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Study area and sampling locationsWe conducted this study in Kedarnath Wildlife Sanctuary (30° 25′–30° 41′ N, 78° 55′–79° 22′ E), located in Uttarakhand state in the western Himalayas of India. This sanctuary covers a broad elevational gradient from 1400 to 4000 m above sea level (asl) (Fig. 1), with corresponding changes in habitat types: from Himalayan moist temperate forests dominated by Quercus spp. at low elevations, to sub-alpine forests dominated by Rhododendron spp. and alpine meadows at high elevations34. This sanctuary is known to harbour 26 species of bats35.Figure 1Map of India showing the location of the study area, Kedarnath Wildlife Sanctuary, and the sampling locations within the study area. Elevation is in m asl. The map was created using QGIS (v 3.6.3-Noosa) (QGIS Geographical Information System, www.qgis.org). Please note that the geographical boundaries represented in the map may contain areas considered disputed.Full size imageWe sampled at four locations spanning an elevational gradient of 2200 m. Sampling points within each location were spread across the elevations mentioned in parentheses: Mandal (1500–1800 m), Ansuya (2000–2200 m), Chopta (2700–3000 m) and Tungnath (3300–3700 m) (Fig. 1). Sampling was conducted between late-March and mid-May in 2018 and 2019, starting at lower elevations and then moving to higher elevations. This sampling duration coincides with summer in the Himalaya. To comprehensively sample the bat diversity, we employed a combination of automated ultrasonic recorders and capture sampling using mist-netting. Fieldwork was approved by the Internal Committee for Ethics and Animal Welfare, Institute for Zoo and Wildlife Research (approval no. 2018-06-01), and conducted under a permit issued by the Uttarakhand State Forest Department, Government of India (permit no. 2261/5-6).Sampling strategyFor acoustic sampling, we placed full spectrum passive ultrasonic recorders (SongMeter SM4BAT, Wildlife Acoustics, Maynard, MA, USA) in different habitat types (open, forest edge, and forest) at each elevation (hereafter, “passive recordings”). The recorders were programmed to record bat calls for two consecutive nights at each sampling point, from dusk to dawn (9–10 h/night), using a sample rate of 500 kHz/s, an amplitude threshold of 16 dB and a frequency threshold of 5 kHz. The dominant habitats at Ansuya and Tungnath are montane evergreen forests and alpine meadows respectively, therefore only these habitats were sampled at these elevations. The exact number of sampling points per habitat for each elevation is given in Table S1. On separate days after completing acoustic sampling at a site, we set up nylon and monofilament mist nets of 4, 6 or 9 m length, 16 × 16 and 19 × 19 mesh sizes (Ecotone GOC, Sopot, Poland) for four hours following dusk (starting between 18.30 h in early summer and 19.30 h in late summer). The captured bats were handled and measured following the guidelines of the American Society of Mammalogists36. To further refine identification in light of the paucity of taxonomic knowledge in the region, we collected only one specimen each of taxonomically-challenging species in accordance with our field research permit. We measured body mass (accuracy 0.1 g) using a spring balance (Pesola, Schindellegi, Switzerland), and forearm length (accuracy 0.01 mm) with vernier calipers (Swiss Precision Instruments SPI Inc., Melville, NY, USA). Next, we gently stretched the left wing and placed the live animal perpendicular to the background of a graph sheet of 1 × 1 cm grids. We photographed the outstretched wing using a Nikon D3400 DSLR camera at 55 mm zoom from a distance of about 90 cm. Subsequently, we released the bats and recorded their echolocation calls at a distance of 5 to 10 m using a handheld ultrasonic detector (Anabat Walkabout, Titley Scientific, Brendale, QLD, Australia) and saved them as audio files of .wav format. These recordings (henceforth referred to as “reference recordings”) formed the dataset used to develop a call library for identification.Call classifier and analysis of passive recordingsReference recordings from 2018 and 2019 were labelled using Raven Pro 1.5 (Cornell Lab of Ornithology, Ithaca, NY, USA) to generate a dataset of acoustic parameters for identification. We visualized calls using a spectrogram with Hanning window, size 1024 samples with 95% overlap. From each recording, we selected 10 clear pulses and measured the following parameters: average peak frequency, maximum peak frequency, centre frequency, minimum peak frequency, peak frequency at the start and end of the call, bandwidth at 90% peak amplitude, average entropy, and call duration. All frequency variables were measured in Hz and time variables in ms. We