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    Simulation-based evaluation of two insect trapping grids for delimitation surveys

    Key delimitation trapping survey performance factorsTrap attractivenessThe performance of the current Medfly design was unexpectedly inferior to that of the leek moth even with a more vagile target insect, 2.8 times greater trap density in the core, and a grid size over three times larger. Despite all those factors, p(capture) for the leek moth grid with 1/λ = 20 m was 15 percentage points greater than that for Medfly at 30 days duration. Thus, trap attractiveness was the key determinant for delimiting survey performance, as it was for detection13.One straightforward way to improve p(capture) and the accuracy of boundary setting, while also cutting costs, would be to develop more attractive traps. Poorly attractive traps include food-based attractants48 and traps based solely on visual stimuli36. But developing better traps is difficult. Pheromone-based attractants generally perform best49, but these are unavailable for many insects. For instance, scientists have searched for decades for effective pheromones for Anastrepha suspensa (Loew) and A. ludens (Loew) without success50. Common issues include the complexity of components, costs of synthesis, and chemical stability.Trap densitiesAll else being equal, increasing the trap density will generally improve p(capture) for any survey grid, and intuitively this can help compensate for using less attractive traps. However, the impact of increasing density is limited when attractiveness is low13,47, and large surveys or grids with many traps can become prohibitively expensive51. The Medfly grid designers likely understood that the available trap and lure was not highly attractive, and used higher densities in inner bands to try to reach some desired (non-quantitative) survey performance level. By contrast, the designers of the leek moth grid used a (constant) density three times smaller, likely because the trap and lure were known to be relatively strong. Here, for both species, marginal ROI decreased as densities increased (Tables 2, 3). Hence, increasing densities has limited benefit, but may be useful when better lures are unavailable13.In that context, the use of variable densities in the Medfly grid is understandable. At its standard size, the survey grid would require 8,100 traps if the core trap density were constant (Table 1). The designers likely intuited that lower densities could be used in outer bands because captures there were less likely. However, doing so reduces the likelihood of detection in outer bands and could increase the possibility of undetected egress, especially with longer survey durations. As far as we know, natural egress has not been raised as a concern following the numerous Medfly quarantines that have used this survey grid over the years, in Southern California in particular52.Generally, however, we think the variable Medfly grid densities run counter to delimitation goals. Greater core and Band 2 densities have proportionally more impact on p(capture), but only a few detections in the core are necessary to confirm the presence of the population (Goal 1), and inner area detections probably contribute little to boundary setting (see below). Therefore, lower or intermediate densities (at most) may be optimal for the core when considering ROI. For the outer bands, increasing densities might improve boundary setting (Goal 2) and help mitigate potential egress, but the sizes of those bands already limit cost efficiency (Table 2), making greater densities less advisable. Our simulation results can help elucidate how to balance these interests to achieve delimitation goals while minimizing costs47.Grid size considerationsThe simulation results indicated that the standard survey sizes for these two pests were excessive. We have verified that empirically for Medfly using trapping detections data53. A 14.5-km grid has been widely used for many other insects in the CDFA (2013) guidelines10, such as Mexfly and OFF, and the same analysis indicated that those are also oversized for use in short-term delimitation surveys53. From the same analysis, the predicted survey radius for leek moth, with D = 500 m2 per day, would be 2,382 m, or a diameter of nearly 4.8 km, which matches the results here. Similarly, Dominiak and Fanson45 analyzed trapping data for Qfly and found that the recommended quarantine area distance of 15 km could be reduced to 3 to 4 km.Grids with radii larger than 4.8-km only seem necessary for highly vagile insects, those with D ≥ 50,000 m2 per day47. This should not be surprising. Small insect populations are unlikely to move very far31,54, especially if hosts are available20,39,55. The (proposed) short duration of a delimitation survey would also limit dispersal potential (see below). Many delimiting survey plans may be oversized, because they were developed before much dispersal research had been done37, thus uncertainty was high. Our dispersal distance analysis included species with a wide range of dispersal abilities, so it can be used generally to choose smaller survey grid radii53.Reducing grid sizes down to about 