from the North-East Greenland shelf during the North Green Expedition onboard R/V Dana in 2017. An age-depth model (Supplementary Fig. 7) and a paleoceanographic reconstruction based on foraminiferal assemblages has been published57.

Subsampling of cores for sedaDNA analysis
The subsampling of Melville Bay 26G and North-East Greenland 73G was carried out at the Globe Institute, University of Copenhagen, whereas subsampling of Hall Basin 24PC and Lincoln Sea 12-GC was carried out at the Center for Paleogenetics, University of Stockholm. In both events, a designated clean sub-sampling laboratory was used that is physically isolated from the molecular biology laboratories. All working surfaces and equipment used during the subsampling were soaked in bleach and subsequently cleaned with ethanol. All people involved in the subsampling process wore appropriate protective clothing, including lab coveralls, two layers of gloves, surgical face masks, and sleeves. We regularly changed gloves and used 5% bleach followed by ethanol to avoid contamination. Initially, each core section was split into one working half and one archive half. We carefully removed a thin layer of sediment (~0.2 cm) using sterile plastic cards first and another thin layer using sterile single-use scalpels just before the actual subsampling of the working half was performed. We subsampled using sterile 3 mL plastic syringes, and samples were immediately frozen to avoid further DNA degradation.

Extraction and library preparation
All pre-PCR laboratory work was performed at the ancient DNA clean lab facilities at the Globe Institute, University of Copenhagen, where strict precautions are taken to avoid contamination116,117. A subset of samples was processed using the semi-automated ancient environmental DNA pipeline operated by the GeoGenetics Sequencing Core facility at the Globe Institute. For these samples, 0.35 g of sediment were subsampled and extracted using the Qiagen® MagAttract® Power Soil Pro kit, with modifications118. After extractions, DNA concentrations were quantified by qPCR and a fixed number of cycles for the library build was determined (17 cycles). The libraries were prepared following the double-stranded protocol119 and unique 10-base pair motifs were used for double-indexing. The amplified libraries were purified and size selected with magnetic beads (MagBioGenomics), targeting 60-600 base pairs (bp; with a 1.6x ratio) and fragment lengths and concentrations were determined using a Fragment Analyzer (Agilent Technologies).

The remaining samples were processed manually using the Qiagen DNeasy® PowerSoil® Pro Kit following the product protocol with minor modifications: an input weight of 0.5–1.0 g sediment was used. We added 25 µL of DTT (Thermo Scientific™; 1 M) and 25 µL of prot K (Sigma-Aldrich®; 2 mg mL⁻¹) to the bead tube containing the beads and sediment sample. The vortex step was performed using a FastPrep-24™ 5G with 2×20 s (4 m s⁻¹). Samples were incubated for ~24 h at 56°C. In the last step of the protocol, 35 µL of elution buffer was added followed by a 5-min incubation. This step was performed twice to yield a total extract volume of 70 µL.

Single stranded libraries were prepared from 1-14 ng of DNA (as determined by Qubit dsDNA HS assay; Thermo Scientific™) following the Santa Cruz Reaction protocol120. For the indexing, two unique 6-bp motifs were used for each library, to minimize the risk of cross-contamination during pooling for sequencing. Blanks were included in both workflows to investigate potential contamination. For shotgun sequencing, indexed libraries were pooled equimolarly (except for blanks which were included with 10% molarity) and sequenced by NovoGene UK on an Illumina NovaSeq 6000 platform.

Hybridization capture
Shotgun sequencing revealed a low number of mammalian sequences, thus we applied hybridization capture to enrich libraries specifically for mitochondrial DNA derived from marine mammals occurring in Greenland seasonally, as well as year-round (Supplementary Data 5 & 9). In preparation of the panel design, which was conducted in collaboration with Daicel Arbor Biosciences myBaits®, the first 80 nucleotides of each mitogenome were added to the end of each mitogenome sequence of interest. Next, runs of ambiguous nucleotides were changed to thymine nucleotides. Finally, to account for the circularity of mitochondrial genomes, a 4x tiling with 80 nt baits was achieved by starting a new bait every 20 nt, resulting in 10,254 unique baits.

The hybridization capture panel used in this study was originally designed for the retrieval of mitochondrial DNA from macrofossils, and therefore includes several species for which we did not expect to find DNA in marine sediments (e.g., polar bears, Ursus maritimus, which mostly live on sea ice and occur in low densities). At the same time, the panel did not include species occurring along the coasts of Greenland in large numbers (e.g., harp seals). However, by lowering the hybridization temperature to 55°C, we could facilitate the retrieval of DNA from closely related species with up to 25% genetic divergence (myBaits® User Manual (v 5.02)), while also accommodating for the expected DNA damage of marine sedimentary ancient DNA47.