used the peak frequency contour to determine start and end frequencies and also used bandwidth at 90% peak amplitude because higher frequencies attenuate quickly with distance from the emitting bat (causing changes to the bandwidth), and these measures are therefore more reliable in field circumstances. Using this labelled call library as a training dataset, we trained a fine K-nearest neighbours classifier using supervised learning within the ‘Classification Learner’ app in MATLAB (Mathworks, Inc., Natick, MA, USA). We further employed fivefold cross-validation to obtain estimates of the accuracy of each classifier in assigning calls to species. Using these pairwise values of relative accuracy (%), we generated confusion matrices for these classifiers where the species identities were represented in the columns and rows as ‘True’ and ‘Predicted’ classes, respectively. Any species with classification accuracy below 85% was clubbed with possible confusion species into a “sonotype”, to improve accuracy of the classifier in the most conservative way possible (Fig. S4). The complete list of sonotypes and their mean echolocation call parameters is presented in Table 1. The classifier identified these sonotypes with  > 80% accuracy, with the exception of Miniopterus and the Plecotus type B call (which, however, we could manually identify because of their call structures and frequencies). For all subsequent analyses on functional diversity and phylogenetic diversity, we used these sonotypes to ensure accurate identification.Table 1 Trait matrix of the sonotypes in our assemblage (FA in mm; fmaxe, pfc.min, and pfc.max in kHz; Duration in ms).Full size tableNext, we analysed the passive recordings manually in Raven Pro. We labelled calls in subsets of 15 min per hour of the passive recordings. For each hour, the 15-min subsets were in the time windows 0–5 min, 20–25 min and 40–45 min, so as to spread out our sampling window across the hour. Following labelling, we obtained sonotype IDs using the classifier, and then verified them manually by visual comparison to the call library to improve discrimination. For every 5-min interval, we made a presence-absence matrix where 1 indicated the presence of a sonotype and 0 indicated its absence. The number of 5-min intervals in which a sonotype was detected (hereby “acoustic detections”) was summed up for each sampling point. We measured the relative abundance of sonotypes as the proportion of its total number of acoustic detections relative to the total number of acoustic detections of all sonotypes in a given elevational location. The use of such a presence-absence framework is akin to ‘Acoustic Activity Index’37 which represents a relatively less biased index of activity that is less affected by differences in vocal behaviour and echolocation frequencies of different species of bats.Assessing detectabilityTo assess the completeness of our species inventory, we estimated the species richness of each sampling point using the first-order Jackknife Estimator (Jack 1)38. Jack 1 is a nonparametric procedure for estimating species richness using presence or absence of a species in a given plot rather than its abundance39. Mean species detectability was calculated as the ratio of the observed to estimated species richness for different sampling point-year combinations40,41. We then assessed whether this mean species detectability depended on the habitat type, year, and location by fitting a linear model with the above-mentioned variables as fixed factor predictors and the mean detectability as a response. We also determined species-level detectability by following the approach of Kéry and Plattner42. If a sonotype was detected by mistnetting or acoustic sampling in sampling event i, we modelled its probability to be detected in sampling event i + 1. For each sonotype, we fitted a generalized linear mixed-effects model (logit link and binomial error distribution) with detection/non-detection as the response variable, and habitat type, location, and year as the fixed factor predictors. Site and species were included as random intercepts. The significance of the fixed effects was assessed with the Likelihood Ratio Test. This test allows one to choose the best of two nested models by assessing the ratio of their likelihoods. The significance of the random effect (species) was assessed by applying a parametric bootstrap (number simulations = 100) to the model with and without the random effect, using the function bootMer of ‘lme4’ package. In short, a parametric bootstrap consists of fitting the model to the data and bootstrapping the obtained residuals. For these and other statistical analyses we used R version 4.0.2 (R Core Team 2020).Taxonomic diversityWe calculated rarefied incidence-based species richness (SR) and Simpson