4.8-km diameters may have little impact on p(capture), since detections in bands outside that distance contributed little to overall performance. The cores of both the leek moth and Medfly grids accounted for 86 percent or more of overall p(capture). While core area detections will confirm the presence of the population, they are less useful for defining spatial extent. The furthest detections from the presumed source are usually used to delimit the incursion46,56 (although in our experience formal boundary setting exercises seem rare). Delimiting surveys may often yield few captures anyway, because adventive populations can be very small and subject to high mortality31. Because size reductions eliminate traps in proportionally larger outer areas, the impact on survey costs is substantial. Removing just the outermost bands of each grid would directly reduce costs by $11,200 for leek moth (400 traps) and by $7,488 for Medfly (288 traps; Table 1).Another reason for the large size of the standard Medfly grid may be that it was designed for monitoring and management in addition to delimitation57. Medfly quarantines end after at least three generations without a detection, so the surveys may last for months. The grid size was reportedly originally determined by multiplying the estimated dispersal distance by three (PPQ, personal communication), to account for uncertainty. This implies that the estimated distance was about 2,400 m per 30 days. Thus, the design may not have been built for the 30-d duration used here, but our recommended design is valid if a shorter delimitation activity without further monitoring is appropriate.Although it seemed too large for leek moth, an 8-km grid for delimitation could be appropriate for some other moths. For example, the delimiting survey plans for Spodoptera littoralis (Boisduval) and S. exempta Walker use this size9. S. littoralis is described as dispersing “many miles”, and S. exempta can travel hundreds of miles9, which clearly exceeds the described dispersal ability of leek moth. On the other hand, the survey plan for summer fruit tortrix moth (Adoxophyes orana Fischer von Röeslerstamm) also specifies an 8-km grid for delimitation but contains little information on dispersal, suggesting only that most movement is local8. Like leek moth, a 4.8-km grid for that species seems likely to be more appropriate.Limiting egress potential is probably the main consideration when setting survey size, but uncertainty about the source population location may also be a factor. Survey grids placed over the earliest insect detection may sometimes be off center from the location of the source population54. However, so far as we know for our agency, most adventive populations have been localized, based on post-discovery detections (PPQ, personal communication). Likewise, we have found53 and other researchers have found that dispersal distances for different species in outbreaks and mark-recapture studies are often less than 1 km58,59,60. That may often be the case for detection networks of traps (e.g., for high risk fruit flies), which increase the likelihood of capture before the population has had much time to grow and disperse. Here, we focused explicitly on localized populations, but allowed for uncertainty in the simulations by varying outbreak locations over one mile in the central part of the grid. If the outbreak population is very large and has extensively spread out (e.g., spotted lanternfly, Lycorma delicatula (White) in 201461), delimitation will not be localized, but “area-wide”2. The results here do not apply to area-wide outbreaks, and we are currently studying how to effectively delimit them.Optimizing delimitation surveysMany trapping survey designs in use were based not on “hard” science but on local experience62. Scientists have recognized the need for more cost-effective surveillance strategies63,64. Quantitatively assessing p(capture) in different designs for the same target pest allows us to determine grid sizes and densities that lower costs while maintaining performance. Results here demonstrated that the sizes and densities of these two survey grids could be optimized to save up to $20,244 per survey for the leek moth and $38,168 per survey for the Medfly. In practical terms, that means more than five leek moth surveys could be run for the cost of one standard design survey. Additionally, over seven Medfly delimitation surveys could be funded by the budget of one standard plan. The magnitudes of reduction seen here may be typical, since about 90 percent of the costs in trapping surveys are for transportation and maintenance related to traps65.Quantifying survey performance was not possible until very recently, so it has been little discussed in the literature5,66, and no standard thresholds exist. We think 0.5 may be a reasonable minimum threshold for the choice of p(capture), to try to ensure that population detection is “more likely than not”. Designs that aim to maximize p(capture) could be realistic with high attractiveness traps, but those designs seem very likely to have lower ROIs (e.g., Table 2). Even for the most serious insect pests, we think targeting near-perfect population detection