Philippa Kaur

Natural diets of tropical birds vary within speciesWe collected 62 regurgitated samples (using the tartar emetic method 22) from multiple tropical bird species representing four bird orders (Columbiformes–Pigeons, Coraciiformes–Kingfishers, Psittaciformes–Parrots, and Passeriformes–Passerines). First, we characterized diet components visually and then through metabarcoding of 52 of these samples using universal primers targeting invertebrates (Cytochrome c oxidase subunit I: COI gene) and plants (Internal transcribed spacer 2: ITS2 gene) (Table S1 and Fig. 2). Through visual identification, we identified plant material in 26 samples. The most common visually identified invertebrate orders were Araneae (spiders—27 samples), and Coleoptera (beetles—27 samples) (Table S2). Metabarcoding sequences were analysed using the OBITools software25. Overall, we found 47 plant operational taxonomic units (OTUs—97% sequence similarity threshold) and 180 invertebrate OTUs (Table S3). Plant items were dominated by the orders Rosales (27.7% OTUs), Fabales (8.5% OTUs), and Sapindales (8.5% OTUs). Except for four OTUs, all plants were identified to the genus level. Of the invertebrate OTUs, 54 belonged to feather mites (known feather symbionts), endoparasites, and rotifers (likely due to accidental consumption along with drinking water), and these OTUs were removed from further analyses, leaving 126 potential dietary invertebrate OTUs. Invertebrate samples were dominated by the classes Insecta (67.5% OTUs) and Arachnida (28.6% OTUs). At the order-level, dietary items were mainly represented by Araneae (spiders—28.6% OTUs), Hemiptera (true bugs—15.9% OTUs), Diptera (flies—14.3% OTUs), and Lepidoptera (moths and butterflies—10.3% OTUs). However, 77% of the invertebrate OTUs could not be identified to genus level, highlighting the limited research on genotyping invertebrate communities in Papua New Guinea.Figure 2Natural diets of wild birds vary between individuals of the same species and the results of the two identification methods of dietary components (visual identification and metabarcoding). Relative abundances based on the presence/absence of data of different dietary components are indicated in colours. Only invertebrates are separated into taxonomic orders as visual identification is unable to identify plant orders. Individuals depicted with asterisks had both crop microbiome and diet samples (dataset 1), while black font represents individuals with both cloacal microbiomes and diet samples (dataset 2). Individuals are clustered according to the species (each species is given a six-letter code name) and their literature-based dietary guilds. The order of the species is indicated with illustrations (Columbiformes–Pigeons, Coraciiformes–Kingfishers, Passeriformes–Passerines and Psittaciformes–Parrots), while ‡ represents diet samples with a complete consensus between the two identification methods.Full size imageDiet item identification differed markedly between visual and metabarcoding methods (Fig. 2, Tables S2 and S3). The diet components of individuals also varied notably within species (Figs. 2 and S1). Only diets of 12 out of 52 individuals were fully congruent between the two methods (Fig. 2). Of these 12 samples, eight had only plant material. Identification of invertebrate orders also differed between the two methods (Fig. 2, Table 1). Both methods identified the arthropod orders Hemiptera, Diptera, Orthoptera (crickets and locusts), and Araneae in the same samples (Fig. 2 and Table 1), while metabarcoding detected lower proportions of Coleoptera than the visual identification (Table 1).Table 1 Comparison between diet items identified in the regurgitated samples from the two approaches (visual identification and metabarcoding).Full size tableComparison of microbiomes and consumed diet itemsFor subsequent comparisons of diets and microbiomes, we utilised individual datasets from both visual identification (diet components identified at the order level) and metabarcoding (both OTU and order level), and a combination (order level) of both approaches (for details see “Methods” section on identifying prey items). Due to differences between the diet identification methods, a combination of the results was used to circumscribe the full diversity of consumed diets and to account for inherent biases associated with the two methods (i.e., the inability to identify plant material and smaller body parts of invertebrates visually, and extraction and sequencing biases associated with metabarcoding). We separated the microbiome dataset into three datasets due to sequencing limitations: dataset 1 included 12 birds with successfully sequenced crop microbiomes and diets identified using both methods, dataset 2 included 27 birds with successfully sequenced cloacal microbiomes and diets, and dataset 3 included 17 birds for which we obtained successfully sequenced crop and cloacal microbiomes (Table S1). Prior to subsequent analyses, each microbiome dataset was rarefied to even sequencing depths using the sample with the lowest number of sequences26 (Fig. S2).Crop microbiome similarity did not align with the consumed diet similarity (dataset 1)Out of the collected crop samples (N = 62), samples from only 19 individuals were successfully sequenced for their microbiomes. Of these individuals, we acquired diet samples for 12 individuals. Bacterial 16S rRNA MiSeq sequences were analysed using the DADA2 pipeline27 within QIIME228. There were 351,867 bacterial sequences (mean ± SD: 29,322 ± 33,009) in the crop microbiomes prior to rarefaction (Table S4). After rarefaction, bacterial sequences were identified to 615 amplicon sequence variants (ASVs—100% sequence similarity). Crop microbiomes were dominated by Proteobacteria (53.6%), Actinobacteria (18.9%), and Firmicutes (17.9%). Alpha diversities of individual microbiomes were calculated using the diversity function in the microbiome package29 and they did not differ significantly between host orders [Chao1 richness: Kruskal Wallis (KW) χ2 = 4.559, df = 3, p = 0.2271; Shannon’s diversity index: χ2 = 