diversity extrapolated to 50 sampling events (the number of sampling events in Mandal) using the ‘iNEXT’ R package43. The calculations were performed on a sonotype-by-sampling point presence-absence matrix with detections from both acoustic sampling and mistnetting pooled together. In the matrix, columns represented sampling units (Night 1, Night 2 and so on) and rows represented sonotype. By using sonotypes instead of species, we likely underestimated the SR, but this underestimation was uniform across elevations and is unlikely to change the pattern of SR with elevation.Functional diversityOur functional trait matrix (Table 1) comprised seven morphological and acoustic traits involved in guild classification, foraging and micro-habitat preferences (abbreviation followed by units): forearm length (FA, mm), aspect ratio (AR), wing loading (WL, N/m2), tip-shape index (I), echolocation peak frequency/frequency of maximum energy (FmaxE, kHz), minimum and maximum frequencies of the peak frequency contour (pfc.min and pfc.max, kHz) and call duration (D, ms). FA was measured in the field using vernier calipers. We used ImageJ (National Institutes of Health, Bethesda, MD, USA)44 to measure total wing area, areas of hand and arm wings and the wingspan from the standardised wing photos that were taken in the field. We calculated AR, WL, and I from these measurements following the equations given in Norberg and Rayner45. AR and WL both represent parameters that are correlated with flight aerodynamics and behaviour. I is influenced by the shape of the wing tip where values of 1 and above indicate broad, triangular tips, while those below 1 indicate acute wing tips. The four acoustic traits represent the shape of the echolocation call and they were measured from the reference recordings using Raven Pro, as described above.We first calculated the means for each of the seven traits across all species within a sonotype (thus obtaining one average trait value for each sonotype) (Table 1) and then used those to compute four multivariate functional diversity (FD) indices: functional richness (FRic), divergence (FDiv), evenness (FEve)46, and dispersion (FDis)47, using the function dbFD() in the ‘FD’ R package47. Our FD measures are unlikely to be underestimated due to the pooling of species into sonotypes because these species were similar in acoustic and morphological traits. FRic is the convex hull volume of the traits of species present in a community, measured in the multidimensional trait space. This measurement is not weighted by abundance, relative abundance or biomass of the species in the community, but, it is standardised such that it ranges from 0 to 1. FDiv reflects the distribution of abundance across taxa (sonotypes in our case) in the functional space. High FDiv means the taxa with extreme trait values are more abundant in a community whereas low FDiv means that those with the trait values close to the centre of the functional space are more abundant48. FEve, on the other hand, measures the evenness in the abundance distribution of taxa in the functional space. FEve is high when all taxa have similar abundances, and it is low when some functional groups are abundant while others are rare48. Lastly, FDis is measured as the mean distance of all taxa to the abundance-weighted trait community centroid. We performed two sets of analyses: one using the number of mistnet captures as a proxy for relative abundance, and another using the number of detections of different sonotypes in 5-min intervals in the passive recordings as a proxy of relative abundance. We did not pool acoustic detections and mistnet captures as they have inherently different detection probabilities and measure different entities (relative number of detections vs. number of captured individuals). Owing to rhinolophid bats at lower elevations being taxonomically and functionally different from the remaining species pool, we performed another set of FD calculations, excluding the four rhinolophid species and using acoustic detections as relative abundance. One species, Tadarida teniotis was commonly detected at all elevations on acoustic recorders, but we were unable to capture it as it foraged high above the ground, and thus were unable to collect morphological trait data. Additionally, in using acoustic detections as a measure of relative abundance, we had to exclude the non-echolocating pteropodid bat Sphaerias blanfordi which was caught only once at Chopta. Therefore, our FD values are likely systematically underestimated across all elevational communities, which does not affect the comparison of community composition across elevations.Phylogenetic diversityUsing the nexus file of a published phylogeny49, we pruned the tree to represent species in the 14 sonotypes. For each of these