We followed the “High Sensitivity” protocol of the myBaits® User Manual (v 5.02) with the following additional modifications: the input mass of each indexed library into each capture reaction was 154 ng. Generally, higher inputs are possible (up to 12 μg per enrichment reaction) but we standardized the input mass to account for libraries with lower DNA concentrations across our sample set. The input volume of baits and water in the hybridization mix was adjusted to 1.1 μL and 4.4 μL, respectively. One round of capture was performed.

We repeated the lab procedure (DNA extraction, library preparation, hybridization capture, and sequencing) for 22 samples to validate the reproducibility of marine mammal detections even with low numbers of DNA sequencing reads. After confirming high overlap of species detections across samples (Supplementary Data 10), we merged the sequencing data of samples deriving from the same depth in the sediment and core after collapsing sequencing pairs and removing sequencing adapters.

Bioinformatic Analysis
Shotgun sequencing. Raw sequencing data were processed using leeHom121 to trim adapters and merge sequencing reads. Merged sequences were complexity-filtered, sequences shorter than 30 bp were discarded and exact duplicates and homopolymers were removed using sga122. For taxonomic assignment of the shotgun sequencing data, a reference index was constructed from the non-redundant NCBI nucleotide database (downloaded on 1st December 2023), the full NCBI RefSeq database (release 213), and a compilation of Arctic plant and animal genomes45. Filtered sequences were taxonomically assigned using bowtie2123 and alignment files were compressed using compressbam of the metaDMG124 suite.

The compressed files were parsed to metaDMG124, which was used to filter alignments using a lowest-common-ancestor approach with a 95% sequence similarity threshold and to assess DNA damage. All downstream visualizations were performed in R111. The taxonomic assignments of the shotgun sequencing data were additionally filtered by a minimum of 10 sequences per taxon and for Fig. S7-S9, only taxa present in at least 2 samples across each core were visualized (for the full list of DNA detections, please refer to Supplementary Data 1). Furthermore, we excluded all taxonomic assignments to prokaryotes, thus only retaining detections of eukaryotes. We calculated relative sequence abundances for each taxon per sample by dividing the number of unique sequences by the number of quality-filtered read pairs, thus providing a representation of the sequencing effort and library complexity.

Using the metaDMG output files, we extracted nucleotide deamination rates, and calculated the mean value across the last three nucleotide bases of both 3’ and 5’ ends of each DNA sequence. For all eukaryotic sequences, we visualized these mean values to provide a representation of DNA damage across sample ages and sediment cores (Supplementary Fig. 1a-d).

Mitochondrial capture. The raw mitochondrial capture sequencing data were processed in the same manner as the shotgun sequencing data, with the following modifications: for taxonomic assignments, a reference database was constructed using all complete vertebrate mitochondrial genomes and the complete refseq database of mitochondrial sequences (downloaded from the NCBI databases on 17th Oct. 2023). To reduce the size of the resulting collection of reference sequences, we retained only one Homo sapiens mitochondrial genome in our database. After the taxonomic assignment, an additional duplicate removal step was included, where sequences with the same start and end position were removed using samtools125.

We also performed an analysis of sequence similarity on mitochondrial genomes to establish a sequence similarity threshold appropriate for the observed genetic divergence within the target group of Arctic marine mammals (Supplementary Fig. 17). Using a low sequence similarity threshold (e.g., 95%) as part of the lowest-common ancestor inference for a target group with moderate genetic divergence between species (interspecific variation) and low genetic divergence within the same species (intraspecific variation) may underestimate the number of detected species, as sequences are classified on a higher taxonomic level (e.g., genus or family). In the same scenario, a high sequence similarity threshold (e.g., 100%) may overestimate the number of detected species based on single nucleotide mismatches deriving from sequencing errors or DNA damage126. Specifically, we downloaded all publicly available mitochondrial genomes belonging to the subfamilies Phocinae, Balaenidae and Monodontidae (downloaded from the NCBI on 25th Mar. 2024). After aligning and trimming the genomes, we generated thousands of sequence fragments of 50 bp length from each genome. We calculated pairwise sequence similarities between the simulated fragments of mitochondrial genomes within the same species and between species. Within species, we observed that for any pair of mitochondrial genomes, 95% of the 50’mers showed sequence similarities between 98-100% whereas only 5% showed sequence similarities below 98% (Supplementary Fig. 17). In contrast, between species of the same subfamily, we observed that for any pair of mitochondrial genomes, only 10% of the 50’mers showed sequence similarities above 98%, whereas 26% showed sequence similarities between 95–98%, and 64% showed sequence similarities below 95% (Supplementary Fig. 17). We thus argue that a 2% threshold is appropriate for our taxonomic target group, to accommodate for the observed high sequence similarity within species and moderate sequence similarity between species.