2.853, df = 3, p = 0.4149], or literature-based dietary guilds (Chao1 richness: KW χ2 = 4.317, df = 2, p = 0.1155; Shannon’s diversity index: KW χ2 = 2.852, df = 2, p = 0.2403) (Fig. S3).The compositional differences of crop microbiomes were investigated with the adonis2 function in the vegan package30 using permutational multivariate analyses of variance tests (PERMANOVA). These analyses revealed that the bird host order did not influence the crop microbiome composition (PERMANOVA10,000 permutations: Bray–Curtis: F = 1.251, R2 = 0.0993, p = 0.1911; Jaccard: F = 1.154, R2 = 0.0962, p = 0.2191) (Fig. S1). The effect of feeding guild was masked by host order as they are strongly correlated in this dataset. Furthermore, the lack of an effect of host taxa on crop microbiomes may be a result of the small sample sizes.We further investigated whether alpha diversity of the crop microbiomes was influenced by the diet item diversity of individuals. The Chao1 richness estimates of the microbiomes and the richness of the consumed diet items (number of different diet items based on the combined results) of individuals were not significantly correlated (Table S5), suggesting that the diet richness does not impact crop microbiome richness. However, Shannon’s diversity index of crop microbiomes and diet diversity were marginally significantly negatively associated (Table S5). This suggests that despite the lack of an association between diet and microbiome richness, crop microbiome evenness could be influenced by diet diversity.We then explored the association between the crop microbiome composition and the consumed diets, investigating correlations between Bray–Curtis and Jaccard dissimilarities of microbiomes, and Jaccard dissimilarity of diets using Mantel tests in the vegan package30. The compositional similarity of the diets based on any of the methods (visual, metabarcoding—both OTU and order-level separately, and combined) did not correlate significantly with crop microbiome compositions (Table 2 and Fig. S4). We observed similar non-significant associations between diets and microbiomes when investigating host orders separately (Table S6). This suggests that overall crop microbiomes of individuals are not completely modelled by the composition of the consumed diets.Table 2 Results of Mantel tests between the crop (dataset 1) and the cloacal (dataset 2) microbiome similarities (measured with both Bray–Curtis and Jaccard distances) and the consumed diet similarities (measured with Jaccard distances).Full size tableHost-taxon specific cloacal microbes are associated with different diet items (dataset 2)We obtained 27 individuals from 15 bird species with successfully sequenced cloacal microbiomes and diet samples (based on both metabarcoding and visual identification). Prior to rarefying, we acquired 818,272 bacterial sequences from the cloacal swab samples (mean ± SD: 30,306 ± 20,903) (Table S7). After rarefaction, bacterial sequences were assigned to 1,324 ASVs that belonged to Actinobacteria (35.9%), Proteobacteria (32.6%), Firmicutes (21.2%) and Tenericutes (5.0%). Cloacal microbiome alpha diversity did not differ significantly between different bird orders (Chao1 richness: KW χ2 = 2.624, df = 3, p = 0.4532; Shannon’s diversity: χ2 = 6.595, df = 3, p = 0.0861) or literature-based dietary guilds (Chao1 richness: KW χ2 = 1.128, df = 3, p = 0.7703; Shannon’s diversity: KW χ2 = 1.673, df = 3, p = 0.6429) (Fig. S5).However, cloacal microbiome beta diversity was significantly influenced by host bird order (PERMANOVA10,000 permutations: Bray–Curtis: F = 2.159, R2 = 0.2055, p  More

Patterns of species abundanceIn their analysis of the fossil assemblage of VM4, Luzón et al.1 indicate that herbivorous taxa comprise the bulk of the fauna. Their data, compiled in Table 1, show that herbivore remains represent 94.2% (1492/1578) of NISP and 78.8% (41/52) of MNI values for large mammals. These figures are close to those of VM3, 93.5% (6570/7027) and 84.4% (287/340), respectively (Table 1). A χ2 test shows that these differences are not statistically significant (p  > 0.3 in both cases). Among herbivores, Luzón et al.1 indicate that E. altidens is the species most abundantly preserved, both in frequency of remains and number of individuals, followed by cervids, bison, caprines, and megaherbivores (i.e., elephant, rhino, and hippo). This is also the situation in VM3 according to data compiled in Table 1: for example, the NISP value of E. altidens represents 31.8% (124/390) of the remains of large mammal identified in VM4 and 49.6% (2937/5924) in VM3. Although this difference is statistically significant (χ2 = 46.408, p  0.75). The difference based on NISP values seems high, but it falls within the range expected from variations in abundance data from different years for the ungulate prey more common in Serengeti, where the frequencies of Thomson’s gazelle, wildebeest, and zebra fluctuated in the late sixties between 18.9–56.3%, 21.3–42.8%, and 11.1–15.7%, respectively15,16. Finally, P. brevirostris is the species most represented among carnivores in both assemblages according to NISP values (Table 1), 26.8% (15/56) in VM4 and 30.0% (122/407) in VM3 (χ2 = 0.241, p  > 0.6), followed by canids, ursids and felids.The distribution of NISP and MNI values among taxa in VM4 and VM3 was further analysed using an approach based on contingency tables. The table for NISP values shows a significant χ2 value (Table 2, left part). This results from some differences in taxa abundance between the assemblages compared, which are reflected in the adjusted residuals: remains of megaherbivores and carnivores (excluding hyaenas) are represented in VM4 by higher frequencies than those expected from a random, homogeneous distribution, while they are underrepresented in VM3. This applies to the estimates obtained for VM4 using the data of Luzón et al.1 and our own data (Tables S1, S2). The NISP values estimated for P. brevirostris by Luzón et al.1 suggest a higher frequency of this carnivore in VM4 than in VM3, as indicated by the adjusted residual. However, the abundance of