types, we chose the species most commonly mist-netted as representative of its group. Published DNA sequences are lacking for some of the species in this region, so we chose their closest relatives from the phylogeny instead. Thus, we made the following replacements: (a) Nyctalus leisleri represented the AMN sonotype, (b) Eptesicus serotinus represented the EH sonotype, (c) Murina aurata for Murina sonotype, (d) Myotis longipes for MS sonotype, (e) Pipistrellus javanicus for MP sonotype, and (f) Plecotus turkmenicus for Plecotus sonotype. After pruning the tree, we calculated three indices of phylogenetic diversity using the ‘picante’ R package50: Faith’s phylogenetic diversity (PD), Mean pairwise distance (MPD) and Mean nearest-taxon distance (MNTD). Faith’s PD is a measure of phylogenetic richness which is obtained by summing the branch lengths of the tree connecting the species in the community. MPD and MNTD measure phylogenetic dispersion of communities; whereas MPD measures the average phylogenetic distance among all the taxa in a community, MNTD measures the same for the nearest neighbouring taxa51. We weighted MPD and MNTD by relative abundance of the sonotypes in each community (like FD, the number of detections in five-minute intervals in the passive recordings was used as a proxy of relative abundance).Null model testingAs FD and PD are strongly correlated to species richness52, we used a null model to assess whether the observed was significantly different than expected due to chance alone. We produced the null distribution of each FD and PD index by randomizing the community matrix 999 times using the ‘independent swap’ method53,54, so as to preserve the species richness at each site and the number of sites in which each species can be found. Our randomization was further constrained by elevation, so that the abundances were randomized among the sampling points within each elevation. The null model allows for calculation of an effect size (difference between the observed value and mean of the null distribution). Given the range of FD and PD values, the effect sizes are not comparable across communities with vastly different species richness55. Therefore, standardized effect sizes (SES) of each index were calculated at each site as the difference between the observed value and the mean of the null distribution, divided by the standard deviation of the null distribution. SES  > 1 and SES  More

Plants and insectsRice (Oryza sativa) cultivar Minghui63 was used in this study. Rice plants were grown in a greenhouse at 27 ± 3 °C with 75 ± 10% RH (relative humidity) and a photoperiod of 16:8 h L:D (light:dark). The cultivation of rice plants followed the same procedure as described previously27. Plants were used for experiments when they were at the tillering stage, which occurred about 44–49 days after sowing.C. suppressalis larvae were reared on an artificial diet as described70. Ten percent honey water solution was provided to supply nutrition for the adults. N. lugens were maintained on a BPH-susceptible rice variety Taichung Native 1 (TN1)38. T. japonicum were obtained from Keyun Industry Co., Ltd (Jiyuan, China). Newly emerged adult wasps were maintained in glass tubes (3.5 cm diameter, 20 cm height) and supplied with 10% honey water solution as a food source and were maintained for at least 6 h to ensure free mating, before females were used for the following experiments. All three species were maintained in climatic chambers at 27 ± 1 °C, 75 ± 5% RH, and a photoperiod of 16:8 h L:D.Performance of caterpillars on insect-infested rice plantsMultiple types of rice plants were prepared: (i) uninfested plants, meaning that potted rice plants remained intact without insect infestation; (ii) SSB-infested plants, each potted rice plant was artificially infested with one 3rd instar SSB larva that had been starved for >3 h for 48 h; (iii) BPH-infested plants, each potted rice plant was artificially infested with a mix of fifteen 3rd and 4th instars BPH nymphs for 48 h; (iv) SSB/BPH-infested plants, each potted rice plant was simultaneously infested with one SSB larva and 15 BPH nymphs for 48 h; (v) SSB → BPH-infested plants, each potted rice plant was artificially infested with one SSB larvae alone for the first 24 h, then 15 BPH nymphs were additionally introduced for another 24 h; (vi) BPH → SSB-infested plants, namely each potted rice plant was artificially infested with 15 BPH nymphs for the first 24 h, then one SSB larvae were additionally introduced for another 24 h. Plant treatments were conducted as described in detail in our previous study27. During herbivory treatment, the uninfested plants were placed in a separate room to avoid possible volatile-mediated interference. During the subsequent bioassays, both SSB caterpillar and