during delimitation is likely not justified. Designs achieving p(capture) from 0.6 to 0.75 could be highly effective in terms of both costs and performance.Another potential area of improvement is grid shape. Circular grids perform as well as square grids but use fewer traps and less service area to achieve equivalent p(capture)47. Moreover, detections in the corners of a square grid are evidence that insects could have traveled beyond the square along the axes, resulting in uncertain boundary setting. Most published survey grids are square10,46, but many field managers tend to use approximately circular trapping grids in the field (PPQ, personal communication). The conversion to a circular grid with a radius of half the square side length reduces the area and number of traps by around 21 percent47. Our findings were consistent with that value.This new quantification ability also indicates that some delimiting survey designs in the U.S.A. may not be performing as well as expected47. For instance, the delimiting survey design for Mexfly uses approximately 31 traps per km2 in the core of a 14.5 km square grid11, but the traps are only weakly attractive (1/λ ≈ 5 m). In this scenario, p(capture) was only around 0.23 with a 30-d survey duration47. A much greater density ( > 80 traps per km2) could be used in the core to achieve p(capture) ≥ 0.5, but this may not be feasible depending on the survey budget.Technical and modeling considerationsExamining diffusion-based movement for these two insects in TrapGrid can give insight into why simulations indicated that smaller grids may be adequate47. The value of σ for Medfly after 30 days is only about 1,550 m. In a normal distribution, σ = 1,550 m gives a 95th percentile distance of 2,550 m, which is similar to the estimated distance above of 2,400 m. Over 90 days, σ = 2,700 m for Medfly, which gives a 95th percentile distance of 4,441 m, still much shorter than the grid radius of 7,250 m. A 95th percentile of 7,250 m requires σ ≈ 4,408 m, which equals t = 253 days. In addition, the maximum total distance (up to 39 days after detection) we observed in trapping detections data for Medfly in Florida was about 4,800 m53.The same calculations for leek moth give σ ≈ 490 m for 30 days, with a 95th percentile distance of only 806 m. That is half the length of the recommended shortened radius above of 2.4 km, and nearly five times shorter than the radius of the standard 8-km grid. A 95th percentile of 4,000 m requires σ = 2,432 m, which implies t = 740 days, which is about two years. Therefore, the leek moth grid is arguably even more oversized than the Medfly grid.The default capture probability calculation in the current version (Ver. 2019-12-11) of TrapGrid is not sensitive to population size32 and does not consider the effects of ambient factors (e.g., wind speed and direction, rainfall, temperature). Many other factors can also impact trapping survey outcomes, such as topography of the environment, availability of host plants, seasonality of pest, and population dynamics. These factors are not considered in the current version of TrapGrid. More

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    Identification of soil particle size distribution in different sedimentary environments at river basin scale by fractal dimension

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    Niche partitioning between planktivorous fish in the pelagic Baltic Sea assessed by DNA metabarcoding, qPCR and microscopy

    High diet overlap is assumed to cause competition between the three dominant pelagic planktivorous mesopredators in the Baltic Sea, sprat, herring, and stickleback11,24,25. Despite this assumption, stickleback populations have increased dramatically over the past decades, which raises the question of whether and how resources are partitioned26. While previous studies of fish diet overlap have mainly relied on microscopic identification of gut content, we implemented a DNA metabarcoding approach targeting two different gene regions, the 18S rRNA gene (18S) and the mitochondrial cytochrome c oxidase I gene (COI) to reveal the taxonomic diversity of prey, and a qPCR step to quantify rotifers that are at times abundant in the Baltic Sea. Our study highlights consistency between methods, with DNA metabarcoding resolving the plankton-fish link at the highest taxonomic resolution. Our results suggest a unique niche of stickleback that may enable high population growth in the open water, despite high competition between mesopredators, although this finding needs to be confirmed at larger scale. More than half of the DNA found in herring and sprat stomach contents was assigned to Pseudocalanus, supporting previous observations of high diet overlap between the two clupeids11,12. On the other hand, the diet of stickleback differed substantially from the two clupeids, with rotifers appearing as main prey DNA in spring. The high rotifer biomass in the environment and lack of competition from other predators indicate that this novel niche utilization may support the drastic increase of pelagic stickleback in the Baltic Sea.We find that copepods dominated the gut content of the two clupeids sprat and herring. Pseudocalanus