hyaena remains in our dataset for VM4 does not depart significantly from the expectations, as happens in VM3. Given that the database of Luzón et al.1 includes less than half of the remains of large mammals included in our database (Table 2), this suggests that the high frequency of P. brevirostris reported in VM4 results from poor sampling. The remains of other carnivores are more abundantly represented in VM4 than in VM3. However, it must be noted that a study of 24 dens of the three living hyaenas showed that the abundance of carnivore remains is highly variable, even among dens of the same species17. The distribution of MNI values among taxa in VM4 and VM3 (Table 2, right part) does not differ from the expectations of a random distribution according to the low χ2 value of the contingency table. Only the adjusted residual for megaherbivores, which are slightly over-represented in VM4 according to the data of Luzón et al.1, is statistically significant, while their abundance in VM3 is slightly lower than expected. Moreover, the probabilities of obtaining in the randomization tests the cumulative χ2 values observed for the NISP and MNI values of each species (p  0.97, respectively; Fig. S4) are equivalent to those obtained with their groupings in Table 2.Table 2 Contingency tables for the abundance of large mammals in the assemblages of the two excavation quarries of Venta Micena compared in this study, VM4 (a: data published by Luzón et al.1 for the fossils unearthed during the years 2005 and 2019–2020; b: unpublished data analysed by M.P. Espigares for the fossils of 2005 and 2013–2015) and VM3 (updated from Ref.9).Full size tableIn summary, the comparison of the faunal assemblages from both excavation quarries (Tables 1, 2) only shows some minor differences in taxa abundance for horse, megaherbivores, and carnivores other than the hyaena, as well as the presence in VM3 of some remains of two small ungulates (a roe deer-sized cervid and a chamois-sized bovid) and two small carnivores (Table 1), which are not reported by Luzón et al.1. Given their comparatively low number of specimens studied at VM4, it is reasonable to expect that the latter taxa, which are poorly represented in VM3, will also appear in VM4 during future excavations.Age mortality profilesLuzón et al.1 indicate that two megaherbivores, elephant Mammuthus meridionalis and rhino Stephanorhinus aff. hundsheimensis, show frequencies of non-adults that are close to, or even higher than, those of adults, as happens in VM3 (Table 1). However, the low MNI counts for these species in VM4 do not allow to state this: for example, elephants are represented by a juvenile and an adult, which gives a frequency of 50% of non-adults; with a sample size of only two individuals, the 95% confidence interval calculated with a binomial approach for this percentage is 1.3–98.7% (Table 1). In S. hundsheimensis, the frequency of non-adults, 80% (4/5), has also a very wide confidence interval (28.4–99.5%). In three species of medium-to-large sized ungulates, E. altidens, the ancestor of water buffalo Hemibos aff. gracilis and P. verticornis, Luzón et al.1 report similar frequencies of adults and non-adults, while they indicate that Bison sp. shows a lower frequency of juveniles (Table 1). This is true for horse and deer (58.3% and 42.9% of non-adults, respectively), but Hemibos is only recorded by one adult individual, which means that the percentage of non-adults for this species is not reliable. Luzón et al.1 calculate the percentage of 33% non-adult bison over a sample of only three individuals, of which one is a juvenile: the confidence interval for non-adults (0.8–90.6%) comprises the frequencies for horse and megacerine deer (Table 1), which rules out their suggestion of a lower frequency of juveniles for this bovid. In contrast to VM4, the abundances of non-adult horse, bison and megacerine deer are similar in VM3 (Table 1), where they are represented by higher MNI counts (which makes their percentages reliable). A similar reasoning can be applied to the claim of Luzón et al.1 that adults outnumber calves and juveniles among smaller herbivores such as the Ovibovini Soergelia minor, the Caprini Hemitraus albus and the cervid Metacervocerus rhenanus: in these species, MNI counts are very low to calculate reliably the percentage of juveniles (see their confidence intervals in Table 1). In fact, Luzón et al.1 acknowledge this limitation when they write that “the total number of individuals in each species is too low to draw reliable conclusions on the resulting patterns” and “a prime-dominant, L- or U-shaped mortality profile cannot be clearly discerned”. The situation in VM3 is quite different (Table 1): MNI counts for the two ungulates better represented in the assemblage, E. altidens and P. verticornis, allowed to reconstruct U-shaped attritional mortality profiles (Fig. 2b), which evidenced that the hypercarnivores focused on young and old individuals in the case of large prey6,7.Patterns of skeletal abundanceThe limitations and inaccuracies cited above result from the small sample analysed by Luzón et al.1 in VM4 (1578 remains of large mammals of which only 420 could be determined taxonomically and anatomically, compared to 8150 and 6331 remains in VM3, respectively: Table 1). These limitations apply also to their inferences on the skeletal profiles of ungulates. For example, they indicate that species of herbivore size class 2 (50–125 kg: M. rhenanus, H. albus, and S. minor) show biased skeletal profiles, with a predominance of teeth and elements of the forelimb over those of the hindlimb. In VM3, these ungulates also show higher frequencies of teeth than of bones, which has been interpreted as evidence of the transport by P. brevirostris of small-to-medium sized ungulates as whole carcasses to their denning site, where the giant hyaenas fractured the bones for accessing their medullary cavities and this resulted in their underrepresentation compared to teeth7,8,9,10. In the case of the major limb bones of these species in VM4, the elements of the forelimb (12.9%, 13 bones out of 101 