BPH nymphs remained in or on the rice plants.Two bioassays were conducted to test the performance of C. suppressalis larvae feeding on differently treated rice plants. The first bioassay included the plant treatments i, ii, iii, and vi, and the second bioassay included the plant treatments i, ii, v, and vi. Three 2-day-old larvae of C. suppressalis were gently introduced onto the middle stem of each rice plant using a soft brush. The infested rice plants were then placed in climatic chambers at 27 ± 1 °C, 75 ± 5% relative humidity, and a photoperiod of 16:8 h L:D. The C. suppressalis larvae were retrieved from the rice plants after 7 days feeding, and they were weighed on a precision balance (CPA2250, Sartorius AG, Germany; readability = 0.01 mg). The mean weight of the three caterpillars on each plant was considered as one biological replicate. The experiment was repeated four times using different batches of plants and herbivores, resulting in a total of 30–46 biological replicates for each treatment.Oviposition-preferences of C. suppressalis females choosing among differently infested rice plantsGreenhouse experimentIn the greenhouse, seven choice tests were conducted with C. suppressalis females including (i) SSB-infested plants versus uninfested plants; (ii) BPH-infested plants versus uninfested plants; (iii) SSB/BPH-infested plants versus uninfested plants; (iv) SSB-infested plants versus BPH-infested plants; (v) SSB-infested plants versus SSB/BPH-infested plants; (vi) BPH-infested plants versus SSB/BPH-infested plants; and (vii) the test in which C. suppressalis females were exposed to all four types of rice plants. The experiments were performed as described in detail by Jiao et al.30. In brief, four potted plants were positioned in the four corners of a cage (80 × 80 × 100 cm) made of 80-mesh nylon nets for each test. For paired comparisons, two potted plants belonging to the same treatment were placed in opposite corners of each age, and in the test with four types of rice plants, each type of plant was positioned in one of the four corners of each cage. Five pairs of freshly emerged moths (less than 1 day) were released in each cage, and a clean Petri dish (9 cm diameter) containing a cotton ball soaked with a 10% honey solution was placed in the center of the cage as food source. After 72 h, the number of individual eggs on each plant were determined. The experiment was conducted in a greenhouse at 27 ± 3 °C, 65 ± 10% RH, and a photoperiod of 16:8 h L:D. Each choice test was repeated with 9–11 times (replicates).Field cage experimentThe oviposition preference of SSB females was further assessed in a field near Langfang City (39.58° N, 116.48° E), China. Four choice tests were conducted: (i) SSB-infested plants versus uninfested plants; (ii) BPH-infested plants versus uninfested plants; (iii) SSB/BPH-infested plants versus uninfested plants; and (iv) SSB/BPH-infested plants versus SSB-infested plants. The treated rice plants were prepared as described above and were transplanted into experimental plots (1.5 × 1.5 m). For each pairwise comparison, six plots of rice plants were covered with a screened cage (8 × 5 × 2.5 m) made of 80-mesh nylon net to prevent moths from entering or escaping. Each of the six plots contained nine rice plants of a particular treatment, with three plots per cage representing the same treatment. Plots were separated by a 1 m buffer and they were alternately distributed in a 3 × 2 grid arrangement in each cage (Supplementary Fig. 4). Approximately 50 mating pairs of newly emerged C. suppressalis adults ( More

Yak and Tibetan sheep thrive under a co-grazing system on the QTP and/or are fed with the same materials; this offers an excellent opportunity to compare the gut microbiota in different host species which share a similar diet. In addition, the grazing systems on the QTP undergo seasonal diets changes in terms of pasture location and forage composition, especially between winter and summer. This presents a good natural “treatment” which helps vary the diets of the yak and Tibetan sheep populations. In the current study, based on a more substantial sample size than the previous study1, we found that diet and environment (represented by seasons winter and summer) superseded host genetics to the family level. That is to say that the gut microbiota of the two animal species showed convergent adaptation to high altitude and harsh environment in QTP, but this convergence had seasonal diets characteristics. These findings may provide a cautionary note for ongoing efforts to link host genetics to gut microbiota composition and function and would provide some food for thought in the breeding of these two livestock groups.The mammalian gut microbiota is acquired from the environment starting at birth, and its assembly