Demographic reconstruction from ancient DNA supports rapid extinction of the great auk.

The great auk was once abundant and distributed across the North Atlantic. It is now extinct, having been heavily exploited for its eggs, meat, and feathers. We investigated the impact of human hunting on its demise by integrating genetic data, GPS-based ocean current data, and analyses of population viability. We sequenced complete mitochondrial genomes of 41 individuals from across the species' geographic range and reconstructed population structure and population dynamics throughout the Holocene. Taken together, our data do not provide any evidence that great auks were at risk of extinction prior to the onset of intensive human hunting in the early 16th century. In addition, our population viability analyses reveal that even if the great auk had not been under threat by environmental change, human hunting alone could have been sufficient to cause its extinction. Our results emphasise the vulnerability of even abundant and widespread species to intense and localised exploitation.

Introduction

The great auk (Pinguinus impennis) was a large, flightless diving bird thought to have once numbered in the millions (Birkhead, 1993). A member of the family Alcidae in the order Charadriiformes, its closest extant relative is the razorbill (Alca torda) (Moum et al., 2002). The great auk was distributed around the North Atlantic and breeding colonies could be found along the east coast of North America, especially on the islands off Newfoundland (Figure 1). The species also bred on islands off Iceland and Scotland, and was found throughout Scandinavia (Norway, Denmark, and Sweden), with evidence of bone finds existing as far south as Florida and in to the Mediterranean (Fuller, 1999; Grieve, 1885).

Figure 1.

The great auk and its former distribution in the North Atlantic.

Red shading indicates the geographic distribution of the great auk, as defined by BirdLife International/IUCN (BirdLife International, 2016a). Sites marked with blue dots represent samples used in our analyses. Black dots denote other sites from which material was obtained, but for which samples were not sequenced or for which sequences did not pass filtering settings. Numbers associated with blue dots correspond to the following sites: 1: Funk Island (n = 14), 2: Qeqertarsuatsiaat (n = 1), 3: Eldey Island (n = 2), 4: Iceland (n = 5), 5: Tofts Ness (n = 2), 6: Bornais (n = 1), 7: Cladh Hallan (n = 1), 8: Portland (n = 1), 9: Santa Catalina (n = 2), 10: Schipluiden (n = 1), 11: Velsen (n = 1), 12: Sotenkanalen (n = 2), 13: Skalbank Otterön (n = 2), 14: Kirkehlleren (n = 1), 15: Storbåthelleren (n = 1), 16: Iversfjord (n = 1), 17: Vardø (n = 2), and 18: Nyelv (n = 1).

The archaeological and historical records show a long history of humans hunting great auks. In prehistoric times, they were hunted for their meat and eggs by the Beothuk in North America (Fuller, 1999; Gaskell, 2000), the Inuit of Greenland (Meldgaard, 1988), Scandinavians (Hufthammer, 1982), Icelanders (Bengtson, 1984), in Britain (Best, 2013; Best and Mulville, 2016), Magdalenian hunter-gatherers in the Bay of Biscay (Laroulandie et al., 2016), and possibly even Neanderthals (Halliday, 1978). Around 1500 AD intensive hunting began by European seamen visiting the fishing grounds of Newfoundland (Bengtson, 1984; Fuller, 1999; Gaskell, 2000; Steenstrup, 1855). Towards the end of the 1700s, the development of commercial hunting for the feather trade intensified exploitation levels (Fuller, 1999; Gaskell, 2000; Kirkham and Montevecchi, 1982). As their rarity increased, great auk specimens and eggs became desirable for private and institutional collections. The last reliably recorded breeding pair were killed in June 1844 on Eldey Island, Iceland, to be added to a museum collection (Bengtson, 1984; Fuller, 1999; Gaskell, 2000; Grieve, 1885; Newton, 1861; Steenstrup, 1855; Thomas et al., 2017).

There are scattered records of great auks dating to later than 1844, including in 1848 near Vardø, Norway (Fuller, 1999; Newton, 1861), and 1852 in Newfoundland (Fuller, 1999; Grieve, 1885; Newton, 1861). BirdLife International/IUCN recognises the last sighting as 1852 (BirdLife International, 2016a). However, uncertainty remains about the reliability of all of these later sightings (Fuller, 1999; Grieve, 1885). There is little doubt that the extensive hunting pressure on the species contributed significantly to its demise. Nevertheless, despite the well documented history of exploitation since the 16th century, it is unclear whether hunting alone could have been responsible for the demise of the great auk, or whether the species was already in decline due to non-anthropogenic environmental changes (Bengtson, 1984; Birkhead, 1993; Fuller, 1999). For example, there is evidence of a decrease in great auk numbers on the eastern side of the North Atlantic, as reflected in a decline in bone finds in England, Scotland, and Scandinavia, which remains unexplained and could have been caused by hunting as well as environmental change (Bengtson, 1984; Best and Mulville, 2014; Grieve, 1885; Hufthammer, 1982; Serjeantson, 2001). To quote Bengtson (1984), ‘In the absence of more detailed information about rate of decline of the bird populations, hunting pressure and environmental changes, we cannot separate the effects of hunting and that of climate change’ (p10).

Reconstructing specific environmental influences on an extinct species can be difficult when there is limited knowledge of the species’ biology. However, if the species had been at risk of extinction prior to the onset of intensive hunting in the 16th century, we would expect to see genetic signatures of population decline, including limited genetic diversity and pronounced population structure. In contrast, the lack of an observable loss in genetic diversity during the last few centuries prior to the extinction would be consistent with a rapid demographic decline at the end. At the same time, human hunting alone can only be considered a reasonable explanation for the extinction of the great auk, if population viability analyses show that extinction could have been caused by harvest rates that would have been realistic for the time and circumstances of the harvest.

Here, we examine the drivers of the extinction of the great auk by analysing whole mitochondrial genome (mitogenome) sequences from across its geographic range, population viability, and harvest rates. We combined these with data from GPS-equipped drifting capsules deployed in the North Atlantic, which allow us to suggest potential migration routes among breeding sites.

Results

Mitogenome sequence data

Using hybridisation capture combined with high-throughput sequencing, we generated short-read sequence data from 66 bone samples of great auk (See Supplementary file 1a for sample information). Following read processing and filtering, 35 samples passed the quality requirements (see Materials and methods) and were suitable for further analysis. In addition to the sequences generated from bones, we included six previously published mitogenome sequences from tissue or feather samples (Thomas et al., 2017) (Supplementary file 1a).

The combined data set comprised 41 complete mitogenomes, representing individuals from across the former range of the great auk and spanning the period 170–15,000 years before present (ybp). For samples in the final data set, the mean average read length of aligned bases to the reference great auk mitogenome (GenBank accession KU158188.1 [Anmarkrud and Lifjeld, 2017]) was 55.12 base pairs (bp), with a range of 41.21–86.95 bp. Unique mitogenome coverage of these samples ranged from 6.39 × to 430.09×, with average coverage of 72.5× (Supplementary file 1c). The final alignment length was 16,641 bp, including 9994 bp (after removal of gaps) that were shared across all 41 mitogenomes.