The resulting taxonomic assignments were filtered using a minimum of 3 unique sequences per taxa and for Figs. 2–4, only species-level marine mammal detections were visualized (for the full list of DNA detections, please refer to Supplementary Data 11). We derived mean nucleotide deamination rates for DNA sequences retrieved through hybridization capture as described for the metagenomic shotgun sequencing data, and included them in Supplementary Fig. 1. In addition, we binned the hybridization capture sequencing data by estimated age windows of 3000 years, and used euka127 on the resulting files to analyze DNA deamination rates, fragment length distributions and coverage across the mitochondrial genome. We identified two taxa (Odontoceti & Phocidae) and visualized the respective DNA characteristics for all DNA sequences assigned to the taxonomic family Phocidae, as it yielded the highest number of sequences across binned samples and cores (Supplementary Fig. 2-5).

Paleoenvironmental and paleoclimatic data for comparison
Published records. For comparison of our DNA data on marine mammal distributions, we compiled existing records on surface and bottom/subsurface water conditions at each study site. Paleoceanographic proxy data was retrieved from the literature for the same cores when available, or else from published records in proximity to the cores.

For Melville Bay 26G, measurements of sea-ice biomarker IP25 (indicative of sea-ice algae productivity), brassica- and dinosterol (indicative of primary productivity) were compiled from a nearby marine sediment core (GeoB19927-3)76.

For Hall Basin 24PC and Lincoln Sea 12-GC, a Holocene air temperature reconstruction from the Agassiz ice cap29 and IP25 as well as brassicasterol measurements from Lincoln Sea 12-GC56 were compiled. In addition, trends in δ13C values of the benthic foraminifera Cassidulina neoteretis and abundance of the benthic foraminifera Nonionellina iridea – indicative of the opening of Nares Strait – were compiled from HLY03-01-05GC51.

For North-East Greenland 73G, measurements of IP25, brassica- and dinosterol were retrieved from PS93/025-299. Furthermore, we included the abundance of the two benthic foraminifera Cassidulina neoteretis and Pullenia bulloides – indicative of relatively warm, saline Atlantic water – previously published for North-East Greenland 73G57.

Analysis of foraminifera assemblage (Melville Bay 26G). For Melville Bay 26G, no foraminiferal data existed and we carried out the analyzes for this study: ~four grams of sediment per sample depth (each sample representing 1 cm of the core) were washed and wet-sieved using a 63 μm sieve. Next, all constituents >63 μm were left in foraminifera storage solution (prepared using 300 ml of ethanol (96%), 700 ml of distilled water, and 1.5 grams of sodium carbonate) for ca. 30–40 minutes to dissolve any cohesive clay clusters that remained after sieving. Afterwards, all samples were washed once more with the foraminiferal storage solution before the foraminiferal assemblage was analyzed using an Olympus stereomicroscope. The following foraminifera species were grouped to indicate influx of chilled Atlantic Water associated with the West Greenland Current36,61: the calcareous species Cassidulina neoteretis, Cassidulina reniforme, Islandiella norcrossi and Pullenia osloensis, as well as the agglutinated species Adercotryma glomerata, Lagenammina difflugiformis, Reophax catella, Reophax pilulifer, and Reophax fusiformis.

Statistical analysis
We performed a statistical analysis on the association between DNA detections and available paleoclimatic data (Figs. 2a–c, 3a and 4a–c) using correlation analyzes and redundancy analysis (RDA) in R111. First, we approximated air temperature anomaly, IP25, foraminifera abundance, brassica- & dinosterol measurements for each estimated sample age using linear interpolation, and standardized all interpolated values to have a mean of zero and a standard deviation of 1. We then calculated pairwise Spearman’s rank correlation coefficients for all species-level detections (derived from hybridization capture), family-level detections (derived from shotgun sequencing) and interpolated paleoenvironmental and paleoclimatic measurements. The resulting correlation matrix was filtered for significant (p < 0.05) correlations (Supplementary Fig. 15; Supplementary Data 7).

In addition, we performed a Redundancy Analysis (RDA) on our data to estimate the contribution of each interpolated proxy measurement to explaining the diversity of the species-level detections based on hybridization capture, and family-level detections based on shotgun sequencing. The significance of the estimated contribution was evaluated using an ANOVA-like permutation test (Supplementary Fig. 16).

All published radiocarbon dates of marine mammal fossils were calibrated in R111 using Marine20113 and region-specific reservoir corrections (Supplementary Data 8).