and composition is largely shaped by factors such as age, diet, lifestyle, hygiene, and disease state. Researchers subconsciously believe that host species play a greater role than environmental factors when it comes to shaping gut microbiota, especially when there is a large taxonomical difference between the host species. So far, the vast majority of research have focused on the ruminal ecosystem because the rumen is primary site of feed fermentation15,16,17. It is rare to find studies that directly compare the gut microbiota of different species. However, evidence showed that energetically-important microbial products, including VFA (10–13% of total GIT VFA) are produced in the ruminant distal gut3. Hence, it is important to study the composition of distal gut microbiota of ruminants.In this study, at the phylum level, the gut microbiota composition in both groups of livestock was dominated by Bacteroidetes and Firmicutes, which was in agreement with previous reports concerning the yak18. At the same time our result consistently with other study in dairy cows that two dominated phyla Bacteroidetes and Firmicutes found in fecal samples in different seasons were abundant19,20. Firmicutes and Bacteroidetes are responsible for digestion of carbohydrates and proteins, Members of Bacteroidetes having extremely stronger ability to degrade crystalline cellulose. The previous report showed that intestinal microbiome plays an important role in digestion and absorption of the food, and maintaining animals’ health21,22. Intestinal tracts of the ruminants are rich in symbiotic bacteria that helps the body digest plant fibers23,24. Glycans are processed by the distal gut microbiota, generating biologically significant short-chain fatty acids (SCFAs, predominantly acetate, butyrate, and propionate), which serve as the principal energy source for colonocytes25. Fibers may be involved in the regulation of food intake and energy balance via the SCFA-mediated modulation of the secretion of gut hormones26. The higher abundance of Firmicutes and Bacteroidetes in yak may be associated with high-energy consumption at high altitude18.It is worth noting that, at the family level, the dominant genera (Unclassified Ruminococcaceae, Bacteroidaceae, Unclassified BS11, Unclassified Prevotellaceae, Unclassified Christensenellaceae, CF231, Unclassified Mogibacteriaceae and Unclassified Paraprevotellaceae) in the intestines of yak and Tibetan sheep were more greatly influenced by season than genetics (Fig. 5). This has not previously been accurately identified, which may be because there have been few studies into the gut microbial communities of the yak and Tibetan sheep in QTP. So, to improve their husbandry, it is important in the future to study their microbiota profiles using more precise methods such as 16S full-length sequencing or metagenomic sequencing. Ruminococcaceae is a family of autochthonous and benignspecies that primarily inhabit in the caecum and the colon27. It is known that Ruminococcaceae are common in the rumen and hindgut of ruminants, capable of degrading cellulose and starch28. As a member of short chain fatty acid (SCFA) producers, Ruminococcaceae is considered to be the most important fiber and polysaccharides-degrading bacterium in the intestine of herbivores, and produces large amounts of cellulolytic enzymes, including exoglucanases, endoglucanase, glucosidases and hemicellulase29. The microbial community of Yak and Sheep is greatly influenced by alterations in dietary nutrition, Bacteroidaceae have the ability to degrade complex molecules (polysaccharides, proteins) in the intestine18, which can promote the Yak utilizes grasses as its major source of nutrition, due to shortage of grain and other nutrients. Prevotellaceae is responsible for hemicellulose, pectin and high carbohydrate food digestion30. The higher abundance of these microbes may contribute to gaining more energy, and play vital roles in the process of adaption of the hosts to the harsh natural environment15. Bacteroidales BS11 gut group are specialized to active hemicellulose monomeric sugars (e.g., xylose, fucose, mannose and rhamnose) fermentation and short-chain fatty acid (e.g., acetate and butyrate) production that are vital for ruminant energy31. The Bacteroidales BS11 was positively correlated with some metabolites that are involved in amino acid metabolism and biosynthesis, as well as the metabolism of energy sources, such as starch, sucrose, and galactose32.At the genus level, 5-7N15 was most abundant in winter in both animals, on the contrary, the Provotella was predominate. Here, our results indicated that seasonal diets change superseded variations derived from genetic differences between the host species, even though the yak and Tibetan sheep are very different, both