determined remains) are twice as abundant as those of the hindlimb (6.9%, 7 bones), but these percentages do not differ statistically (χ2 = 2.028, p = 0.1544), which indicates the effects of poor sampling. In the species of herbivore size class 3 (125–500 kg), Luzón et al.1 indicate that they are well represented by all anatomical elements (e.g., craniodental elements account for ~ 30% of the remains, while both axial and appendicular elements show frequencies  > 20%). This pattern is like the one reported in VM3 for medium-to-large sized ungulates7,8,9,10. However, Luzón et al.1 indicate a bias in the disproportionate amount of posterior limb remains compared to anterior limb specimens, which in their opinion contrasts with the more balanced representation of these elements observed in VM3. Specifically, the number of forelimb bones (13.8%, 54 out of 392 bones) is about half the abundance of hindlimb bones (25.3%, 99 bones). This difference is statistically significant (χ2 = 16.460, p  More

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Hydrothermal vent rock and sediment sample collectionRock no. NA091-R045 (source of Ca. H. endolithica PR6, Ca. H. repetitus FW102 and Thorarchaeote FW25) and rock no. NA091-R008 (source of Heimdall group Gerdarchaeote AC18) were retrieved from the Auka hydrothermal vent site situated on the margin of the southern Pescadero Basin of the Gulf of California using remotely operated vehicle Hercules during research expedition NA091 on E/V Nautilus on 2 November 2017. Local venting fluids have a measured temperature approaching 300 °C, contain hydrocarbons and hydrogen and are precipitating minerals, such as calcite and barite15. R045 was collected during dive H1658 at coordinates 23.956987786° N, 108.86227922° W at a water depth of 3,674 m, near shimmering water, a sign of locally focused hydrothermal fluid discharge. R008 was collected during dive H1657 at coordinates 23° 57′ N, 108° 52′ W at a water depth of 3,651 m. After shipboard recovery, rock samples were placed in Mylar bags prefilled with 0.2 µm filtered bottom seawater collected during the same dive, flushed with N2 gas for 10 min, sealed and stored at 4 °C until preparation for incubations in the laboratory.Sediment sample no. FK181031-S0193-PC3 (source of Ca. H. aukensis) was collected during the research expedition FK181031 on R/V Falkor to the southern Pescadero Basin on 14 November 2018. The sample was collected during dive S193 at the Auka hydrothermal vent site (23.954822° N, 108.863009° W, water depth of 3,657 m), near the site where rocks nos. NA091-R045 and NA091-R008 were collected in 2017. The sediment push core was extruded upwards and sectioned into discrete 3 cm depth horizons on board immediately after recovery, transferred into sterile Whirl-Pak bags and sealed in a larger Mylar bag, flushed with argon gas, heat-sealed and stored at 4 °C until use in the laboratory.Sample collection permits for the expedition were granted by the Dirección General de Ordenamiento Pesquero y Acuícola, Comisión Nacional de Acuacultura y Pesca (Permiso de Pesca de Fomento no. PPFE/DGOPA-200/18) and the Dirección General de Geografía y Medio Ambiente, Instituto Nacional de Estadística y Geografía (authorization no. EG0122018), with the associated diplomatic note no. 18-2083 (CTC/07345/18) from the Secretaría de Relaciones Exteriores-Agencia Mexicana de Cooperación Internacional para el Desarrollo/Dirección General de Cooperación Técnica y Científica.Artificial seawater medium recipeArtificial seawater was prepared as described in Scheller et al.47 with minor modifications. Briefly, 1 l of artificial seawater (ASW) medium contained 46.6 mM MgCl2, 9.2 mM CaCl2, 485 mM NaCl, 7 mM KCl, 20 mM Na2SO4, 1 mM K2HPO4, 2 mM NH4Cl, 1 ml of 1,000× trace element solution, 1 ml of 1,000× vitamin solution and 0.5 mg of resazurin and was buffered by 25 mM HEPES buffer adjusted to pH 7.5. One litre of 1,000× trace element solution contained 50 mM nitrilotriacetic acid, 5 mM FeCl3, 2.5 mM MnCl2, 1.3 mM CoCl2, 1.5 mM ZnCl2, 0.32 mM H3BO3, 0.38 mM NiCl2, 0.03 mM Na2SeO3, 0.01 mM CuCl2, 0.21 mM Na2MoO4 and 0.02 mM Na2WO4. One litre of 1,000× vitamin solution contained 82 μM d-biotin, 45 μM folic acid, 490 μM pyridoxine, 150 μM thiamine, 410 μM nicotinic acid, 210 μM pantothenic acid, 310 μM para-aminobenzoic acid, 240 μM lipoic acid, 14 μM choline chloride and 7.4 μM vitamin B12.Enrichment cultivationRock no. NA091-R045 was anaerobically fragmented; then, approximately 5 g wet weight was crushed using a sterile agate mortar and pestle on 8 November 2018 and immediately immersed in anaerobic ASW medium in 25–125 ml of butyl rubber-stoppered serum bottles supplemented with different carbon/energy sources, including lactate, H2/CO2, hexane and decane and incubated in the dark at 40 °C (Extended Data Fig. 1a). The headspace for all cultures was flushed and overpressurized with N2 gas (2 atm). For the H2-containing cultures, the N2 gas headspace was replaced with H2/CO2 at an 80:20 mixture by flushing for 1 min and subsequent equilibration at 2 atm. After 33 d of incubation, the lactate-fed first-generation culture produced 5 mM sulphide, indicating active sulphate reduction. This enrichment was mixed by gentle shaking and diluted 1:100 vol/vol into fresh anaerobic ASW medium containing the same suite of carbon/energy sources as described above (Extended Data Fig. 1b). A transfer using the liquid fraction-lacking rock particles from the primary lactate enrichment was also included to enrich for members of the planktonic community alone with lactate as the carbon and energy source. This enrichment was later found to be devoid of the AAG (Heimdall) phylotype. Third- and fourth-generation cultures were set up in the following months through 1:100 dilution (Extended Data Fig. 1b). Further details of microbial community development in these enrichments are provided in Supplementary Note 1 and Supplementary Tables 1–3.R008 was prepared as above except using 2 atm of methane in the headspace as the sole carbon source and electron donor. The culture was passaged twice using