Peer review rounds
[{"round": 1, "reviewer_comments": {"reviewer_1": "The paper is about the distribution of marine mammals in northern Greenland during the Holocene. To this end, sediment\ncores from four different locations were examined and the occurrence of various species was detected using aDNA analysis.\nIn addition, further environmental information from proxy investigations of the same sediments was used to link the\ndistribution of the animals with the prevailing environmental conditions. The result significantly expands our previous\nknowledge of the animals' distribution, as the fossil record from coastal sites is patchy. I consider this work to be highly\nrelevant and innovative because it combines biological techniques and geological archives and research questions.\nFor this review the focus is on the chronologies of the sediment records.\nThe age-depth models of the four cores are based on radiocarbon ages. Two of the models were taken from existing\npublications, one was created by correlation with a dated core, and the other was generated using newly obtained 14C\nages.\nThe age models differ in their data basis (number of age constraints) and the cores differ in their temporal resolution.\nAt this point, I highlight the core from Hall Basin, whose age model seems to be the weakest. Therefore, it is important to\nprovide a comprehensive description of the approach and to give a detailed discussion on the limitations of the age-depth\nmodel of the core. This is not properly elaborated in the manuscript at the moment and should be added/modified. Although\nthe correlation to a dated neighboring core is plausible, there is no dating for the base of the core, whose age is only\nestimated. This should be explained in more detail at some point. Furthermore, the last c. 7000 years seem to be very\ncondensed in the record, or it could also be that the core is incomplete. The difficulty in estimating the age of this core (and of\nsediment cores from polar regions in general) cannot be avoided, but it must be explained more clearly and taken into\naccount when interpreting the aDNA and other proxy data in terms of “age”. I think, this is widely taken into account in the\ndiscussion, but it is not worked out clearly enough in the results/methods. More detailed comments and specific suggestions\nare given in the commented version of the main text and the supplement that I provide with this review.", "reviewer_2": "This paper uses shotgun sequencing and hybridization capture to identify marine mammals from 4 cores around the\nnorthern shelf edges of the Greenland ice-sheet and land-mass. The results do indeed provide both a remarkable marine\npalaeo-record and also provide novel insights into the Lateglacial-Holocene dynamics of the Arctic and north Atlantic ocean\nsystems around Greenland. This research area is critically important for studying future changes in these currents and their\neffects on marine resources in the face of climate change. This paper is also important in two other respects; firstly, it is one\nof very few and first long-term sedaDNA studies of marine systems and secondly it integrates marine mammals with other\nproxies, in this case forams. The methodology is sound and my only significant criticisms revolve around some more\ntransåparency of the data sources and some improvement in clarity of discussion. Major points for the authors consideration:\n1. The damage patterns from the shotgun sequencing - are both quite low for their age and also show considerable scatter\nwith a weak relationship to depth/age.. a bit more mention or discussion of this would be an improvement --and since these\nare means - on how many sequences are they based and could this be added to the diagram (there are some different ways\nof showing this data).\n2. The dating is critical and not too bad for most of the cores but there are problems e.g. Hall Basin has a top problem - and it\neffects the 'timing' of the detections - what happens to the narrative if the upper 4 samples are all clustered between c. 7 ka\nand 4 ka as might be the case if this is an eroding site?\n3. Shotgun.. was it not possible to take the eukaryote families such as Phocidae using standard reference libraries? if not\nwhy not? Any fragment length data?\n4. This leads to the question of the sedimentological environment of each cores (not just depth and location) - Lincoln Sea\ncore seems off the mouth of a fjord system. If not space in this paper can the reader be directed to papers on these cores if\nthey exist (which is not clear).\n5. It is as clear from the above what has been done on these cores before and what for this study?\n6. Figs - whilst OK - it would be vary much better to try and combine the hybridization capture DNA records records together\nso the reader can see how the changes in the text effect the whole system?\nSince the word count is over 2000 I think you can have more than 4 figures - I think the paper warrents at least 6 figures..\n7. The discussion pages 9-17 seems a bit rambling and would be really helped also by a figure as suggested above.\n8. The discussion on detection and preservation is a bit weak - what mineralogy of the sediments and did this vary - it is not\nclear from the data and this refers back to the sedimentology and sediment inputs.\n9. Lastly, a new proxy is mentioned - IP25 of algal productivity - and although a reference given this needs more explanation\nhere.