and Temora occupied most of the sequence reads of the clupeid metabarcoding, two species that are often reported as preferred prey in previous studies11,12. Despite high contributions of these two copepods, Pseudocalanus was more than four times as abundant as Temora in clupeid gut contents. A strong preference for this copepod with marine origin can further confirm the increased competition between the clupeids, as Pseudocalanus has decreased due to decreased salinity12 and shares a similar vertical distribution as clupeid during daytime27. Our study using metabarcoding further reveals a large relative quantity (11%) of the ctenophore Mertensia in the gut samples of both clupeids. Similar, Clarke et al.28 reported an important contribution of gelatinous zooplankton to upper trophic levels in the Southern Ocean. Despite high abundances of ctenophores in the Baltic Sea and their assumed importance in marine food webs19, they are not reported as food for planktivorous fish. A possible explanation is the difficulty observing them microscopically, as their digestion rate is faster than crustaceans29, and no hard parts remain in the digestive system. Further, COI detected the presence of cladocerans, which was confirmed by the microscopic survey, but underrepresented with 18S that strongly amplify copepods20. Interestingly, more than twice annelid COI reads, including the benthic macroinvertebrates Bylgides and Marenzellaria, were associated to stickleback (15%) and herring (8%) than to sprat (4%), highlighting their ability to migrate vertically. These interactions suggest that together stickleback and herring contribute to benthic-pelagic coupling when oxygen is not restricting vertical migration in the southern Baltic Sea30.Sprat and herring share a similar feeding niche, which may explain previously observed declines in body mass and stomach fullness, and supports the theory of competition between the two species31. In contrast, stickleback revealed little diet overlap with the other mesopredators. The low relative abundances of Pseudocalanus (1–8%) in metabarcoding analyses indicates that the density-dependent competition may not limit the population growth of stickleback. The copepods that were shared in the diet of stickleback, sprat, and herring were Temora, Acartia, and Centropages have increased over the last decades, as opposed to Pseudocalanus32. Our results show that stickleback are able to feed on a broader spectrum of prey and highlight that stickleback utilizes the rotifer Synchaeta baltica as prey, which is an important component of the plankton community composition in the Baltic Sea18,20. Due to the difference of prey size, we can expect an overrepresentation of copepod to rotifer sequences compared with microscopic count data. High predation rate on S. baltica is supported by both the qPCR assay as well as microscopic counts, although only the eggshells were visible but not the soft-bodied rotifer. Despite the considerably lower carbon content per S. baltica (ca. 6 µg C ind−1) compared to copepods (ca. 20 µg C ind−1)33, the high number of rotifers likely act as a major food source for stickleback. These results propose that stickleback, due to their opportunistic feeding behaviour34 and smaller size35, have a distinct feeding niche from sprat and herring in the open water, as they feed on a smaller size class of zooplankton compared to the clupeids. Thus, we cannot assume the same process of competition between clupeids and stickleback.Rotifers can at times be very abundant in the Baltic Sea, reaching densities up to 25,000 ind m−3, but their natural predators are poorly studied. An increasing trend in biomass of the two main rotifer genera (Synchaeta and Keratella) was observed since the 1990s36. In a recent study, we showed that rotifers might occupy a unique feeding niche, as direct grazers of dinoflagellate spring bloom, as well as in the recycling of organic matter in summer20. The low level of predation on rotifers by clupeid adults ( More

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    Understanding social–ecological systems using social media data

    Ecosystem services are the contributions of nature to human well-being — for example, the provision of raw materials, carbon sequestration and recreation. Although relatively new, the study of these essential services has developed rapidly and is now included in many global policies and assessments. However, mapping and modelling these services is restricted by the availability of data that can account for the multidimensional traits of ecosystem services and model coupled social–ecological systems. Traditional datasets, including surveys, interviews, and focus groups, are often not viable on the scale necessary for many ecosystem service assessments. More

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    Long-term observation of the egg and chick size in the nests of Larus ichthyaetus in Lake Chany, Russia