Genetic diversity and population structure

Haplotype diversity among the great auk mitogenomes was high, with only two individuals yielding identical haplotypes across the 9994 bp covered by all 41 mitogenomes. The two identical sequences differed in age, so that when divided into different age groups, each age group contained a unique set of haplotypes. No reduction of haplotype diversity could be identified in more recent samples (Figure 2).

Figure 2.

Statistical parsimony network showing haplotype diversity of great auk mitogenomes through time.

In each age category observed haplotypes are shown in colour, absent haplotypes are shown as empty circles, and mutations between haplotypes are marked as black dots. All samples have been included in this figure.

We observed no structure in the distribution of haplotypes using any of our four approaches to reconstruct phylogeographic and temporal relationships among the samples: Bayesian analyses using BEAST (Appendix 1—figure 1 and Appendix 1—figure 2); maximum-likelihood phylogenetic analysis using RAxML; statistical parsimony network analysis using TempNet (Figure 2); and median-joining network analysis using PopART (Figure 3).

Appendix 1—figure 1.

Phylogenetic tree showing the relationships among dated mitogenomes from the great auk.

This maximum-clade-credibility tree was inferred by Bayesian analysis in BEAST. Nodes are labelled with posterior probabilities. The tree is drawn to a timescale, as indicated by the horizontal scale bar. Samples included in the analysis are those with associated date information (see Supplementary file 1e). For samples with a stratigraphically assigned date the median age has been used. Tip labels give the sample names, sampling locations, and sample ages (years before present, with the exception of mounted specimens labelled YA- years ago).

Appendix 1—figure 2.

Phylogenetic tree showing the relationships among dated and undated mitogenomes from the great auk.

This maximum-clade-credibility tree was inferred by Bayesian analysis in BEAST. Nodes are labelled with posterior probabilities. The tree is drawn to a timescale, as indicated by the horizontal scale bar. Samples included in the analysis are those with and without associated date information (Supplementary file 1e). For samples with a stratigraphically assigned date the median age has been used. Tip labels give the sample names, sampling locations, and sample ages (years before present, with the exception of mounted specimens labelled YA- years ago).

Figure 3.

Median-joining network of great auk mitogenomes.

The network was inferred in PopART18 and shows a lack of phylogeographic structure among the dated and undated samples of great auks. Haplotypes are coloured according to sampling location.

Ocean current data

To evaluate potential reasons for the observed lack of population structure, we sourced data from GPS-equipped drifting capsules that had been deployed in the North Atlantic as part of the ‘Message in a Bottle’ project by Verkís Consulting Engineers. As the great auk was flightless, ocean currents might have influenced its migration patterns. The route taken by the capsules connects some of the main breeding colonies in St Kilda (Scotland), Geirfuglasker/Eldey Island (Iceland), and Funk Island (Canada) (Figure 4).

Figure 4.

Routes taken by GPS capsules in the North Atlantic.

The map shows GPS data from two capsules (green and yellow lines). These tracks show possible routes that the great auk might have used to move between colonies, aided by ocean currents, waves, and wind. Legend: Red Star: Known breeding sites of the great auk (Funk Island, New Newfoundland; Eldey Island, Iceland; St Kilda, Scotland). Green line: GPS capsule 1. Yellow line: GPS capsule 2. Pink arrows: Warm sea currents (Gulf Stream and North Atlantic Drift). Dark blue arrows: Cold sea currents (East Greenland Current and Labrador Current).

The extrapolation of present-day ocean current data into the past and the interpretation of the data in the context of great auk movements is merely speculative. However, if ocean currents today are comparable to those of past millennia, then the data do at least provide a possible explanation for how great auks travelled across their former range and between breeding colonies (Figure 4). A full description of the routes taken by the capsules is provided in Appendix 2.

Demographic history and effective population size

We reconstructed the demographic history of the great auk using the 25 dated mitogenomes (see Materials and Methods for definition of ‘dated’ samples) and found support for a constant population size through time, with no evidence of a population decline. Despite having a high haplotype diversity, our samples had a shallow divergence and their most recent common ancestor was dated to 42,188 ybp (95% credibility interval 24,743–84,894 ybp; see Appendix 3). The effective female population size (Nef) was estimated at 9558 (95% credibility interval 4548–19,665), assuming a generation interval of 12 years (BirdLife International, 2016a). To examine the effect of including the undated samples, we repeated the analysis on the complete data set while accounting for the uncertainty in the ages of the undated samples. This second analysis also yielded support for a constant population size, with an effective female population size of 7331 (95% credibility interval 2477–19,492). Census size (Nc) estimates based on the effective population size and the range of known Ne/Nc ratios (Frankham, 1995) yielded an expectedly wide range of 12,292–756,346 individuals.

Population viability analyses and sustainable harvest rates

To assess the feasibility of a ‘hunting-only’ scenario of extinction, we used population viability analysis to estimate the proportion of the population that would need to have been harvested in order to cause extinction within 350 years. Population sizes for our simulations were conservatively based on the upper margin of the census size estimates outlined above, consistent with the large census sizes described in historic documents (Birkhead, 1993) (see also Appendix 8). The estimate of 756,346 mature birds is slightly below the census size estimates for the great auk’s closest relative, the razorbill (Alca torda;~1 million mature birds) and significantly below those of common and thick billed murre, also from the Alcidae family (Uria aalge and Uria lomvia; 3 million mature birds each) (BirdLife International, 2016a; BirdLife International, 2016b; BirdLife International, 2016c; BirdLife International, 2017). Given historic reports of millions of great auks (Birkhead, 1993) and in order to reduce the risk of underestimating the census size of great auks, we ran simulations for population sizes of 1 million and 3 million mature birds (2 million and 6 million birds total size including juveniles). All simulation settings were ‘optimistic’ and biased strongly towards survival. This included conservatively high estimates of reproductive success and conservatively low estimates of natural mortality. For a subset of simulations, we also introduced a further, population density dependent, linear reduction of natural mortality to half our already low rates of natural mortality. Furthermore, in order to provide maximum sustainable harvest rate estimates for more ‘realistic’ settings, we ran simulations using estimates for reproductive success and natural mortality obtained from the razorbill.

We found that under our conservative settings, annual harvest rates up to 9% of the pre-hunting population were sustainable. For example, for a pre-hunting population size of 2 million individuals, this corresponds to an annual harvest rate of 180,000 birds. In contrast, an annual harvest rate of 10% of the pre-hunting population combined with an annual egg harvest rate of 5% led to extinction in a large proportion of our simulations. A harvest rate of 10.5% (egg harvest rate 5%) of the pre-hunting population led to extinction within 350 years in all of our simulations. Assuming a density-dependent reduction of mortality had only a small effect on sustainable harvest rates (Table 1). Furthermore, even if no eggs at all were harvested, the population was still at risk of extinction at 10.5% bird harvest rate, with extinction probabilities between 15% (population size 6 million, density-dependent mortality) and 81% (population size 6 million, no density-dependent mortality, [Table 1]). These results were robust to the definition used for extinction. For comparison, when using the much higher mortality rate of the razorbill, with a starting population of 2 million birds and slightly more realistic settings for reproductive age and success, harvest rates are only sustainable up to about 40,000 birds per year even if no eggs are harvested and mortality is gradually reduced to 50% of the starting value as the population density declines (see Supplementary file 2b).