a 1:100 dilution under the same culturing conditions; the cell fraction was collected by centrifugation after a total of 22 months for metagenomic sequencing (described below).For sediment enrichment cultivation, the top 3 cm section of the sediment core was mixed with anaerobic ASW at a 1:4 vol/vol ratio; a total of 60 ml volume each was dispensed into seven 125 ml glass serum bottles sealed with butyl rubber stoppers. The headspace was replaced by ethane (2 atm) in 2 bottles (Supplementary Table 5), while the headspace in 1 bottle was replaced by 100% N2 gas (2 atm). The cultures were incubated at 37 °C in the dark. Further details on microbial community development are provided in Supplementary Note 1 and Supplementary Table 4.Mineralogical analysesThe mineralogical composition of rocks NA091-R045 and R008 was characterized on a PANalytical X’Pert Pro X-Ray diffractometer. A dried rock aliquot was finely powdered using a clean agate mortar and pestle and scanned from 3 to 75° (2θ angle) at a 0.0167° step size. Mineral identification was performed with the X’Pert HighScore software v4.1 using the search and march algorithm.DNA extractionCombined cells with rock or sediment substrate were pelleted through centrifugation at 13,000 r.p.m. for 3 min. For amplicon sequencing, unless specified in Supplementary Table 6, DNA was extracted using the Qiagen DNeasy PowerSoil kit (catalogue no. 47014) according to the manufacturer’s instructions as described previously48 with a minor modification, where mechanical shearing was carried out using the MP Biomedicals FastPrep-24 system (catalogue no. 116004500) at level 5.5 for 45 s. For genomic sequencing, incubated rock and sediment cultures were extracted using multiple approaches, including the Qiagen DNeasy PowerSoil kit, ZymoBIOMICS 96 MagBead DNA Kit (catalogue no. D4302; Zymo Research Corporation), Quick-DNA 96 Kit (catalogue no. D3010; Zymo Research Corporation), ZymoBIOMICS DNA Microprep Kit (catalogue no. D4301; Zymo Research Corporation) and a standard phenol/chloroform-based protocol. The list of samples and their extraction methods are provided in Supplementary Table 6.16S rRNA gene amplicon sequencingFor amplicon (iTAG) sequencing of 16S rRNA genes, extracted DNA was amplified using primer pair 515f/806r GTGCCAGCMGCCGCGGTAA/ GGACTACHVGGGTWTCTAAT, barcoded and sequenced at Laragen using the Illumina MiSeq platform and analysed using Qiime v.1.8.0 (ref. 49) as described previously48. Taxonomic assignment was based on the SILVA 138 database (https://www.arb-silva.de)50.Full-length 16S archaeal rRNA gene sequences were amplified using the archaeal primer pair SSU1Arf/SSU1492Rngs TCCGGTTGATCCYGCBRG/ CGGNTACCTTGTKACGAC as described by Bahram et al.51, multiplexed as instructed by PacBio and sequenced using the PacBio Sequel II at the Brigham Young University DNA Sequencing Center and then analysed using the DADA2 package v1.9.1 in R v3.6.0 as described in Callahan et al.52 using the SILVA 138 database for taxonomic classification. Note that in the SILVA 138 database, all Asgard archaea clades are classified under Asgardarchaeota.Metagenomic sequencingA total of 11 metagenomic sequencing runs were performed using the Illumina and Oxford Nanopore platforms, with details listed in Supplementary Table 6. For Illumina short-read sequencing, libraries were constructed using the NEBNext Ultra and Nextera Flex Library kits as specified in the Supplementary Table 6. Sequencing was carried out using a HiSeq 2500 system (single-end, 100 bp) at the Caltech Genetics and Genomics Laboratory and HiSeq 4000 system at Novogene (paired-end, 150 bp). Only paired-end data were used for assembly, while all data were used for error correction. Due to the low DNA quantity obtained from the sediment incubation that yielded Ca. H. aukensis, we used multiple displacement amplification with the QIAGEN REPLI g Midi Kit before library preparation for Nanopore sequencing. Oxford Nanopore sequencing libraries were constructed using the PCR Barcoding Kit (catalogue no. SQK-PBK004) and were sequenced on MinION flow cells FLO-MIN106. Base calling was performed with the ONT Guppy software v.3.4.5.Genome assembly, error correction and read coverage mappingTwo different approaches were used to assemble contiguous genomes from metagenomes. For species of interest, if Nanopore sequencing yielded high read coverage and read lengths N50  > 2 kb, we obtained more contiguous genomes through de novo assembly purely based on Nanopore reads. If Nanopore sequencing did not yield a high number of reads or exhibited low read lengths, we obtained more contiguous genomes through de novo assembly first based on Illumina reads and then joined using Nanopore reads.For Ca. H. endolithica, Nanopore sequencing data were assembled de novo using Canu17 v.2.1, which yielded a 30 Mbp assembly, including a 3.4 Mbp contig. The approximate 40 kilobase (kb) regions at two ends of an approximate 3.4 Mbp contig were repetitive. This repeated region was deleted at one end and the two ends were joined to result in a circular genome. The resulting genome was mapped using BamM (http://ecogenomics.github.io/BamM/, based on Burrows–Wheeler Aligner53 mapping) with 150 bp Illumina paired-end reads (88× coverage on average) and 100 bp single-end reads (20× coverage). Mapped reads were then used for error correction through pilon54 v.1.22. To account for the reduced mapping at the edges (approximate 50 bp region), the two ends of the genomic sequence were joined, read-mapped and error-corrected again using the same methods. After the genome was annotated, it was rotated such that the genomic sequence ended with tRNA (GlyCCC), which was the integration site of the putative provirus HeimV1. All sequencing reads derived from incubations of the same rock were mapped onto the final genome using BamM, which was then used for coverage calculation through bedtools (https://bedtools.readthedocs.io/en/latest/).For Ca. H. aukensis, Illumina PE150 bp sequencing data were assembled using SPAdes18 v.3.14.1 with the ‘-meta’ option and k-mers 21,33,55,77,99. The assembly was then