    We surveyed three islands of Lake Chany: Uzkoredkii (54° 58′ 15′′ N, 77°27′04′′ E), Reden’kii (54° 56′ 05′′ N, 77° 22′ 27′′ 52 E), Korablik (54° 59′ 31′′ N, 77° 40′ 38′′ E). The studied intertidal habitats are rarely reached by humans.Gull nests were counted in colonies by regular surveys over eight years (1993, 1994, 1996–1998, 2001–2003) on the islands of Lake Chany. Colonies were visited daily or sometimes every other day. To minimize the disturbance caused by the investigation, the time spent working, within view of the gulls was restricted to a maximum of forty minutes per study plots. We noted nest content at every visit for the presence of eggs or chicks. In total, there were 1 164 nests under observation. Nests contained 1 (n = 140), 2 (n = 518), 3 (n = 504) or 4 (n = 2) eggs. Modal clutch size of the great black-headed gull is two or three eggs, varying seasonally. The length and width of the eggs were measured using Vernier calipers (division accuracy 0,1 mm) and numbered with a waterproof marker. Egg volumes were estimated using Hoyt’s equation: Volume = 0.51 * Length * Width * Width/100013. We determined the volume of 2117 great black-headed gull eggs.As the laying of eggs has already started by the first visit to the colony, the date of the beginning of egg laying was calculated by subtracting the average length of the incubation period of great black-headed gulls (27 days) from the hatching date of first chick in the nest (n = 559 nests). If the hatching date was not known, the clutch initiation date was determined by subtracting the number of days of incubation from the date that the nest was first discovered (n = 469 nests). The stage of incubation was estimated from the change in position of an incubated egg placed in water14,15. The technique’s accuracy varied throughout incubation and mean prediction error fall between 0–4 days. On average, egg flotation estimated an embryo’s developmental age to within 1.9 ± 1.6 days (mean ± 1 SD)16. Only 47 nests were found during egg laying. Great black-headed gulls usually laid eggs at intervals of two days. Incubation started as soon as the first egg was laid, so eggs hatched asynchronously, one or two days apart.Whenever possible, we determined the within-clutch laying sequence of eggs (1st, 2nd, 3rd, and 4th). A complete laying sequence was established by observation in 47 cases. In about 48% of clutches the position in laying sequence was established on the basis of the sequence of hatching. In other cases, if we could distinguish within-clutch distinct flotation levels of eggs, we numbered eggs according to the stage of incubation. Sometimes this technique for distinguishing egg laying order were used in other seabirds17,18.We recorded the pipping date (i.e. appearance of star-like bursts) and the actual hatching date of the individual eggs. Wet chicks were registered as hatchlings of that day; dry chicks were registered as 1 day old. Chicks older than two days left the nest and moved to a location nearby. Newly hatched gull chicks were captured by hand at nests, ringed, and measured. We determined wing, tarsus, and head length using a ruler with zero-stop and vernier calipers and body weight measured using Pesola spring balances for 747 chicks of great black-headed gulls, and 457 of them hatched from eggs that were measured. More

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    Priority effects shape the structure of infant-type Bifidobacterium communities on human milk oligosaccharides

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    Grey wolf genomic history reveals a dual ancestry of dogs

    Sampling, DNA preparation and sequencingStockholmSamples LOW002, LOW003, LOW006, LOW007, LOW008 and PON012 were processed at the Archaeological Research Laboratory at Stockholm University, Sweden, following methods previously described8. In brief, this involved extracting DNA by incubating the bone powder for 24 h at 37 °C in 1.5 ml of digestion buffer (0.45 M EDTA (pH 8.0) and 0.25 mg ml–1 proteinase K), concentrating supernatant on Amicon Ultra-4 (30-kDa molecular weight cut-off (MWCO)) filter columns (MerckMillipore) and purifying on Qiagen MinElute columns. Double-stranded Illumina libraries were prepared using the protocol outlined in ref. 48, with the inclusion of USER enzyme and the modifications described in ref. 49.Samples 367, PDM100, Taimyr-1 and Yana-1 were processed at the Swedish Museum of Natural History in Stockholm, Sweden, following previously described methods8. In brief, this involved extracting DNA using a silica-based method with concentration on Vivaspin filters (Sartorius), according to a protocol optimized for recovery of ancient DNA50. Double-stranded Illumina libraries were prepared using the protocol outlined in ref. 48, with the inclusion of USER enzyme.Samples ALAS_024, VAL_033, ALAS_016, VAL_008, HMNH_007, HMNH_011, VAL_050, VAL_005, DS04, VAL_037, VAL_012, VAL_011, VAL_18A, IN18_016 and IN18_005 were processed at the Swedish Museum of Natural History in Stockholm, Sweden, following previously described methods for permafrost bone and tooth samples51. In brief, this involved DNA extraction using the methodology of ref. 52 and double-stranded Illumina library preparation as described in ref. 48, with dual unique indexes and the inclusion of USER enzyme. Between eight and ten separate PCR reactions with unique indexes were carried out for each sample to maximize library