Table 1.

Population viability analysis.

Extinction is defined as ‘only one sex remains’. The number of mature individuals was estimated in Vortex 10.2.8.0, assuming a stable age distribution and given our fixed mortality rates. ‘Maximum- number of eggs’ refers to the number of eggs that would be produced if all mature individuals were breeding. ‘Harvest rate’ describes the percentage of the population that is harvested annually, with egg harvest rate calculated from the maximum number of eggs in parentheses. ‘DD’ refers to density-dependent reduction of mortality. ‘Number of birds’ is the total number of birds killed annually, which was split between the age cohorts (see Appendix 8). ‘Number of eggs’ is total number of eggs harvested annually.

Conservative settings
Population size (total)	Mature birds (>4 years)	Maximum number of eggs	Harvest rate (% of starting population size)	DD	Number of birds	Number of eggs	Probability of extinction within 350 years
2,000,000	1,027,532	513,766	9 (5)	No	180,000	25,688	0.00
2,000,000	1,027,532	513,766	10 (5)	No	200,000	25,688	0.79
2,000,000	1,027,532	513,766	10 (5)	Yes	200,000	25,688	0.22
2,000,000	1,027,532	513,766	10.5 (5)	Yes	210,000	25,688	1.00
2,000,000	1,027,532	513,766	10.5 (0)	No	210,000	0	0.71
2,000,000	1,027,532	513,766	10.5 (0)	Yes	210,000	0	0.19
6,000,000	3,082,594	1,541,297	9 (5)	No	540,000	77,065	0.00
6,000,000	3,082,594	1,541,297	10 (5)	No	600,000	77,065	0.86
6,000,000	3,082,594	1,541,297	10 (5)	Yes	600,000	77,065	0.33
6,000,000	3,082,594	1,541,297	10.5 (5)	Yes	630,000	77,065	1.00
6,000,000	3,082,594	1,541,297	10.5 (0)	No	600,000	0	0.81
6,000,000	3,082,594	1,541,297	10.5 (0)	Yes	630,000	0	0.15
‘Realistic’ settings
Population size (total)	Mature birds (>5 years)	Maximum number of eggs	Harvest rate (% of starting population size)	DD	Number of birds	Number of eggs	Probability of extinction within 350 years
2,000,000	1,027,532	513,766	2 (0)	Yes	40,000	0	0.19–0.33 (range across multiple repeat simulations)

Discussion

Our analyses of the demographic history of great auks support a constant population size within the temporal resolution of our data (back to the most recent common ancestor of all samples 24,000–85,000 ybp). Therefore, we find no evidence of a decline in the population prior to the onset of intensive hunting. We also observed high haplotype diversity across the sampling period, right up to the demise of the species. If the great auk had been at risk of extinction prior to the onset of intensive human hunting, for example as a result of long-term suboptimal habitat or environmental change, we would expect to see genetic evidence of such stress, as for example observed in studies of cave bears (Stiller et al., 2010) and bison (Shapiro et al., 2004). If, on the other hand, the population declined rapidly, for example as a result of extensive hunting, genetic data would have only very limited power to detect such a decline in a long-lived species. Mitochondrial DNA studies of New Zealand moa found no evidence of a population decline prior to extinction (Allentoft et al., 2014; Rawlence et al., 2012) and a study of the endemic Hawaiian Petrel came to a similar conclusion (Welch et al., 2012). In fact, even a recent whole-genome study of two extinct New Zealand songbirds (huia and South Island kõkako), which disappeared after human settlement within 700 years, found no genetic evidence of population decline prior to the disappearance of the species (Dussex et al., 2019). Therefore, our results are consistent with a rapid decline of great auks. It is important to keep in mind, though, that our results simply indicate that the demise of the great auk was beyond the detection limit of genetic data. They do not necessarily confirm whether the rapid demise that must have taken place prior to extinction started before or after the onset of extensive human hunting, nor do the results provide an indication of whether there was more than one population decline. A localised, unexplained decline in great auk numbers on the eastern side of the North Atlantic over the past 2,000 years, for example, which has been inferred from a decline in bone finds in England, Scotland, and Scandinavia (Bengtson, 1984; Best and Mulville, 2014; Grieve, 1885; Hufthammer, 1982; Serjeantson, 2001), does not appear to have been severe enough to leave a genetic signature.

The estimated female effective population size is considerably smaller than the census size, which has been estimated to be in the millions (Birkhead, 1993). This is noteworthy because it suggests that the species went through a severe bottleneck in the recent past. The shallow divergence of less than 90,000 years between the sequenced individuals suggests a population decline in the late Pleistocene, potentially associated with climate fluctuations. However, the wide 95% credibility intervals of our divergence-time estimates prevent us from narrowing down the cause of the bottleneck to any specific event. In any case, the high percentage of singleton haplotypes in our data, which is characteristic of a population expansion following a bottleneck (Slatkin and Hudson, 1991), together with the large census size at the onset of intensive hunting, suggest that the great auk had successfully recovered from the bottleneck.

Our genetic analyses failed to detect any female population structure in space or time, indicating a lack of marked barriers to dispersal among populations across the species’ range. This is inconsistent with predictions of limited or no interbreeding between populations from either side of the North Atlantic (Burness and Montevecchi, 1992), and suspected regional philopatry in this species (Bengtson, 1984; Montevecchi and Kirk, 1996). Such a lack of structure is, however, common in seabirds, and has been observed in several relatives of the great auk, such as the thick-billed murre (Uria lomvia; no structure within ocean basins) (Tigano et al., 2015), common murre (Uria aalge; structure in the Atlantic but not in the Pacific) (Morris-Pocock et al., 2008), ancient murrelets (Synthliboramphus antiquus; no genetic differentiation in the North Pacific) (Pearce et al., 2009), and little auk (Alle alle; no structure in the Arctic) (Wojczulanis-Jakubas et al., 2014). While all of the great auk’s closest relatives are capable of flight, which would aid population connectivity, a lack of population structure has similarly been report from some penguin species. For example, little or no population structure has been reported for the emperor penguin (Aptenodytes forsteri) (Cristofari et al., 2016), chinstrap penguin (Pygoscelis antarcticus) (Mura-Jornet et al., 2018), and Adélie penguin (P. adeliae) (Gorman et al., 2017; Roeder et al., 2001).

We can only speculate what factors may have driven this lack of population structure, but the data collected from the GPS-enabled drifting capsules are consistent with hypotheses put forward by a number of authors. It has been suggested that migrations occurred in both northward and southward directions between breeding and wintering sites, aided by ocean currents such as the East Greenland Current (Brown, 1985; Meldgaard, 1988; Montevecchi and Kirk, 1996). However, as these preliminary data were only available from two GPS-enabled drifting capsules and as ocean currents may have changed significantly over the past few centuries, the conclusions that we can draw from such data are somewhat limited. Furthermore, it is possible that these currents can change throughout the year. Thus, these data must be considered with caution and pending far more detailed studies of ocean currents in the North Atlantic throughout the year. Nevertheless, high vagility of the great auk is further supported by its ability to track its habitat in response to climate change, as evidenced by archaeological records (Bengtson, 1984; Campmas et al., 2010; Meldgaard, 1988; Serjeantson, 2001).