\nThe manuscript is clean and well written.", "reviewer_3": "This work presents an overview of ~12 thousand years of marine mammal habitation in northern Greenland. It notes the\nappearance of some taxa in the sedaDNA record much earlier than the palaeontological record. The authors also try to draw\ninferences on the abundance (or lack thereof) of certain taxa across this time period. The results are interesting, and I have\nno large problems with the methodology (at least as it pertains to the ancient DNA – I cannot speak to the core age\nmodeling), and again serve to highlight the usefulness of sedaDNA as a complement to traditional palaeontological\nanalyses.\nI think the authors do a good job with the interpretation of their results when it comes to the identification of which taxa are\npresent, and this is where I think the paper is strongest. However, I feel the argument suffers a bit when attempting to draw\nconclusions based on the absence of species, particularly when the presence of those taxa in identified bins is also quite\nlow. This is most problematic in the discussion section titled “Episodic marine mammal detections in north-east Greenland\nover the past 10 ka”, for which I’ve detailed my concerns below.\nI’m not entirely sure I’m seeing the link the authors want me to see between harp seal presence/absence and primary\nproductivity. While I again don’t question the detection of taxa from this core, the authors also mention that the detection is\nquite poor (<10 reads). However, to elucidate a pattern of appearance/disappearance requires that periods of presence and\nabsence are strongly separated, and when the presences are so weak it leads doubt to whether something is truly there and\nnot being detected or actually absent. I suspect part of this is due to the extraction kits the authors chose to use – the\nPowerSoil kits have poor DNA recovery for ancient remains, although they generally manage to capture most of the most\nabundant taxa; see for example the comparison in Murchie et al. (2020; https://doi.org/10.1017/qua.2020.59). I would\nrecommend swapping to a more sensitive extraction methodology for future work.\nI’m also not entirely sure I’m correlating the shifts within the graphs in Fig. 4A and B with the harp seal abundance. Part of\nthis may be my own unfamiliarity with benchmarks for these metrics (i.e. are there certain thresholds below which hard seals\nare never found?), but I’m not sure I see meaningfully different levels when harp seals are present or not. For example, the\nharp seal signature ends at ~ 7 ka BP right when 4B appears to show a local maxima, and levels similar to when harp seals\nare present continue for ~1.5 ky after they disappear. I think this section needs some caveats but would also benefit with\nbetter explanations that guide the reader through the correlations, especially as this journal has a broad scope.\nAdditional points:\n- Line 131: I had a hard time linking samples/cores back to the Data Tables. For example, I’m wondering why data table 2\nonly has 66 libraries instead of the 109 mentioned here.\n- Line 155 and Fig. S1: I don’t quite understand what exactly is being shown in Fig. S1 and/or what the authors are trying to\nconvey displaying the data this way. The main text appears to indicate the deamination patterns are split by taxa, but it is not\ndiscernable which taxa is which (or why this might be relevant) from the figure. I would at least supplement this with one\nmore supplementary figure showing the mapped data for their key taxa (lumping across time points if necessary) and\nrunning it through MapDamage 2.0 to produce full deamination plots. I think a sentence or two in the methods explaining\nhow exactly the deamination of these final 3bp was calculated wouldn’t be remiss.\n- Line 188: It is unclear to me how these numbers relate to Data Table 1. For example, the first library eDNALib006_050 has\nmore than the upper limit mentioned here at 8133 reads assigned across Prokaryota and Eukaryota. The average for the\nlibraries is also higher.\n- Line 189: Also, not sure as to the source of these numbers. The lowest amount assigned to prokaryotes appears to be 64%\nin eDNALib006_016. I suspect this may be a relic from an earlier analysis?\n- Line 215: Why is this window so broad? The sample ages spanning for most whales don’t appear to produce such a large\nwindow. And if it’s to include the seals harp seals (listed in this sentence), they appear to be detected from samples ~1 ka\nBP.\n- Line 231: There should be a figure callout here as this starts a new section.\n- Line 235: I’m having difficulty linking the cores and samples mentioned here to ones in the Data Tables. It would be great if\nthey could have the same name. I believe the two for this are the ones labelled Ryder19_12_GC and Ryder19_24_PC.\n- Line 247: This should specifically reference Fig. 4E.\n- Line 275: I’m not sure the evidence for this claim comes across super strong by this point in the paper. It would be better\nremoving this or moving it to the conclusion.\n- Line 327: Latitude limits are mentioned here and in other parts of the paper. If not too much work (depending on how the\nmap was made) it might be worth adding latitude lines to the Greenland blow-up in Fig. 1.\n- Line 413: This shouldn’t be capitalized as I assume this is not referring to the time period known as the Late Pleistocene\n(the last interglacial to the end of the Pleistocene), but instead the end of the Pleistocene. Maybe rephrase to something like\n“Towards the end of the Pleistocene …”\n- Line 532: This sentence serves no purpose and should be excluded. Or it needs to be caveated with why northernmost is a\nmeaningful/interesting metric in the same way as oldest might be.\n- Line 681: This should specify that you are removing mapped sequences as the previous sentences are about your\nreference database construction.\n- Line 766: Raw sequencing data should always be uploaded to NCBI to allow for reanalysis in the future as better\nbioinformatic tools and reference databases become available."