complexity. The libraries were sequenced alongside samples HOV4, AL2242, AL2370, AL2893, AL3272 and AL3284 across three Illumina NovaSeq 6000 lanes with an S4 100-bp paired-end set-up at SciLifeLab in Stockholm.PotsdamSamples JAL48, JAL65, JAL69, JAL358, AH574, AH575 and AH577 were processed at the University of Potsdam. Pre-amplification steps (DNA extraction and library preparation) were conducted in separated laboratory rooms specially equipped for the processing of ancient DNA. Amplification and post-amplification steps were performed in different laboratory rooms. DNA was extracted from bone powder (29–54 mg) following a protocol specially adapted to recover short DNA fragments52. Single-stranded double-indexed libraries were built from 20 µl of DNA extract according to the protocol in ref. 53. The libraries were sequenced on an HiSeq X platform at SciLifeLab in Stockholm.Tübingen/JenaSamples JK2174, JK2175, JK2179, JK2181, JK2183, TU144, TU148, TU839 and TU840 were processed at the University of Tübingen, with DNA extraction and pre-amplification steps undertaken in clean room facilities and post-amplification steps performed in a separate DNA laboratory. Both laboratories fulfil standards for work with ancient DNA54,55. All surfaces of tooth and bone samples were initially UV irradiated for 30 min, to minimize the potential risk of modern DNA contamination. Subsequently, DNA was extracted by applying a well-established guanidine silica-based protocol for ancient samples52. Illumina sequencing libraries were prepared by using 20 µl of DNA extract per library48; afterwards, dual barcodes (indexes) were chemically added to the prime ends of the libraries56. For the samples from Auneau (TU839 and TU840), five sequencing libraries each were prepared; for all other samples processed in Tübingen, three sequencing libraries each were prepared. To detect potential contamination of the chemicals, negative controls were conducted for extraction and library preparation. After preparation of the sequencing libraries, DNA concentration was measured with qPCR (Roche LightCycler) using corresponding primers48. The DNA concentration was given by the copy number of the DNA fragments in 1 µl of the sample.Amplification of the indexed sequencing libraries was performed using Herculase II Fusion under the following conditions: 1× Herculase II buffer, 0.4 µM IS5 primer and 0.4 µM IS6 primer48, Herculase II Fusion DNA polymerase (Agilent Technologies), 0.25 mM dNTPs (100 mM; 25 mM each dNTP) and 0.5–4 µl barcoded library as template in a total reaction volume of 100 µl. The applied amplification thermal profile was processed as follows: initial denaturation for 2 min at 95 °C; denaturation for 30 s at 95 °C, annealing for 30 s at 60 °C and elongation for 30 s at 72 °C for 3 to 20 cycles; and a final elongation step for 5 min at 72 °C. Thereafter, the amplified DNA was purified using a MinElute purification step and DNA was eluted in 20 µl TET. The concentration of the amplified DNA sequencing libraries was measured using a Bioanalyzer (Agilent Technologies) and a DNA1000 lab chip from Agilent Technologies.The sequencing libraries were sequenced on an Illumina HiSeq 4000 platform at the Max Planck Institute for Science of Human History in Jena. The samples from Auneau (TU839 and TU840) were paired-end sequenced applying 2 × 50 + 8 + 8 cycles. All other libraries prepared in Tübingen were single-end sequenced using 75 + 8 + 8 cycles.OxfordSamples AL2657, AL2541, AL2741, AL2744, AL3185, AL2350, CH1109, AL2370, AL3272 and AL3284 were processed at the dedicated ancient DNA facility at the PalaeoBARN laboratory at the University of Oxford, following methods described previously8. In brief, double-stranded libraries were constructed following the protocol in ref. 48. These libraries were sequenced on a HiSeq 2500 (AL2657, AL2541, AL2741, AL2744) or a HiSeq 4000 (AL3185, AL2350, CH1109) instrument at the Danish National Sequencing Center or on a NextSeq 550 instrument (AL2741) at the Natural History Museum of London. For samples AL2370, AL3272 and AL3284, between six and eight separate PCR reactions with unique indexes were carried out on their libraries and they were sequenced alongside samples HOV4, VAL_18A and IN18_016 on an Illumina NovaSeq 6000 lane with an S4 100-bp paired-end set-up at SciLifeLab in Stockholm.CopenhagenSamples CGG13, CGG17, CGG19, CGG20, CGG21, CGG25, CGG26, CGG27, CGG28, CGG34, Tumat1 and IRK were processed at the GLOBE Institute, University of Copenhagen. All pre-PCR work was performed in ancient DNA facilities following ancient DNA guidelines57. The details of extraction, library construction and sequencing for the samples with CGG codes are described in ref. 21, in relation to the publication of mitochondrial data from these specimens. The Tumat1 sample was processed following the exact same protocol. In brief, DNA extraction was performed using a buffer containing urea, EDTA and proteinase K50, double-stranded libraries were prepared with NEBNext DNA Sample Prep Master MixSet 2 (E6070S, New England Biolabs) and Illumina-specific adaptors48, and sequencing was performed on an Illumina HiSeq 2500 platform using 100-bp single-read chemistry. For