We find no evidence in our genetic data that would suggest that great auk populations were at risk of extinction at the time when human hunting intensified. However, the strength of our conclusions is limited in a number of respects. The mitochondrial genome is only a single genetic marker and our samples were insufficiently preserved to yield nuclear SNP data (Appendix 9), which would have offered a greater degree of resolution with the potential to detect population structure. Similarly, as a result of limitations in sample preservation and availability, the sample size of 41 is relatively small for population genetic analysis and could have limited our ability to resolve changes in population structure and size.

The key question, therefore, is whether it is at all feasible to assume that the intensive hunting of the 16th–19th centuries alone led to the extinction of the great auk. Our population viability analysis shows that, independent of the population size, harvest rates that would cause extinction under all of the conditions explored in our simulations are well below reasonable estimates of harvest rates as inferred from historical sources. For example, a total population size of 2 million birds corresponds to 1 million mature individuals. This is higher than the upper margin of our census size estimates and is consistent with the census size currently estimated for the great auk’s closest relative, the razorbill. At this census size, an annual harvest of 210,000 birds and fewer than 26,000 eggs would have caused the extinction of the great auk within 350 years.

Actual hunting pressure on great auks is likely to have far exceeded 210,000 birds annually. From 1497 AD, when Europeans discovered the rich fishing grounds of Newfoundland, fleets of 300 to 400 ships from various European countries were drawn annually to this region, which is likely to have had the highest population density of great auks (Bengtson, 1984; Steenstrup, 1855). Fishing stations were set up near colonies of the great auk and other seabirds, and these colonies were heavily exploited (Pope, 2009). Great auks were also likely to have been caught by fishing lines and in fishing nets (Montevecchi and Kirk, 1996; Piatt and Nettleship, 1985; Piatt and Nettleship, 1987; Pope, 2009). Contemporary reports document a case in which approximately 1000 great auks were caught and killed within half an hour by two fishing vessels off the coast of Funk Island (Bengtson, 1984; Grieve, 1885). Thus, if each of the 400 vessels in the region spent only half an hour a year harvesting great auks at this rate, that would already correspond to 200,000 birds a year.

At a total population size of 6 million birds, corresponding to the estimated 3 million mature individuals of common murre and thick-billed murre in the North Atlantic, an annual harvest of 630,000 birds and 77,000 eggs would cause certain extinction. Even this number does not appear unrealistically high when considering that great auks were also targeted for the feather trade, with hunters living on Funk Island throughout the summer with the purpose of killing the birds (Gaskell, 2000; Kirkham and Montevecchi, 1982). Adding to the effects of excessive hunting, the great auk laid only one egg a year, which was not replaced if removed (Bengtson, 1984). Thus, replenishing the large number of birds lost annually would have been highly improbable (Gaskell, 2000).

Critically, our estimates of harvest rates leading to extinction are likely to be conservatively high, because they are based on some unrealistically optimistic assumptions. For example, our settings assume that 100% of mature birds breed, that they had 100% breeding success, and that their offspring was independent from the time the egg was laid (hence no negative effect of parents being killed). Furthermore, we assumed the lowest natural mortality observed among all alcids for each age class and in some simulations reduced these mortality rates by half when population density declined, thereby considering the positive effects of increased availability of resources and reduced competition. Detrimental effects of small population sizes, such as inbreeding depression, were not included in our simulations. Because very little is known about the biology of the great auk, we chose to use such conservative settings to reduce the risk of underestimating the sustainable harvest rate. However, this brings an increased risk of overestimating the number of birds that could have been sustainably harvested. Using the mortality rate of the razorbill and allowing for more variation in reproductive success (see Supplementary file 2a) reduces the sustainable harvest rate for a population of 2 million birds to as few as 40,000 birds per year. However, the razorbill can produce a second egg per season if the first one is lost, so applying razorbill mortality rates to the great auk likely leads to an underestimation of the sustainable harvest rate.

Our conservative simulations require high harvest rates to cause the extinction of the great auk, but these values are largely consistent with harvest rates for present-day species. For example, until recently, between 200,000 and 300,000 murres (Uria spp.) were killed legally every year off the eastern Canadian coast (Wilhelm et al., 2008). Harvest rates were even higher before the mid-1990s, when between 300,000 and 700,000 thick-billed murres alone were being harvested annually (Wilhelm et al., 2008). In Iceland, 150,000 to 233,000 Atlantic puffins were once killed annually, representing about 2–3% of the population. In contrast, 25–30% of the populations of species of black-backed gulls are killed annually (Merkel and Barry, 2008). Although current figures for annual harvest rates of auk species are considerably lower than those given above and continue to decline (e.g.,~25,000 puffins were killed in Iceland in 2016 compared with ~233,000 in 1995 [Statistics Iceland, 2016]; also see Frederiksen et al., 2016), the harvesting rates required to cause the extinction of the great auk would not be considered excessive even by modern standards.

The roles of humans and environmental changes in causing extinctions have long been debated, not only for the great auk but also for other lost species (Cooper et al., 2015; Lorenzen et al., 2011; Shapiro et al., 2004). In contrast with most studies of Pleistocene extinctions, which have argued for at least some level of climate-driven environmental contributions to species extinction, we have found little evidence that the great auk was at risk of extinction prior to the onset of intensive human hunting. Critically, this does not mean that our study provides unequivocal evidence that humans alone were the cause of great auk extinction. To test this hypothesis, simulations of great auk population dynamics in response to environmental change throughout the Holocene would be required. However, with little information about great auk biology, such simulations would be highly speculative. What our study has demonstrated though, is that human hunting pressure alone was very likely to have been high enough to cause extinction even if the great auk population was not already under threat of extinction through environmental change.

Our findings highlight how industrial-scale commercial exploitation of natural resources have the potential to drive even an abundant, wide-ranging, highly vagile, and genetically diverse species to extinction within a short period of time. This echoes the conclusions drawn for the passenger pigeon (Murray et al., 2017), which occurred in enormous numbers prior to its extinction in the early 20th century. Our findings emphasise the need for thorough monitoring of commercially harvested species, particularly in poorly researched environments such as our oceans. This will lay the platform for sustainable ecosystems and ensure the evidence-based conservation management of biodiversity.

Materials and methods

Sampling and DNA extraction

We obtained great auk material for ancient DNA (aDNA) analyses from various institutions (Supplementary file 1a). Samples were chosen to represent individuals from the major centres of the former geographic distribution of the species (Figure 1), spanning as wide a time period as possible (Supplementary file 1a). The samples range from about 170 years old to about 13,000–15,000 years old. Sample dates are stratigraphically assigned (archaeological material), based on documented information (e.g., dates on which mounted specimens were killed), or estimated from known site information to give dated constraints (e.g., Funk Island material was collected from the top layers of the islands, so the bones are most likely from individuals killed during the intense hunting period that began ~500 years ago). Bones were sampled via drilling using a Dremel 107 2.4 mm engraving cutter to obtain powdered bone (Figure 5) or using a Dremel cutting wheel, which allowed removal of sections of bones that were later powdered using a sonic dismembrator.

Figure 5.

Great auk humeri following sampling.