scaffolded using Nanopore reads through two iterations of LRScaf55 v.1.1.10. The Ca. H. aukensis genome was joined after trimming the identical sequences at the two ends. The end-joining region was verified through PCR amplification and Sanger sequencing using the primer pair CGCTTTCTTCAAACAATATTTCTGGTG/CTTACTTTCTCTCGGTCCATTTTTCAC. Finally, a 1 kbp stretch of unresolved genomic sequence at an approximate 2.9 Mbp position was resequenced through PCR amplification and Sanger sequencing using the primers GAGTTTTTTCAATCTTATAATGCCAAACTAAAAAATAG (forward), CAGTCAGATTTGACACAATTTTGGTC (reverse) and GCTGGACTCAACCTATAACTAATAGT (reverse). The final assembly was read-mapped, error-corrected through pilon v.1.24 using 346× coverage. It was rotated as described above to place the tRNA gene GlyCCC at the end.The metagenome containing the Lokiarchaeote Ca. H. repetitus FW102 was assembled using Canu v.2.1, as described for the Ca. H. endolithica genome, and then binned using metabat2 v.2.15 (ref. 56) with default parameters. The bin was then used to recruit long reads using minimap2 v.2.17 and reassembled and binned again. We then used LRScaf to scaffold the contigs and used ten iterations of pilon v.1.24 to achieve error correction and resolve ambiguous bases.The Thorarcheote FW25 MAG was assembled using the hybrid assembly of Illumina reads and Nanopore reads using SPAdes v.3.14.1 with k-mers 21,33,55,77,99, and then binned using metabat2 v.2.15 with default parameters. The MAG bin was then used to recruit reads through MIRAbait in the MIRA v.4 package (http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#chap_intro). These reads were then used for hybrid assembly with Nanopore long reads via SPAdes v.3.14.1 with k-mers 21,33,55,77,99. It was then binned again using metabat2 v.2.15 with default parameters to yield the final Thorarcheote FW25 MAG.The metagenome containing Gerdarchaeote AC18 was assembled from Illumina reads using SPAdes v.3.14.1 with k-mers 21,33,55,77,99 and then binned using metabat2 v.2.15 with default parameters. The MAG bin was then used to recruit reads through MIRAbait in the MIRA v.4 package and then reassembled and binned using SPAdes and metabat2 to yield the final Gerdarchaeote AC18 bin.Alignment fraction, ANI and AAIANI and alignment fraction values, independently calculated for rRNA, tRNA and coding gene sequences were obtained using ANIcalculator57 2014-127, v.1.0 (https://ani.jgi.doe.gov/html/download.php?). Note that Lokiarchaeote FW102 contains 2 copies of 16S rRNA genes at 99% identity with each other, and Thorarchaeote BC has a partial 16S rRNA gene. The alignment of 16S rRNA was carried out using SINA58 v.1.2.11. The AAI values of translated proteomes were obtained with the enveomics package v1.8.059. The final output is shown in Supplementary Table 7.Genome and mobilome annotationsGene calling was done using a combination of Prodigal v.2.6.3 and Glimmer v.3.0.2 using translation code 11 within the RASTtk60 pipeline, now under the PATRIC package v1.03261. Translated coding sequences were annotated and domain-assigned using eggNOG mapper39 v.2. The tRNA, 16S rRNA and 23S rRNA genes were identified using RNAmmer62 v.1.2 embedded in RASTtk. Thus far, 5S rRNA gene sequences could not be predicted through the existing HMM using various approaches. Long, non-tandem repeats were identified using RASTtk with the default cut-off of 95% identity and 100 bp. Tandem repeat sequences were identified using RASTtk, Prokka v1.14.6 and CRISPRCasTyper 1.1.463. Prokka and CRISPRCasTyper both employ MinCED (https://github.com/ctSkennerton/minced) to identify repeats and detect intragenic tandem repeats, which were manually removed from the CRISPR–Cas analyses. The Cas genes were annotated using CRISRCasTyper.All identified Heimdallarchaeum mobilomes were further analysed using PSI-BLAST 1.10.064, CDD search v3.1965 and PhANNs webserver (version March 2021)37.Genome evaluation and HMM constructionMarker coverage was carried out using a two-step process. First, we used the automated marker analyses via CheckM66 v.1.1.3 with the lineage_wf option and the default HMM E value cut-off, which included the 149 standard archaeal single-copy marker set. Next, each of the missing markers was examined with hmmer67 v.3.3.2 using the hmmsearch option with manual inspection of alignment regions and bitscores. This rescued markers unidentified through the default cut-offs by CheckM as well as divergent variants that most likely functionally replace the genuinely missing marker. The detailed description of markers missed by CheckM can be found in Supplementary Note 2 and the final evaluation of marker presence is displayed in Extended Data Fig. 4a and Supplementary Table 15. Next, we constructed an updated HMM set to replace the CheckM set by (1) updating all HMM to the most recent versions, (2) removing the six commonly missing or duplicated markers shown in Extended Data Fig. 4a from the list and (3) overcoming the pitfall of existing HMMs constructed using only a few sequences acquired from Euryarchaeota and Crenarchaeota. We manually constructed Asgard-specific versions based on the 282 Asgard archaea genomes. The HMMs constructed in this study are PF00832.ASG, PF00861.ASG, PF01194.ASG, PF01287.ASG, PF01667.ASG, PF03874.ASG, PF03876.ASG, PF13656.ASG, TIGR00270.ASG, TIGR00336.ASG, TIGR00442.ASG, TIGR02338.ASG and TIGR03677.ASG. The updated HMM file has been provided as a supplementary data file. The updated HMM was used to evaluate the 282 genomes reported in this study and in the literature3,6,7,8,9,10,11,12,16,23,26,68,69,70,71,72,73,74,75,76,77 through (1) CheckM, which uses Prodigal for gene calling, and (2) the more up to date HMMER3.2.2 on our gene calls described above. The latter generally produced slightly higher completeness and redundancy values (Supplementary Tables 8 and 9). For the expanded set of Asgard archaea genomes used for the phylogenomic analyses shown in Extended Data Fig. 4b, we applied the following filtering criteria: ≤100 contigs, >96% marker completeness and 20% sequence identity, >85% sequence alignment and 30% sequence identity, >90% sequence alignment and More