the IRK sample, DNA was extracted from three subsamples and purified as described in ref. 21. The three DNA extracts and the purified pre-digest of one subsample were incorporated into double-stranded libraries following the BEST protocol58, with the modifications described in ref. 59, and sequenced on a BGISEQ-500 platform using 100-bp single-read chemistry.Santa CruzSamples SC19.MCJ017, SC19.MCJ015, SC19.MCJ010 and SC19.MCJ014 were processed at the UCSC Paleogenomics Lab and were provided by the Yukon Government Paleontology program. All pre-PCR work was performed in a dedicated ancient DNA facility at the University of California, Santa Cruz, following standard ancient DNA methods60. Subsamples (250–350 mg) were sent to the UCI KECK AMS facility for radiocarbon dating, and the remaining amounts were powdered in a Retsch MM400 for extraction. For each sample, ~100 mg of powder was treated with a 0.5% sodium hypochlorite solution before extraction to remove surface contaminants61 and then combined with 1 ml lysis buffer for extraction, following the protocol in ref. 52. Samples were processed in parallel with a negative control. We quantified the extracts using a Qubit 1× dsDNA HS Assay kit (Q33231) before preparing libraries. We prepared single-stranded libraries following the protocol in ref. 62 and amplified the libraries for 9–16 cycles as informed by qPCR. After amplification, we cleaned the libraries using a 1.2× SPRI bead solution and pooled them to an equimolar ratio for in-house shallow quality-control sequencing on a NextSeq 550 paired-end 75-bp run. We then sent the libraries to Fulgent Genetics for deeper sequencing on two paired-end 150-bp lanes on a HiSeq X instrument.ViennaSample HOV4 was processed at the Department of Anthropology, University of Vienna. The sample is a canine tooth, which after sequencing was determined to derive from a dhole (Cuon alpinus). DNA was extracted from its cementum using the methods described in ref. 63 with a modified incubation time of ~18 h. The library was prepared according to the protocol in ref. 48 with the modifications from ref. 64. Five separate PCR reactions with unique indexes were carried out on the library and were sequenced alongside samples VAL_18A, IN18_016, AL2242, AL2370, AL2893, AL3272 and AL3284 on an Illumina NovaSeq 6000 lane with an S4 100-bp paired-end set-up at SciLifeLab in Stockholm.An overview of all samples and their associated metadata is available in Supplementary Data 1.Genome sequence data processingFor paired-end data, read pairs were merged and adaptors were trimmed using SeqPrep (https://github.com/jstjohn/SeqPrep), discarding reads that could not be successfully merged. Reads were mapped to the dog reference genome canFam3.1 using BWA aln (v.0.7.17)65 with permissive parameters, including a disabled seed (-l 16500 -n 0.01 -o 2). Duplicates were removed by keeping only one read from any set of reads that had the same orientation, length and start and end coordinates. For sample Taimyr-1, previously published data13 were merged with newly generated data. Data from samples processed in Copenhagen were processed as described previously66 except that they were also mapped to canFam3.1. Post-mortem damage was quantified using PMDtools (v0.60)67 with the ‘–first’ and ‘–CpG’ arguments.Genotyping and integration with previously published genomesTo construct a comparative dataset for population genetic analyses, we started from a published variant call set compiling 722 modern dog, wolf and other canid genomes from multiple previous studies (NCBI BioProject accession PRJNA448733)40. To this, we added additional modern whole genomes from other studies: 4 African golden wolves and 15 Nigerian village dogs (Genome Sequence Archive (http://gsa.big.ac.cn/), accession PRJCA000335)68, 12 Scandinavian wolves (European Nucleotide Archive accession PRJEB20635)69, 9 North American wolves and coyotes (European Nucleotide Archive accession PRJNA496590)25 and 8 other canids (African hunting dog, dhole, Ethiopian wolf, golden jackal, Middle Eastern grey wolves) (European Nucleotide Archive accession PRJNA494815)22. Reads from these genomes were mapped to the dog reference genome using bwa mem (version 0.7.15)70, marked for duplicates using Picard Tools (v2.21.4) (http://broadinstitute.github.io/picard), genotyped at the sites present in the above dataset using GATK HaplotypeCaller (v3.6)71 with the ‘-gt_mode GENOTYPE_GIVEN_ALLELES’ argument and then merged into the dataset using bcftools merge (http://www.htslib.org/). The following filters were then applied to sites and genotypes across the full dataset: sites with excess heterozygosity (bcftools fill-tags ‘ExcHet’ P value 5.8×. For divergence time analyses, haploid X chromosomes from two different male genomes were combined and the point at which the inferred effective population size for this ‘pseudodiploid’ chromosome increased sharply upwards was taken to correspond to a population divergence. Results were scaled using a mutation rate of 0.4 × 10−8 mutations per site per generation13,87 (with a 25% lower rate for X-chromosome analyses) and a mean generational interval of 3 years13. For effective population size inferences, transition