Great auk humeri, collected from Funk Island, following sampling to collect bone powder for use in DNA extraction. Bones part of the collection at the American Museum of Natural History (Credit: J. Thomas).

All laboratory work prior to polymerase chain reaction (PCR) amplification was carried out in the designated aDNA laboratories of the Natural History Museum of Denmark and the University of Otago. Strict aDNA protocols were followed to avoid contamination. For each DNA extraction and library build, no-template controls were used to test for contamination by exogenous DNA. All post-PCR work was carried out in separate laboratory facilities (Knapp et al., 2012).

Genomic DNA was extracted from 20 to 60 mg of bone powder (Supplementary file 1b) using the method described by Dabney et al. (2013). In short, the bone powder was digested using an EDTA-based extraction buffer and DNA purified using a Qiagen MinElute column. After washing with ethanol-based wash buffers (Qiagen), the DNA was eluted in TE buffer for storage.

DNA sequence data

Single-stranded sequencing libraries were prepared from aDNA extracts following the protocol by Gansauge and Meyer (2013), with modifications as described by Bennett et al. (2014). For some samples, double-stranded libraries were also built using the protocol described by Meyer and Kircher (2010) (Supplementary file 1b). Hybridisation capture was used to enrich libraries for great auk mitochondrial DNA following the MYcroarray MYbaits Sequence Enrichment protocol v2.3.1 (MYcroarray MYbaits, 2014). Bait design details can be found in Appendix 4 and Appendix 4—figure 1.

Appendix 4—figure 1.

Hybrid reference mitogenome used for bait design.

Illustration of the hybrid reference mitogenome constructed using the killdeer (Charadrius vociferous) mitogenome, with orthologous gene regions replaced by those of the great auk (Pinguinus impennis), or razorbill (Alca torda), when great auk data were unavailable. Annotations correspond to the various regions of the mitogenome: those in blue show where great auk or razorbill genes have been used; yellow corresponds to coding regions; green shows all gene regions; the D-loop is shown in gold; rRNA regions are in red; tRNA regions are in pink; and any miscellaneous features are in grey. The numbers on the outer black circle correspond to the base position of the mitogenome.

Samples were sequenced on Illumina platforms (HiSeq 2500 and MiSeq; further details in Supplementary file 1b) at the Danish National High-Throughput DNA Sequencing Centre or by New Zealand Genomics Limited. Demultiplexing of raw sequence data was performed by the respective sequencing centres. Read processing of demultiplexed sequence data was performed as described by Thomas et al. (2017) using the PALEOMIX v1.2.5 pipeline (Schubert et al., 2014), details of which can be found in Appendix 5.

Demographic history analyses

To reconstruct the demographic history of the great auk through time, we performed a Bayesian phylogenetic analysis of the mitogenome sequences from the 25 dated samples (‘dated’ being defined here as those with associated date information, such as stratigraphically assigned dates; undated refers to those for which there is no associated dating information, such as the Funk Island samples) (Supplementary file 1e). The sequence alignment was analysed using BEAST 1.8.4 (Drummond et al., 2012). Full details of the BEAST analysis, including details of the data-partitioning scheme, can be found in Appendix 6.

To test hypotheses of constant population size through time vs. population size increase or decline, we compared the marginal likelihoods of constant-size and exponential-growth coalescent tree priors for our data set. The exponential-growth coalescent tree prior with a positive growth rate yielded a higher marginal likelihood than the constant-size tree prior, suggesting that it was the best model of population dynamics in the great auk. However, the posterior distribution of the population growth rate was highly right-skewed with a mode very close to zero, so we conservatively used the constant-size coalescent tree prior for our analysis.

A second analysis was performed in BEAST, in which the 16 undated mitogenomes were included in the data set. A uniform prior of either (0,1000) or (0,5000) was specified for the ages of these mitogenomes, depending on independent information about the context of the samples (Shapiro et al., 2011). All other settings and priors matched those used in the analysis of the 25 dated samples. The extended data set was still best described by a constant-size coalescent prior.

Network analyses

Population structure was investigated by inferring a haplotype network using median joining (Bandelt et al., 1999) in PopART (Leigh and Bryant, 2015). Genetic diversity through space and time was visualised using statistical parsimony and a temporal haplotype network, as implemented in TempNet (Prost and Anderson, 2011) (see Appendix 7 for details on TempNet age categories and Supplementary file 1e).

Population viability analysis

We performed a population viability analysis using the software Vortex 10.2.8.0 (Lacy and Pollak, 2014) in order to estimate the number of great auks that were hunted annually, as well as the rate at which a given intensity of hunting would result in population collapse and extinction. Full details of the simulations performed and parameter justifications can be found in Appendix 8 and Supplementary file 2a, 2b and 2c.

Tracking migration routes using GPS capsules

To achieve a better understanding of the feasibility of great auk movement between colonies of the North Atlantic, we accessed data that were initially generated as part of the ‘Message in a Bottle’ project by Verkís Consulting Engineers in Iceland. Two GPS-equipped drifting capsules were released on 10th January 2016 from a helicopter around 40 km southeast of the Reykjanes peninsula (southwestern Iceland). Each of the capsules contained a North Star TrackPack GPS tracking device (https://www.northstarst.com/asset-trackers/trackpack/), which uploaded precise location data six times a day for up to two years, through the GlobalStar satellite network.

In the interests of transparency, eLife publishes the most substantive revision requests and the accompanying author responses.

Acceptance summary:

This paper reports an exciting attempt to draw new inferences about the extinction history of the Great Auk. Generating a large number of mitogenomes from an extinct species requires considerable effort, and has so far only been achieved for very few taxa (e.g., mammoth and cave bear). The reviewers noted that additional nuclear markers would have significantly strengthened analyses, but appreciated that obtaining this information proved methodologically difficult. While some uncertainty remains, this study represents an important step in advancing our understanding of humans' role in the extinction of the iconic Great Auk.

Decision letter after peer review:

Thank you for submitting your article "Demographic reconstruction from ancient DNA supports rapid extinction of the Great Auk" for consideration by eLife. Your article has been reviewed by four peer reviewers, and the evaluation has been overseen by Christian Rutz as Reviewing Editor and Ian Baldwin as Senior Editor. The following individual involved in the review of your submission has agreed to reveal their identity: Paul Wade.

The Reviewing Editor has consolidated the reviewers' feedback and drafted this decision letter, to help you prepare a revised submission.

Essential revisions:

1) Study assumptions:

The reviewers noted that some aspects of the study inevitably remained quite speculative, and felt that this should be better acknowledged throughout. Therefore, please state explicitly the assumptions, and degree of certainty, for all results and conclusions; all key information should be contained in the main text, and not just the online supplement.

2) GPS Drift capsules:

There was broad agreement that this was one of the weaker aspects of the study. Specifically, it is not clear whether currents can be reliably mapped with just two capsules, and whether it is possible to use these data to make robust inferences about currents thousands of years ago. Furthermore, are currents assumed to be stable throughout the year? Adult Great Auks would presumably have only moved at certain times of the year, and because they were almost certainly philopatric, the map's uni-directional arrows raise the question of how they returned to their colonies. Please tone down the inferences drawn from the drift capsule dataset, highlight ocean current modelling as a challenge for future work, and provide better justification for this line of enquiry (the Great Auk was a flightless bird and therefore may have relied on, or at least been affected by, ocean currents).