Generation timeDuring the infectious period, an infected individual may produce a secondary infection. However, the individual’s infectiousness is not constant during the infectious period, but it can be approximated by the probability distribution of the generation time (GT), which accounts for the time between the infection of a primary case and the infection of a secondary case. Unfortunately, such distribution is not as easy to estimate as that of the serial interval, which accounts for the time between the onset of symptoms in a primary case to the onset of symptoms of a secondary case. This is because the time of infection is more difficult to detect than the time of symptoms onset. Ganyani et al.27 developed a methodology to estimate the distribution of the GT from the distributions of the incubation period and the serial interval. Assuming an incubation period following a gamma distribution with a mean of 5.2 days and a standard deviation (SD) of 2.8 days, they estimated the serial interval from 91 and 135 pairs of documented infector-infectee in Singapore and Tianjin (China). Then, they found that the GT followed a gamma distribution with mean = 5.20 (95% CI = [3.78, 6.78]) days and SD = 1.72 (95% CI = [0.91, 3.93]) for Singapore (hereafter GT1), and with mean = 3.95 (95% CI = [3.01, 4.91]) days and SD = 1.51 (95% CI = [0.74, 2.97]) for Tianjin (hereafter GT2). Ng et al.28 applied the same methodology to 209 pairs of infector-infectee in Singapore and determined a gamma distribution with mean = 3.44 (95% CI = [2.79, 4.11]) days and SD 2.39 (95% CI = [1.27, 3.45]; hereafter GT3). Figure 3 shows the probability density functions (PDF) of such distributions, fGT. The differences between them are remarkable. For example, the 54.5%, 81.0%, and 80.7% of the contagions are produced in a pre-symptomatic stage (in the first 5.2 days after primary infection) assuming GT1, GT2, and GT3, respectively.Figure 3Probability density function of the generation time distribution, fGT(t), of GT1 (blue line; Singapore27), GT2 (yellow line; Tianjin27), GT3 (red line; Singapore28), and GTth (black line; theoretical distribution). Bars are the discretized version, (widetilde{{f_{GT} }}left( n right)), of the PDF of GTth.Full size imageTheoretically, assuming that the incubation periods of two individuals are independent and identically distributed, which is quite plausible, the expected/mean values of the GT and the serial interval should be equal29,30. The mean of the serial interval is easier to estimate than that of the GT. For that reason, we assume a mean serial interval as estimated from a meta-analysis of 13 studies involving a total of 964 pairs of infector-infectee, which is 4.99 days (95% CI = [4.17, 5.82])31, is more reliable than the aforementioned means of the GT. This value is within the error estimates of the means of GT1 and GT2, but not for GT3. Then, we construct a theoretical distribution for the GT that follows a gamma distribution (hereafter GTth) with mean = 4.99 days and SD = 1.88 days. This theoretical distribution can be seen in Fig. 3 and approximates the average PDF of three gamma distributions with mean = 4.99 and the SD of GT1, GT2, and GT3. We assume a conservative CI = [1.51, 2.39] for the theoretical SD, defined with the minimum and maximum SD values of GT1, GT2, and GT3. GTth shows 63.1% of pre-symptomatic contagions.
R

0

from r
In theory, the basic reproduction number R0 can be estimated as far as the intrinsic growth rate r, and the distributions of both the latent and infectious periods are known26,32,33,34. The latent period accounts for the period during which an infected individual cannot infect other individuals. It is observed in diseases for which the infectious period starts around the end of the incubation period, as happened with influenza35 and SARS36. However, from Fig. 3 it is inferred that COVID-19 is transmissible from the moment of infection, and we will assume a null latent period. Then, if the GT follows a gamma distribution, R0 can be estimated from the formulation of Anderson and Watson32, which was adapted to null latent periods by Yan26 as$$ R_{0} = frac{{mean_{GT} }}{{1 – left( {1 + mean_{GT} cdot r cdot frac{1}{{shape_{GT} }}} right)^{{ – shape_{GT} }} }} cdot r, $$
(4)
where meanGT is the mean GT and shapeGT is one of the two parameters defining the gamma distribution, which can be estimated as$$ shape_{GT} = frac{{left( {mean_{GT} } right)^{2} }}{{left( {SD_{GT} } right)^{2} }}. $$
(5)
For GTth, we get R0 = 1.50 (CI = [1.41, 1.61]) for REMEDID I(n) and R0 = 1.76 (CI = [1.60, 1.94]) for official I(n). For the other three GT distributions, R0 ranges from 1.39 (CI = [1.27, 1.58]) to 1.51 (CI = [1.34, 1.80]) for REMEDID I(n) and from 1.59 (CI = [1.40, 1.88]) to 1.78 (CI = [1.51, 2.23]) for official I(n) (Table 1). In all cases, R0 from GTth are within those from the three known GT distributions and indistinguishable from them within the error estimates. The lower (upper) bound of the CI is estimated as the minimum (maximum) R0 obtained from all the possible combinations of 100 evenly spaced values covering the CI of r, meanGT and SDGT. Then, following the Bonferroni correction, the reported CI present at least a 85% of confidence level for GT1, GT2, and GT3, but it cannot be assured for GTth since the CI of its SD is unknown. In general, all these R0 estimates are lower than those summarised by Park et al.20.Table 1 R0 and HIT values of the ancestral SARS-CoV-2 variant estimated from GT1, GT2, GT3, and GTth, and REMEDID and official infections. For date0, “Dec.” means December 2019, and “Jan.” means January 2020.Full size tableAlternatively, R0 can be estimated by applying the Euler–Lotka equation29,33,$$ R_{0} = frac{1}{{mathop smallint nolimits_{0}^{ + infty } e^{ – rt} cdot f_{GT} left( t right)dt}}. $$
(6)