variants were ignored and results were scaled using a transversions-only mutation rate inferred from results on modern genomes. For more details on the MSMC2 analyses, see Supplementary Information section 3.Selection analysesSelection analysis was performed using PLINK (v1.90b5.2)88. This analysis used the 72 ancient wolf genomes and 68 modern wolf genomes (with the latter including a historical Japanese wolf genome73 treated as ancient for analysis purposes, with its age set to 200 bp). A list of the genomes used for this analysis is available in Supplementary Data 2 (“Used for selection scan” column). All SNPs, not only transversions, were used for this analysis. The age of each wolf was set as the phenotype, with values of 0 for modern wolves, and the ‘–linear’ argument was used to test for an association between SNP genotypes and age, also applying the ‘–adjust’ argument to correct P values using genomic control. The application of genomic control34 here aimed to use the magnitude of temporal allele frequency variance observed across the genome to account for what was observed from genetic drift alone given wolf demographic history. Only results for the following sets of sites were retained and included in the Manhattan plot: sites where at least 40 ancient genomes had a genotype call, sites with a minor allele frequency among the ancient wolves of ≥5% and sites that had at least 7 neighbouring sites within a 50-kb window with a P value that was at least 90% as large (on a log10 scale) as the P value of the site itself. The last ‘neighbourhood filter’ aimed to reduce false positives by requiring similar evidence across multiple nearby sites. As a P-value significance cut-off to correct for the genome-wide testing, we used 5 × 10−8, which is commonly used in genome-wide association studies in humans and also in dogs89. We excluded 15 regions where only a single variant reached significance. A detailed table with the 24 detected regions is available in Supplementary Data 3. To test the robustness of this analysis to false positives arising from genetic drift alone, we applied the same analysis to data from neutral coalescent simulations generated using ms90 and found no false positives. For more details, see Supplementary Information section 4.Ancestry modelling with qpAdm and qpWaveWe used the qpAdm and qpWave methods43 from ADMIXTOOLS (v5.0)84 to test ancestry models for wolf and dog targets postdating 23 ka. For the primary analyses, we used the following set of candidate source populations (age estimate in brackets, years bp): Armenia_Hovk1.HOV4 (ancient dhole), Siberia_UlakhanSular.LOW008 (70,772), Germany_Aufhausener.AH575 (57,233), Siberia_BungeToll.CGG29 (48,210), Germany_HohleFels.JK2183 (32,366), Siberia_BelayaGora.IN18_016 (32,020), Yukon_QuartzCreek.SC19.MCJ010 (29,943), Altai_Razboinichya.AL2744 (28,345), Siberia_BelayaGora.IN18_005 (18,148) and Germany_HohleFels.JK2179 (13,229). We used a rotating approach in which, for each target, we tested all possible one-, two- and three-source models that could be enumerated from the above set. Individuals from the set that were not used as a source in a given model served as thereference set (or the ‘right’ population in the qpAdm framework). This means that, in every model, each of the above individuals was always either in the source list or in the reference list. We ranked models on the basis of their P values, but prioritized models with fewer sources using a P-value threshold of 0.01: if a simpler model (meaning a model with fewer sources) had a P value above this threshold, it ranked above a more complex model (meaning a model with more sources) regardless of the P value of the latter. We also failed models with inferred ancestry proportions larger than 1.1 or smaller than −0.1. For single-source models, qpWave was run instead of qpAdm. Both programs were run with the ‘allsnps: YES’ option (without this option, there was very little power to reject models). We describe ancestry assigned to the ancient dhole source (Armenia_Hovk1.HOV4) as ‘unsampled’ ancestry; note that this does not imply that such ancestry is of non-wolf origin, only that it is not represented by (that is, diverged early from and lacks shared genetic drift with) the ancient wolf genomes in the reference set.To test whether any post-23 ka or modern wolf genome available might be a good proxy for the western Eurasian wolf-related ancestry identified in Near Eastern and African dogs, we added the 9,500-year-old Zhokhov dog17 to the rotating set of candidate source populations. Chosen for its high coverage, early date and easterly location, this makes the assumption that the Zhokhov dog is a good representative for the eastern dog ancestry component. Using the African Basenji dog as a target, models involving the Zhokhov dog plus another given wolf thus allowed us to test whether that wolf was a good match for the additional component of ancestry. For more details on the qpAdm and qpWave analyses, see Supplementary Information sections 2 (wolf targets) and  5 (dog targets).Reporting summaryFurther information on research design is available in the Nature Research Reporting Summary linked to this paper. More