taxonomically and in terms of body size. In summer, the forage grass on the Qinghai-Tibet Plateau is dominated by Agropyron cristatum, Elymus nutans, Festuca ovina, Kobresia humilis, Poa pratensis, Stipa aliena, Kobresia pygmaea, Oxytropis biflora, Saussurea hieracioides, Astragalus arnoldii Hemsl. In winter, the main forage was Brachypodium sylvaticum. Carex crebra, Trisetum spicatum and Bupleurum smithii. Stipa has both high palatability and nutritional value, with a high content of crude protein, crude fat, and nitrogen- free extract, and low levels of crude fiber33. The levels of crude protein, crude fat, and nitrogen-free extracts of Brachypodium sylvaticum. Carex crebra, Trisetum spicatum and Bupleurum smithii were lower than that of Stipa, whereas the content of crude fiber was higher than that of Stipa34. Crude protein is the main nutrient of herbage. Crude fat and nitrogen-free extracts provide heat and energy33.Lopes et al. reported that some OTUs known to be functionally relevant for fiber degradation and host development were shared across the entire gastrointestinal tract and present within the feces35. Microbial diversity increases in the distal segments of the gastrointestinal tract. Microbial fermentation appears to be reestablished in the large intestine, with the proportion of acetate, propionate and butyrate being similar to the rumen.Several explanations for this phenomenon are possible. Firstly, both the yak and Tibetan sheep are ruminants. In herbivores, the gut microbiota is dominated by Firmicutes and Bacteroides, the functions of which are related to cellulose digestion36. Therefore, ruminant microbes could possibly be more similar across species than gut microbes from elsewhere.Secondly, the yaks and Tibetan sheep in our study co-grazed from birth to death. As such, the initial gut microbiota source, responsible for populating the remainder of the gut in the months and years after the initial seeding at birth, would necessarily come from the same environment. It has been established that early life events are critical for gut microbiota development and for shaping the adult microbiota. Lifestyle and diet will further influence the composition and function of the gut microbiota. In our study, the investigated animals shared a very similar lifestyle and obtained their diets from the same source. The results revealed that sheep and yaks presented almost identical gut microbiota compositions in the winter, but by the date of collection of the summer samples they were quite different. The reason for this could be that during summer and summer there is pronounced pastoral grass growth, giving the animals more variety and choice in their diets; it is known, after all, that sheep have different diet preferences to yaks37. However, during the winter, the animals have no option but to eat the same food in order to survive until winter.Thirdly, there could be a convergent evolution of gut microbiomes in yaks and Tibetan sheep due to the extremely harsh environment in high-altitude regions1,38. When compared with their low-altitude relatives, cattle (Bos taurus) and ordinary sheep (Ovis aries), metagenomic analyses revealed significant enrichment in rumen microbial genes involving volatile fatty acid-yielding pathways in yaks and Tibetan sheep, whereas methanogenesis pathways were enriched in the cattle metagenome. Analyses of RNA transcriptomes revealed significant upregulation in 36 genes associated with volatile fatty acid transport and absorption in the ruminal epithelium of yaks and Tibetan sheep. This suggests that, aside from host genetics, long-term exposure to harsh environments has allowed the gut microbiome to adapt in order to boost health and survival. In other words, although yaks and Tibetan sheep are very different genetically, their gut microbiota could be similar due to the selection pressures of the high altitude at which they live. Meanwhile, from our data based on functional gene composition (Fig. S3), it is also worth noting that there were no groups clearly distinguished from one another, although the PERMANOVA results indicated both a host and season effect, with the interaction between them being statistically significant. Though factors such as environment and diet (represented by seasons) can trump host genetics, we could not ignore the interplay of these factors as gut microbes are a very complex community.Winter is the harshest period for the survival of yak and Tibetan sheep. To maintain the survival, it’s best to feed the animals with a high protein content. Furthermore, to get more detailed data in different seasons and various dietary habits of yak and sheep, more study should be assessed about intestinal microbiota by collecting feces. More

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