}, "author_response": "Response: We now provide a much more comprehensive description of the age model for the Hall\nBasin core and how it was derived (L601-621). This includes how the age for the transition into the\nbasal diamict was derived – which is consistent with previous work on this site (Jakobsson et al.,\n2018, Jennings et al., 2022). An important fact that we now explicitly highlight in the manuscript is\nthat the drop in sedimentation rates for samples younger than 8-7 ka is not something unique to\nRyder19-24PC. In fact this same pattern is seen across the Nares Strait and Hall Basin, as illustrated\nby Jennings et al., 2022, and north of the Robeson Channel in the Lincoln Sea (Detlef et al., 2023).\nThere are no indications of hiatus in the core, and the changes in sedimentation rate are linked to\nchanges in ice shelf sedimentation processes. With regards to our earliest DNA detections it is\nimportant to highlight that all marine mammal detections were found in the sediment layers above\nthe deepest radiocarbon age, so our ecological inferences are not affected by the estimated age for\nthe top of the diamict.\nSpecific comments:\n1. x-Axes labelling: Please use Age (cal ka BP). Ka = kilo year\nResponse: We have adjusted the x-axes labelling for all figures generated for this study to\n‘Age (cal ka BP)’ as suggested.\n2. Species names in panel b in italics; Note formatting in panel b: 13 superscript\nResponse: We have changed the font to italics for latin species names and adjusted the\nspelling of δ13C as suggested.\n3. What is the age range you found? Give reference to the 14C data table and mention results\nin text.\nResponse: We have added a reference to the 14C data table (Table S2) and mention the\ncalibrated radiocarbon dates in the text (L167-169).\n4. What did you use as an age constraint?\nResponse: We have added information on the upper age constraint (year = 2021 CE), which\nrelates the surface of the sediment core to the year of retrieval; the core was collected in\n2021 (L171).\n5. Add to which age this depth corresponds\nResponse: We have added the calibrated age of the depth where the sedimentology\nchanges: 213 cm depth corresponds to 12.3 ± 1.4 cal ka BP (L179).\n6. Add reference to Figure S4 and Table S2 and S1 (presumably)\nResponse: Done.\n7. Give core ID in table caption\nResponse: Done.\n8. Please check the axis labelling: probably “cal yr BP” and not “cal ka BP”?\nResponse: The x-axis title did not match the x-axis labels in the previous version of Fig. S10.\nIn the new version of the figure, the x-axis title and x-axis labels match.\n9. Please report original 14 age (as given in the publication by Bennike et al 1989) and calibrate\nthe age. Calibration should be performed with marine20 and with and appropriate DR.\nResponse: We have created a new table in the supplement (Table S7), where we present the\noriginal fossil 14C ages, reservoir offsets, and newly calibrated ages (using Marine20).\n10. This is a description of the method and not of the results. It is important to know how many\nage tiepoints were used, what ages they have and what the age model looks like. For\nexample, the mid and late Holocene is not well resolved in this core either. The last dating\npoint is 6900 cal yr BP. Was it also ensured for this core that the core top is the modern\nsediment surface and therefore a low sedimentation rate can be assumed, or is it possible\nthat parts of the core are missing? Please add these aspects to the description. It is\nimportant for the discussion to point out the weaknesses of the age assignment in this\nrecord.\nResponse: As further detailed above, we have revised the age model for the Hall Basin core\nand provided a more comprehensive description in the Methods section (L601-621). We\nhave also revised the respective description in the Results section, including the same details\nand structure as for the Melville Bay core (L187-205). Reduced sedimentation rates younger\nthan 8-7 ka are a robust feature in all records from the Nares Strait region. And thus, we do\nnot think that this site suffers from local erosion. We agree that this adds some uncertainty\nto the exact timing of events in the Mid-to-Late Holocene for samples with estimated ages\nyounger than the oldest radiocarbon date (6.9 ± 0.1 cal ka BP). Therefore, our discussion of\nmarine mammal detections for both Hall Basin 24PC and Lincoln Sea 12-GC focuses mainly\non the earliest detection of marine mammals in the region (L439-484).\n11. Why did you use marine13 and not marine20 (as for the core from Melville Bay)?\nResponse: We have changed this now and re-calibrated all ages using Marine20. Originally,\nwe adopted the reported dates from Jennings et al., 2022 – and simply wanted to be\nconsistent. After a required adjustment to the local reservoir correction (subtracting 150\nyears to translate dR13 to dR20) we generated a new age model using OxCal. There is very\nlittle difference between these age models, except for a 400-year difference at the base of\nthe sequence, where the calibrated age for the top of the diamict is now younger (see Figure\n1 below). The reason for this difference is that in the original submission we assumed a basal\nage of 9600 cal yrs BP, which was based on the calibrated age (using Marine 13) for the ice\nmargin retreat provided by Jakobsson et al. 2018. However, this was the oldest estimate\nthey reported and was derived by assuming no reservoir correction. In our revised Hall Basin\n24PC chronology, the uncalibrated age for the ice margin retreat is basically the same as for\nthe deepest benthic radiocarbon date in the record. It is apparent that the laminated\nsediments were very rapidly deposited. Without direct age constraints, the exact timing for\nthe deposition of the laminated sequence remains uncertain. However, this part of the core\ndid not contain any positive reads for marine mammal DNA and thus it doesn’t impact the\nenvironmental interpretations of this manuscript.