3) Genomic analyses:

The reviewers have raised several issues about the genomic analyses that need addressing.

a) There is a hint that a Spanish sample may have been differentiated from the Northern ones, and could represent a refugial population. Were there any partial mtDNA data from the other 8 samples from Spain that could be used to explore this further?

b) It is unfortunate that the Funk Island samples had no date and were excluded from analyses, although their addition with a wide prior had little effect on results; please add the corresponding tree to the online supplement (like Appendix—figure 4). Are there no additional historical museum samples, or feather specimens, available that might yield more and better quality sequence data than the old subfossil bones?

c) The complete lack of phylogeographic structure is surprising. Such lack of structure is usually explained either by high dispersal or a relatively recent bottleneck, followed by range expansion. Since the Great Auk was a flightless bird, it would be very interesting if you could add a comparison to the phylogeographic structure (or lack thereof) found in penguins (e.g., Discussion, third paragraph).

d) Related to the previous comment, the manuscript could be improved by a brief comparison, perhaps in the Discussion, with what previous studies have found when analysing temporally sampled mtDNA data across demographic declines (e.g., in either extinct species or species that are critically endangered today). The manuscript does not appear to cite any papers that analysed genetic changes across the time scales explored here (i.e., a few centuries). Perhaps the human-caused decline in the Great Auk was even more rapid than the declines that have been observed in many species during the last century? Do you have enough samples (i.e., power) to detect a decline in genetic diversity in the last 100 years prior to the Great Auk's extinction?

e) Supplementary Figure 4: Please add a higher-resolution version of the TempNet figure as a main figure, instead of as a supplementary item. The reason for this is partly that there is currently no easily accessible information in the main text on how the samples are temporally distributed, which is important for context. Furthermore, the finding that diversity was still high in the last time bin (<250 years) is very interesting, and should be discussed in more detail.

4) Population viability analyses:

The reviewers generally found the population viability analyses (PVA) well implemented, but highlighted a few points that need addressing.

a) You chose to specify a fairly optimistic life history scenario for the Great Auk, reasoning that, if the model predicts extinction even under these conditions, it can be safely concluded that extinction risk must have been high in the real world. While this is a reasonable approach, the PVA settings were perhaps a touch too optimistic, with zero environmental variation in reproduction, and very low variation in mortality rates (set at 1% for all age classes). Furthermore, it seems that Vortex was run with harvest rate set as a constant percentage of population size (please clarify in the revision whether this was actually the case, as it was hard to tell from either the manuscript or the Vortex documentation), even though it is conceivable that humans may have continued harvesting a constant number (at least for a while), as it would have been relatively easy to find the birds on their nesting colonies. When run on such basic settings, the PVA comes close to being a deterministic model, and a simple lambda calculation could have yielded the same insight: using life history parameters from Supplementary file 2A and B, lambda can be estimated as ~1.12, and one would conclude that a harvest rate of 12% would clearly be unsustainable in a deterministic manner. Please consider exploring a more realistic suite of settings, and provide some further context to justify your PVA approach.

b) In general, the life history parameters seem carefully chosen, but it is slightly odd that annual juvenile mortality (13%) is higher than hatchling/fledgling mortality (9%). Can this be justified, or adjusted? Furthermore, estimates for age of first breeding and adult survival probably need amending.

c) Is there more historical information on harvest rates, such as numbers of birds or eggs taken from a particular nesting colony, that would allow the calculation of site- and time-specific harvest rates?

Essential revisions:

1) Study assumptions:

The reviewers noted that some aspects of the study inevitably remained quite speculative, and felt that this should be better acknowledged throughout. Therefore, please state explicitly the assumptions, and degree of certainty, for all results and conclusions; all key information should be contained in the main text, and not just the online supplement.

Thank you for this feedback. Where appropriate, we have tried to improve the clarity of our assumptions, the degree of certainty of various results and conclusions. Specifically, we discussed in more detail our conclusions of a rapid population decline and what our data does and does not show (first paragraph of the Discussion). We have also more explicitly identified speculations in the discussion of the GPS data. Furthermore, we have added vortex simulations with “realistic” mortality and reproduction rates derived from the razorbill to put our conservative sustainable harvest rate estimates into context and highlight the uncertainty of our estimates. Finally, we moved the TempNet figure into the main text as requested by the reviewers.

2) GPS Drift capsules:

There was broad agreement that this was one of the weaker aspects of the study. Specifically, it is not clear whether currents can be reliably mapped with just two capsules, and whether it is possible to use these data to make robust inferences about currents thousands of years ago. Furthermore, are currents assumed to be stable throughout the year? Adult Great Auks would presumably have only moved at certain times of the year, and because they were almost certainly philopatric, the map's uni-directional arrows raise the question of how they returned to their colonies. Please tone down the inferences drawn from the drift capsule dataset, highlight ocean current modelling as a challenge for future work, and provide better justification for this line of enquiry (the Great Auk was a flightless bird and therefore may have relied on, or at least been affected by, ocean currents).

We have amended the manuscript in several sections that discuss the GPS capsule data. The changes made are as follows:

Results: Ocean current data: To evaluate potential reasons for the observed lack of population structure, we sourced data from GPS-equipped drifting capsules that had been deployed in the North Atlantic as part of the “Message in a Bottle” project by Verkís Consulting Engineers. As the great auk was flightless, ocean currents might have influenced its migration patterns. The route taken by the capsules connects some of the main breeding colonies in St Kilda (Scotland), Geirfuglasker/Eldey Island (Iceland), and Funk Island (Canada) (Figure 4). The extrapolation of present-day ocean current data into the past and the interpretation of the data in the context of great auk movements is merely speculative. However, if ocean currents today are comparable to those of past millennia, then the data do at least provide a possible explanation for how great auks travelled across their former range and between breeding colonies (Figure 4). A full description of the routes taken by the capsules is provided in Appendix 1.

Discussion: We can only speculate what factors may have driven this lack of population structure, but the data collected from the GPS-enabled drifting capsules are consistent with hypotheses put forward by a number of authors. It has been suggested that migrations occurred in both northward and southward directions between breeding and wintering sites, aided by ocean currents such as the East Greenland Current (Brown, 1985; Meldgaard, 1988; Montevecchi and Kirk, 1996). However, as these preliminary data were only available from two GPS-enabled drifting capsules and as ocean currents may have changed significantly over the past few centuries, the conclusions that we can draw from such data are somewhat limited. Furthermore, it is possible that these currents can change throughout the year. Thus, these data must be considered with caution and pending far more detailed studies of ocean currents in the North Atlantic throughout the year. Nevertheless, high vagility of the great auk is further supported by its ability to track its habitat in response to climate change, as evidenced by archaeological records (Bengtson, 1984; Campmas et al., 2010; Meldgaard, 1988; Serjeantson, 2001).

We hope that this now makes it clear that although the data has been included in the Discussion and used in supporting some of our conclusions, it is from a small, preliminary dataset and should therefore be viewed that way.

3) Genomic analyses:

The reviewers have raised several issues about the genomic analyses that need addressing.

a) There is a hint that a Spanish sample may have been differentiated from the Northern ones, and could represent a refugial population. Were there any partial mtDNA data from the other 8 samples from Spain that could be used to explore this further?