In this case, we get values closer to previous estimates20. In particular, for GTth, we get R0 = 2.12 (CI = [1.81, 2.48]) for REMEDID I(n) and R0 = 2.92 (CI = [2.28, 3.75]) for official I(n). For the other three GT distributions, R0 ranges from 1.63 (CI = [1.43, 1.90]) to 2.21 (CI = [1.59, 2.95]) for REMEDID I(n) and from 1.97 (CI = [1.59, 2.54]) to 3.11 (CI = [1.84, 4.90]) for official I(n) (Table 1). The CI are estimated as in Eq. (4).R0 from a dynamical modelWe designed a dynamic model with Susceptible-Infected-Recovered (SIR) as stocks that accounts for the infectiousness of the infectors. Such a model is a generalisation of the Susceptible-Exposed-Infected-Recovered (SEIR) model37. Births, deaths, immigration and emigration are ignored, which seems reasonable since the timescale of the outbreak is too short to produce significant demographic changes. For the sake of simplicity, the recovered stock includes recoveries and fatalities, and it is denoted as R(t). A random mixing population is assumed, that is a population where contacts between any two people are equally probable. Time is discretized in days, so the real time variable t is replaced by the integer variable n. As a consequence, the derivatives in the differential equations defining the dynamic model explained below are discrete derivatives.The size of the population is fixed at N = 100,000, and then, for any day n we get$$ tilde{S}left( n right) + left( {mathop sum limits_{k = 0}^{20} tilde{I}left( n-k right)} right) + tilde{R}left( n right) = N, $$
(7)
where (tilde{S}left( n right)), (tilde{I}left( n right)), and (tilde{R}left( n right)) are the discretized versions of S(t), I(t), and R(t) and (tilde{I}) is assumed to be null for negative integers. The summation is a consequence of the infectiousness, which is approximated according to the GT, whose PDF is discretized as$$ widetilde{{f_{GT} }}left( n right) = mathop smallint limits_{n – 1}^{n} f_{GT} left( t right) dt, $$
(8)
from n = 1 to 20. Figure 3 shows (widetilde{{f_{GT} }}left( n right)) for GTth. Truncating at n = 20 accounts for 99.99% of the area below the PDF of all the GT. Then, an infected individual at day n0 is expected to produce on average$$ widetilde{{R_{e} }}left( {n_{0} + n} right) cdot widetilde{{f_{GT} }}left( n right) $$
(9)
infections n days later, where (widetilde{{R_{e} }}left( n right)) is the discretized version of Re(t). From this expression, it is obvious that values of (widetilde{{R_{e} }}left( n right) < 1) will produce a decline of infections. Conversely, infections at day n0 are produced by all individuals infected during the previous 20 days as$$ tilde{I}(n_{0} ) = tilde{R}_{e} left( {n_{0} } right) cdot left( {mathop sum limits_{n = 1}^{20} tilde{I}left( {n_{0} - n} right) cdot widetilde{{f_{GT} }}left( n right)} right), $$ (10) whose continuous version has been reported in previous studies29,38. The expression in brackets is called total infectiousness of infected individuals at day n039. According to Eq. (1), Eq. (10) can be expressed in terms of R0 as$$ tilde{I}(n_{0} ) = R_{0} cdot frac{{tilde{S}left( {n_{0} } right)}}{N} cdot left( {mathop sum limits_{n = 1}^{20} tilde{I}left( {n_{0} - n} right) cdot widetilde{{f_{GT} }}left( n right)} right). $$ (11) As we want a dynamic model capable of providing (tilde{I}left( {n_{0} } right)) from the stocks at time step n0 − 1, we replaced (tilde{S}left( {n_{0} } right)) by (tilde{S}left( {n_{0} - 1} right)) in Eq. (11). This assumption makes sense in a discrete domain since the infections at time n0 take place in the susceptible population at time n0 − 1. Then, assuming that all stocks are set to zero for negative integers, our dynamic model can be expressed in terms of Eq. (7) and the following differential equations:$$ delta tilde{I}(n_{0} ) = R_{0} cdot frac{{tilde{S}left( {n_{0} - 1} right)}}{N} cdot left( {mathop sum limits_{n = 1}^{20} tilde{I}left( {n_{0} - n} right) cdot widetilde{{{text{f}}_{GT} }}left( n right)} right) - tilde{I}(n_{0} - 1), $$ (12) $$ delta tilde{S}left( {n_{0} } right) = {-}tilde{I}left( {n_{0} } right), $$ (13) $$ delta tilde{R}left( {n_{0} } right) = tilde{I}left( {n_{0} - 21} right), $$ (14) where (delta tilde{I}), (delta tilde{S}), and (delta tilde{R}) are the (discrete) derivatives of (tilde{I}), (tilde{S}), and (tilde{R}), respectively. Applying the initial conditions (tilde{S}left( 0 right) = N - 1), (tilde{I}left( 0 right) = 1), and (tilde{R}left( 0 right) = 0), it is assumed that the outbreak was produced by only one infector. The latter is not true in Spain, since several independent introductions of SARS-CoV-2 were detected40. However, for modelling purposes it is equivalent to introducing a single infection at day 0 or M infections produced by the single infection n days later. Then, the date of the initial time n = 0 is accounted as a parameter date0, which is optimised, as well as R0, to minimise the root-mean square of the residual between the model simulated (tilde{I}left( n right)) and the REMEDID and official I(n) for the period from date0 to n0.The model was implemented in Stella Architect software v2.1.1 (www.iseesystems.com) and exported to R software v4.1.1 with the help of deSolve (v1.28) and stats (v4.1.1) packages, and the Brent optimisation algorithm was implemented. For REMEDID I(n) and GTth, we obtained date0 = 13 December 2019 and R0 = 2.71 (CI = [2.33, 3.15]). Optimal solutions combine lower/higher R0 and earlier/later date0 (Fig. 4), which highlights the importance of providing an accurate first infection date to estimate R0. When the other three GT distributions were considered, we obtained similar date0, ranging from 12 to 17 December 2019, and R0 values ranging from 2.08 (CI = [1.86, 2.42]) to 2.85 (CI = [2.05, 3.25]; see Table 1). For official infections, date0 was set to 1 January 2020 for all cases, and R0 ranged from 1.81 (CI = [1.64, 2.07]) to 2.41 (CI = [1.80, 2.91]). The CI are estimated as in Eq. (4).Figure 4Root-mean square (RMS) of the residuals between infections from the model, which depends on date0 (x-axis) and R0 (y-axis), and REMEDID (from MoMo ED) and official infections. Parameters optimizing the model are highlighted in purple. RMS larger than 1275 (left panel) and 103 (right panel) are saturated in white.Full size image More

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