\nFigure 1. Comparison of the age model used in our first submission and the revision, after we\nhave addressed the reviewer’s request to update the calibration (and hence the dR) using\nMarine20, and adjusting the age for the top of the diamicton.\n12. Why do you use a value of 510 years for DR? It is much higher than values reported for\nnorthern Greenland (DOI:10.5194/gchron-5-451-2023) Please add some discussion on this.\nResponse: A dR of 510 years for benthics (using Marine 13) is consistent with recent\nliterature for other marine sediment cores from Hall Basin\n(doi.org/10.1016/j.quascirev.2022.107460). We have adjusted the dR for calibration with\nMarine20 (L607-610).\n13. Explain briefly why you set the onset of marine deposition at this location to 9600 years BP\nResponse: We have added this explanation to the text (L610-616).\n14. Why do you use clam for this core and BACON for the other?\nResponse: There was no particular reason. We have now used OxCal to model the\nages, so all reported models are based on Bayesian statistics. .\n15. Please structure the section in the same way as for the Melville Bay core: number of 14C\nages, number and definition of age constraints other than 14C ages, which calibration did\nyou use and which DR.\nResponse: Thank you, we have re-structured the respective section according to this\nsuggestion (L187-205).\n16. The age estimate of the base of the record is not derived from 14C age (as indicated in data\ntable 4) and should differ graphically from the calibrated 14C ages.\nResponse: We have updated the chronology of Hall Basin 24PC (Fig. S10) and the age\nestimate of the base of the record now differs graphically from the 14C ages.\n17. I think the presentation of the age ranges for each sample is a good idea. However, the way\nit is presented is unsuitable for the upper part of the Hall Basin core. The bars suggest that\nthe age assessment for the sample points is very precise, but in fact it is purely speculative.\nResponse: We have argued that the low sedimentation rates between the uppermost\nradiocarbon date at Hall Basin 24PC (circa 6900 14C years) and the surface of the core\n(about 4.3 cm/ka) is very much consistent with other records from the Hall Basin and Lincoln\nSea (i.e the region around the Nares Strait). We do not think there is evidence for local on-\ndeposition here. We accept that there is uncertainty beyond the reported calibration and\nmodelling uncertainties, however this is true for all age models. We can arbitrarily increase\nthe uncertainty by changing the potential error of the reservoir correction - but our\njustification for not doing this is to remain consistent with previous work in the area (e.g.\nJakobsson et al. 2018; Jennings et al. 2022; Detlef et al. 2023) .\n18. Reporting of 14C ages: Give F14C values and apply rounding convention of reported 14C\nages. What is meant by “modeled ages”- if you refer to calibration, please use the terms 14C\nages and calibrated ages instead.\nResponse: We have updated Table S2 by adding F14C values in a new column,\nrounded ages to the closest decade, and adjusted the table legend as suggested.\n19. This interpretation should be made with caution: the oldest foraminifer age obtained from\nthe core is 9.3-10.9 ka, so it can be stated that the first occurrence of marine mammal DNA\npre-dates this. Is it plausible to expect the presence of marine mammals at this site prior to\nice sheet retreat?\nResponse: We have adjusted the reporting of the estimated age of this particular sample to\nbe ≥11.6 - 11.0 cal ka BP (L231). This is more consistent with our interpretation that samples\nof this core with depths ≥213 cm were likely deposited at or just prior to 11.6 ka BP. While\nthere is no further age constraint for these samples, we cannot exclude the possibility of\nmarine mammal DNA deposition in the sediment under a marine-based ice shelf, prior to the\nice-sheet retreat recorded on land.\nResponse: We have added four new figures to the supplement (Fig. S2 - S5) showing damage\npatterns for DNA sequences assigned to Phocidae (seals) across the four marine sediment cores,\nincluding fragment length distributions and coverage estimates (L778).\nResponse: This is a fair observation that we have addressed in the revised manuscript (L601-621).\nWe have better described how the age model for this core was constructed and added a facies\ninterpretation to go along with the correlation of physical and chemical proxies (MSCL and XRF). An\nimportant fact that we now highlight in the manuscript is that the reduction in sedimentation rates\nyounger than 8-7 ka is not something unique to Ryder19-24PC. In fact this same pattern is seen\nacross the Nares Strait and Hall Basin, as illustrated by Jennings et al., 2022, and north of the\nRobeson Channel in the Lincoln Sea (Detlef et al., 2023). There is no reason to assume that this core\nsuffers from erosion of near-surface sediments.\nResponse: Using shallow shotgun sequencing, we anticipated not recovering the complete\neukaryote community (L212-216). We refrained from deeper shotgun sequencing due to the high\ncosts of generating enough data for recovering rare DNA sequences (as expected for marine\nmammal DNA). We have added fragment length data (Fig. S2 - S5) for the hybridization capture data\nassigned to Phocidae.