Thank you for this observation. We have explored this further as good as possible with limited data (see below). Our results suggest that there is no evidence for a refugial population in Spain. Samples from Spain are similarly spread across the tree as samples from other regions. Below, we have summarized the additional analyses we have conducted. However, as they do not show any pattern that is unobserved in the data we use for this publication, we would prefer to leave this section out of the manuscript. We feel that it would impact the flow and clarity of the manuscript without adding any crucial information. We are of course open to including this section, for example in the appendix, if the editor sees this fit.

Additional analyses Spanish samples.

In the phylogenetic tree of Great Auks that yielded sufficient sequence data as per our filtering criteria (Appendix 4) the sample MK40_Spain appeared to be differentiated from the rest of the samples which came from the northern regions of their distribution. This raises the question whether the sample could represent a refugial population in Spain. In order to test this, we re-examined the phylogenetic relationships between samples with the addition of the other Spanish samples we sequenced but which did not fulfil the filtering criteria for inclusion in our final dataset. These samples included MK37, MK42, MK44 and MK45. These samples were characterized by poor coverage (average coverage ranged from 0.18-2.07) and over 33% of bases missing from consensus sequence (consensus sequence length ranged from 36bp to 5468bp). Sequences generated as described using the Paleomix pipeline (Appendix 4) for samples MK37, MK42, MK44 and MK45 were manually aligned to the reference genome using Bioedit v7.2.5 (Hall, 1999) and Tablet v1.16.09.06 (Milne et al., 2013) to view the rescaled Binary Alignment Map (BAM). As MK37 and MK45 were of very poor quality, we were unable to use them in this additional analysis. However, we were able to produce an alignment of 859bp that included the additional Spanish samples MK42 and MK44. A Neighbour-joining analysis of the alignment based on p-distances (Saitou and Nei, 1987) using MEGAX (Kumar et al., 2018) yielded a very poorly resolved phylogeny (Author response image 1). Critically, the new Spanish samples do not group with the outlier MK40, thereby not supporting a hypothesis of a Spanish refugial population.

Author response image 1.

The evolutionary history was inferred using the Neighbor-Joining method [Saitou and Nei, 1987].

The optimal tree with the sum of branch length = 0.01164144 is shown. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches [Felsenstein, 1985]. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the p-distance method [Nei and Kumar, 2000] and are in the units of the number of base differences per site. This analysis involved 43 nucleotide sequences. All positions containing gaps and missing data were eliminated (complete deletion option). There were a total of 859 positions in the final dataset. Evolutionary analyses were conducted in MEGA X [Kumar et al., 2018].

b) It is unfortunate that the Funk Island samples had no date and were excluded from analyses, although their addition with a wide prior had little effect on results; please add the corresponding tree to the online supplement (like Appendix—Figure 4).

We agree that it is unfortunate that the Funk Island samples do not have date information, however, sadly that is the nature of the sample from this site which is essentially a mass grave yard of great auks, with hundreds of bones from the period of intense hunting. It would certainly be interesting future work to be able to carbon date some of the samples from Funk Island to add this information to the data set. However, for now we have added all undated samples to the tree and added it to the supplement as requested (New Appendix—figure 5).

Are there no additional historical museum samples, or feather specimens, available that might yield more and better quality sequence data than the old subfossil bones?

This study was part of a PhD project that was completed in 2017, therefore, unfortunately, funding and personnel to facilitate further sampling is no longer available. During the project extensive sampling was carried out, sourcing samples that represented individuals from as much of the former great auk range as possible, and over as great a period as possible. Samples were collected from number of museums, worldwide. As we wanted to include samples in the dataset which had as much information as possible, we chose not to include many mounted museum specimens as the vast majority of these do not have sample date or sample location information.

c) The complete lack of phylogeographic structure is surprising. Such lack of structure is usually explained either by high dispersal or a relatively recent bottleneck, followed by range expansion. Since the Great Auk was a flightless bird, it would be very interesting if you could add a comparison to the phylogeographic structure (or lack thereof) found in penguins (e.g., Discussion, third paragraph).

Thank you for the suggestion to compare our result to the penguins. It helps to put our findings from the great auk in context and shows that while the lack of population structure in great auks is surprising, it does not actually appear to be unusual in flightless seabirds. We have now added a paragraph that reads: While all of the great auk’s closest relatives are capable of flight, which would aid population connectivity, a lack of population structure has similarly been report from some penguin species. For example, little or no population structure has been reported for the emperor penguin (Aptenodytes forsteri) (Cristofari et al., 2016), chinstrap penguin (Pygoscelis antarcticus) (Mura-Jornet et al., 2018), and Adélie penguin (P. adeliae) Gorman et al., 2017; Roeder et al., 2001).

d) Related to the previous comment, the manuscript could be improved by a brief comparison, perhaps in the Discussion, with what previous studies have found when analysing temporally sampled mtDNA data across demographic declines (e.g., in either extinct species or species that are critically endangered today). The manuscript does not appear to cite any papers that analysed genetic changes across the time scales explored here (i.e., a few centuries). Perhaps the human-caused decline in the Great Auk was even more rapid than the declines that have been observed in many species during the last century? Do you have enough samples (i.e., power) to detect a decline in genetic diversity in the last 100 years prior to the Great Auk's extinction?

This was indeed an obvious omission in our Discussion. We have now added a section to the first paragraph of the Discussion which discussed this point as follows:

If the great auk had been at risk of extinction prior to the onset of intensive human hunting, for example as a result of long-term suboptimal habitat or environmental change, we would expect to see genetic evidence of such stress, as for example observed in studies of cave bears (Stiller et al., 2010) and bison (Shapiro et al., 2004). If, on the other hand, the population declined rapidly, for example as a result of extensive hunting, genetic data would have only very limited power to detect such a decline in a long-lived species. Mitochondrial DNA studies of New Zealand moa found no evidence of a population declines prior to extinction (Allentoft et al., 2014; Rawlence et al., 2012) and a study of the endemic Hawaiian Petrel came to a similar conclusion (Welch et al., 2012). In fact, even a recent whole-genome study of two extinct New Zealand songbirds (huia and South Island kõkako), which disappeared after human settlement within 700 years, found no genetic evidence of population decline prior to the disappearance of the species (Dussex et al., 2019). Therefore, our results are consistent with a rapid decline of great auks. It is important to keep in mind, though, that our results simply indicate that the demise of the great auk was beyond the detection limit of genetic data. They do not necessarily confirm whether the rapid demise that must have taken place prior to extinction started before or after the onset of extensive human hunting, nor do the results provide an indication of whether there was more than one population decline. A localised, unexplained decline in great auk numbers on the eastern side of the North Atlantic over the past 2,000 years, for example, which has been inferred from a decline in bone finds in England, Scotland, and Scandinavia (Bengtson, 1984; Best and Mulville, 2014; Grieve, 1885; Hufthammer, 1982; Serjeantson, 2001), does not appear to have been severe enough to leave a genetic signature.

e) Supplementary Figure S4: Please add a higher-resolution version of the TempNet figure as a main figure, instead of as a supplementary item. The reason for this is partly that there is currently no easily accessible information in the main text on how the samples are temporally distributed, which is important for context. Furthermore, the finding that diversity was still high in the last time bin (<250 years) is very interesting, and should be discussed in more detail.