\nResponse: We have now carefully checked, and all relevant papers are referenced for the cores (L\n586-630; L785-796). For Melville Bay 26G, a detailed description of the sedimentological\nenvironment is currently being prepared for submission. For Lincoln Sea 12GC, we added a\npreviously missing reference (Cronin et al. 2022) describing the oceanographic conditions and glacial\nhistory of Southern Lincoln Sea (L452).\nResponse: In the methods, we include a section titled “Paleoenvironmental and paleoclimatic data\nfor comparison”. This section provides details on previously published paleoenvironmental data\nfrom the same or nearby sediment cores and newly generated data as part of this study (L785-796).\nResponse: We now include a figure where the hybridization capture data are presented for each\nmarine mammal species, across cores (Fig S14). It is in the SI, to avoid presenting the same findings\ntwice in the main text.\nResponse: We have added the requested figure to the SI, which we hope will aid the reader. We\nhave revised sections of the discussion to make it more succinct (L508-525). However, there are so\nmany exciting findings and inferences to highlight, that the discussion still has some length.\nResponse: We acknowledge the reviewer’s point. This is an emerging field within sedaDNA studies\nand we have initiated XRD (X-ray diffraction) analyses of marine sediments from the region for\nanother ongoing study where we aim to reconstruct the entire ecosystem going further back in time.\nHowever, a detailed mineralogical analysis of these Holocene records is beyond the scope of this\nstudy, where we followed a targeted approach (hybridization capture of marine mammals).\nResponse: We have included an explanation on the use of IP25 in the context of paleoceanographic\nreconstructions (L366-368).\nResponse: We renamed this section of the discussion (L502) and toned down the interpretations,\nespecially the correlation of sparse detections with paleoceanographic reconstructions (L508-525).\nThe discussion now focuses more on broad detection patterns and acknowledges the overall sparsity\nof marine mammal DNA in this record. We will consider using an alternative, more efficient\nextraction protocol for future laboratory work on marine sediment cores.\nResponse: We revised this section of the discussion (L508-525) as described for the previous\ncomment.\nResponse: The data tables in our original submission only contained samples and taxonomic\nassignments containing at least 3 unique sequences (hybridization capture) or 10 unique sequences\n(shotgun sequencing). We have revised the tables containing the taxonomic assignments of shotgun\nsequencing and hybridization capture. Table S1 (shotgun sequencing) contains all 55 samples & ten\nblanks; Table S9 (hybridization capture) now contains all 116 samples, and 25 blanks.\nResponse: We have added four new figures to the supplement (Fig. S2 - S5) showing damage\npatterns for DNA sequences assigned to Phocidae across the four marine sediment cores,\nincluding fragment length distributions and coverage estimates (L778). We have also added a more detailed\ndescription about the data underlying Fig. S1 in the methods section (L769-778).\nResponse: The reason for the mismatch between the numbers in the main text and the numbers in\nthe table stems from the table only listing taxonomic assignments above the threshold of 10 reads,\nwhile the numbers in the text were based on all taxonomic assignments, including those with less\nthan 10 reads. We have revised the numbers in the main text to match the numbers in the table\n(L208-210).\nResponse: We have revised the numbers, as stated in the previous response.\nResponse: We adjusted the window to 8 - 7 cal ka BP to account for the fact that most of the listed\nspecies were only detected in that period (L237).\nResponse: We added a figure reference (Fig. 3e) at the end of the sentence (L474).\nResponse: We have adjusted the core names in the Data Tables (now called Table S1 & S9) so they\nmatch the main text.\nResponse: We added the figure reference at the end of the sentence (L523).\nResponse: We have removed the sentence.\nResponse: Thank you, we have added latitude lines to Fig. 1 to make cross-referencing of the\nlatitudes mentioned in the main text easier.\nResponse: Thank you, we have adopted the proposed phrasing (L443).\nResponse: We have removed the sentence.\nResponse: We have rephrased the sentence for clarification (L739-740).\nResponse: We have created a SRA BioProject (PRJNA1211513) with the raw sequencing files for the\nmetagenomic shotgun sequencing data and hybridization capture sequencing data. The data\navailability was updated with the SRA BioProject reference (L830-831). The project will be made\npublicly available upon publication."}, {"round": 2, "reviewer_comments": {"reviewer_1": "The paper is about the temporal and spatial distribution of marine mammals in Greenland. The use of ancient DNA analyses\non sediment cores from different regions has provided new insights into the timing of the first appearance of specific species\nand on the prevailing environmental conditions that may explain the pattern of species occurrence throughout the Holocene.\nThe chronology of the investigated sediment cores is fundamental for the interpretation of the temporal changes and\ncorrelation between regions/records. The authors used the widely accepted method of 14C dating for this purpose. In the\noriginal manuscript version, I had noted that in a few places a more detailed description of the procedures of reservoir\ncorrections, age-depth modelling and correlations was necessary to make the quality of the age information more\nassessable to the reader. The authors responded to this and fully improved the points mentioned.", "reviewer_3": "My revisions have been addressed adequately. I have no further revisions."}, "author_response": ""}]

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