We have added a higher-resolution image of the TempNet figure and moved this to the main text (Figure 2). We hope that the resolution of the image now meets your requirements.

4) Population viability analyses:

The reviewers generally found the population viability analyses (PVA) well implemented, but highlighted a few points that need addressing.

a) You chose to specify a fairly optimistic life history scenario for the Great Auk, reasoning that, if the model predicts extinction even under these conditions, it can be safely concluded that extinction risk must have been high in the real world. While this is a reasonable approach, the PVA settings were perhaps a touch too optimistic, with zero environmental variation in reproduction, and very low variation in mortality rates (set at 1% for all age classes).

To provide some comparative data with more “realistic” settings, we have now added a simulation with mortality rates derived from the razorbill (including higher standard variation), an increased reproductive age (from 4 to 5 years) and a reduced maximum reproductive age (down to 20 years from 25) See Supplementary file 2B). These simulations yield a sustainable harvest rate of approximately 40,000 birds a year without any egg harvest. This is likely an underestimation, as the razorbill does have a higher reproductive rate than the great auk, and can therefore tolerate a higher mortality. This simulation and its results are now introduced and discussed in appropriate sections throughout the manuscript.

Furthermore, it seems that Vortex was run with harvest rate set as a constant percentage of population size (please clarify in the revision whether this was actually the case, as it was hard to tell from either the manuscript or the Vortex documentation), even though it is conceivable that humans may have continued harvesting a constant number (at least for a while), as it would have been relatively easy to find the birds on their nesting colonies. When run on such basic settings, the PVA comes close to being a deterministic model, and a simple λ calculation could have yielded the same insight: using life history parameters from Supplementary fie 2A and B, λ can be estimated as ~1.12, and one would conclude that a harvest rate of 12% would clearly be unsustainable in a deterministic manner.

Sorry, this was not well described in our manuscript. We actually did use constant numbers rather than a constant percentage. We have now clarified this where appropriate throughout the manuscript.

Please consider exploring a more realistic suite of settings, and provide some further context to justify your PVA approach.

b) In general, the life history parameters seem carefully chosen, but it is slightly odd that annual juvenile mortality (13%) is higher than hatchling/fledgling mortality (9%). Can this be justified, or adjusted?

The reasoning behind the somewhat odd distribution of mortality rates was that we wanted a rigorous way to decide on rates in the absence of biological information. Hence we decided on the criterium of “lowest rates of any alcid found in the literature”. And the lowest rates we could find for the 0-1 year timeframe are lower than those for the later time frames. We could have increased the 0-1 values, but it would have been arbitrary, so we decided against it. However, we have now also included analyses with the complete razorbill set of mortality rates and higher standard variations to provide a comparison how our simulations would look with less conservative, but still species derived settings. We have also added a further explanation of our reasoning behind the conservative values into the manuscript which reads (Appendix 7):

“Strictly applying the rule that we use the lowest mortality rate of any alcid species found in the literature leads to some settings that are questionable from a biological perspective. For example, our 0-1 year hatchling mortality is lower than our 1-4 years juvenile mortality. However, as we have no information about actual mortality rates in great auks, any adjustment of these settings would be arbitrary. We therefore chose to strictly use the lowest mortality rates found in the literature for each age class. For comparison, we added a simulation based on known mortality rates of the razorbill, which have a more biological realistic distribution of mortality rates, albeit perhaps somewhat too high for the great auk (see Discussion and Supplementary file 2B).”

Furthermore, estimates for age of first breeding and adult survival probably need amending.

We have now done that in our “realistic settings” analyses (see Supplementary file 2A and B).

c) Is there more historical information on harvest rates, such as numbers of birds or eggs taken from a particular nesting colony, that would allow the calculation of site- and time-specific harvest rates?

Unfortunately, we could not find such information despite extensive literature searches. This was in fact the main reason why we decided on running the analyses with unrealistically conservative settings.

Appendix 6—table 1.

Marginal likelihoods of six partitioning schemes and two tree priors for the 25 dated mitogenomes.

Partitioning schemea	Marginal likelihoodb
	Constant size	Exponential growth
Unpartitioned	−24,151.6	−24,143.6
two subsets: (CR rRNA tRNA) (PC1 PC2 PC3)	−24,222.3	−24,212.4
three subsets: (CR) (rRNA tRNA) (PC1 PC2 PC3)	−24,162.4	−24,150.1
four subsets: (CR) (rRNA tRNA) (PC1 PC2) (PC3)	−23,659.7	−23,647.5
five subsets: (CR) (rRNA tRNA) (PC1) (PC2) (PC3)	−23,248.7	−23,235.9
six subsets: (CR) (rRNA) (tRNA) (PC1) (PC2) (PC3)	−23,229.1	−23,217.5

aComponents of the mitogenome are the ribosomal RNA genes (rRNA), transfer RNA genes (tRNA), three codon positions of the protein-coding genes (PC1, PC2, and PC3), and the control region (CR). bMarginal likelihoods were estimated by stepping-stone sampling with 25 path steps, each with a chain length of 2,000,000 steps.

Appendix 9—table 1.

Estimated coverage information from the twelve sequenced samples.

The estimated coverage of the 495 targeted genes and estimated coverage of the reads that mapped to the razorbill genome is reported.

Sample	Country	Estimated coverage of razorbill genome	Estimated coverage of targeted genes
MK49	Norway	0.0101	0.0152
MK50	Iceland	0.0190	0.0155
MK78	Funk Island	0.0022	0.0018
MK83	Funk Island	0.00006	0.0071
MK103	Funk Island	0.0011	0.0150
MK106	Sweden	0.0172	0.0105
MK115	Norway	0.0012	0.0021
MK131	Iceland	0.0090	0.0423
MK133	Skin Mystery	0.0190	0.0154
MK134	Skin Mystery	0.0179	1.2592
MK135	Skin Mystery	0.0073	0.0106
MK136	Skin Mystery	0.0021	0.0128

Appendix 9—table 2.

Coverage range of captured markers.

Numbers in square brackets represent the number of markers which have 0 coverage. Genes with the highest coverage are shown in brackets.

Sample	Country	Coverage range of captured markers
MK49	Norway	0 [125] – 0.4898 (Fam174b)
MK50	Iceland	0 [157] – 0.2204 (Isca2)
MK78	Funk Island	0 [379] – 0.1087 (Mrp130)
MK83	Funk Island	0 [223] – 0.2960 (Nipbl)
MK103	Funk Island	0 [164] – 0.7049 (Glrx5)
MK106	Sweden	0 [190] – 0.2403 (Pcp4)
MK115	Norway	0 [366] – 0.2263 (Tmem60)
MK131	Iceland	0[78] – 1.5238 (Ssna1)
MK133	Skin mystery	0 [129] – 0.3061 (Fam174b)
MK134	Skin mystery	0.0628 (TPK1) – 17.7232 (Ssna1)
MK135	Skin mystery	0 [172] – 0.2580 (myct1)
MK136	Skin mystery	0 [142] – 0.4067 (myct1)