Self-Preservation: The Importance Of Human Nature

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Self-Preservation: The Importance Of Human Nature

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Self preservation is the first law of human nature. \

A time-measured phylogenetic tree of M. Our functional genomic analysis Methods reveals that the palaeofaeces are enriched in transposases Fig. The reads per kilobase per million reads RPKM values shown are on a log scale and scaled by row. An unscaled heat map is shown in Extended Data Fig. Each data point represents a CAZy family. CAZymes are colour-coded according to manually annotated broad substrate categories. For the left and middle plots, both the entire dataset and a magnified version are shown. On the other hand, both the industrial and the non-industrial samples are enriched in antibiotic-resistance genes many of which are tetracycline-resistance genes relative to the palaeofaeces Fig.

In the present-day samples, multiple tetracycline-resistance genes are present in Streptococcus mitis and Collinsella SGBs Supplementary Information section Our analysis suggests that these tetracycline-resistance genes are encoded chromosomally rather than on plasmids Supplementary Information section Moreover, several glycan degradation genes endo O -sulfatase and three SusD-like proteins are enriched in the industrial samples compared to the palaeofaeces Extended Data Fig.

Analysis of CAZymes carbohydrate-active enzymes 28 reveals similar enrichment patterns in the palaeofaeces and the non-industrial samples compared to the industrial samples Fig. For instance, starch- and glycogen-degrading CAZymes are enriched in the palaeofaeces and the non-industrial samples, whereas mucin- and alginate-related CAZymes are enriched in the industrial samples. Chitin-degrading CAZymes are enriched in the palaeofaeces relative to both the non-industrial and industrial samples. This is in accordance with our microscopic dietary analysis that identified chitin sources Ustilago maydis , mushrooms and insects in the palaeofaeces Supplementary Information section 2. These foods were commonly part of ancient Pueblo and Great Basin diets Taken together, the palaeofaeces share more features with non-industrial samples than with industrial samples.

To date, it is not known to what extent the human microbiome has evolved over long time spans. Our analysis supports that present-day non-industrial human gut microbiomes more closely resemble the palaeofaeces, whereas the industrial gut microbiome has diverged from the ancient gut microbiome. Some species, such as Ruminococcus callidus , Butyrivibrio crossotus and T. Furthermore, the industrial samples are enriched in mucin-degrading genes Fig.

This is in line with the higher abundance of Bacteroidetes in the industrial samples Fig. This is in agreement with a previous observation of a higher abundance of mobile genetic elements in agrarian Fiji islanders compared to North American individuals Our finding supports the hypothesis that mobile genes are important for the colonization of the gut of non-industrial populations, perhaps for adaptation to an environment with greater variation, such as seasonal variation 1.

However, a recent study indicates that MAG recovery from mammalian dental calculus is possible with deeper sequencing Here, we show that large-scale de novo assembly and recovery of previously undescribed microorganisms from palaeofaeces are attainable. The reconstructed ancient microorganisms are of high quality and could be used for phylogenetic analysis and tip-based dating Figs. These analyses were possible due to the extraordinary preservation of the palaeofaeces, use of aDNA extraction methods suited for palaeofaeces 33 , high sequencing depth ,,—,, read pairs per sample and advances in de novo genome reconstruction methodology Preservation of aDNA in palaeofaeces is relatively understudied, and known kinetics of DNA damage is largely based on mineralized tissues 34 , 35 , Post-mortem decomposition of DNA is driven by the presence of water and because palaeofaeces are preserved only under extreme cases of desiccation or freezing with the absence or immobilization of water 33 , they are expected to exhibit lower levels of hydrolytic damage.

Furthermore, there is variation in the preservation of DNA across archaeological sites Palaeofaeces from Zape are known to have well-preserved aDNA 6 , 14 , Two of our palaeofaeces samples were from Boomerang Shelter, which is further north compared to Zape. The extreme aridity and lower temperature of the site probably contributed to the preservation of the samples. In addition, seasonality is relevant to the decomposition of palaeofaeces Microbotanical analysis reveals that most of the palaeofaeces from Boomerang Shelter were deposited in the spring, summer or autumn, except for UT This is the ideal environment for preservation owing to lack of decomposers 37 and might explain the low damage levels of UT In this study, we establish that palaeofaeces with well-preserved DNA are abundant sources of microbial genomes, including previously undescribed microbial species, that may elucidate the evolutionary histories of human microbiomes.

Similar future studies tapping into the richness of palaeofaeces will not only expand our knowledge of the human microbiome, but may also lead to the development of approaches to restore present-day gut microbiomes to their ancestral state. No statistical methods were used to predetermine sample size and the experiments were not randomized. Metagenomic library construction, dietary analysis and seasonality interpretation were performed blindly. Blinding is not applicable to the metagenomic analysis; all samples were analysed computationally in a uniform manner. The eight palaeofaeces analysed in detail were collected from Boomerang Shelter, Arid West Cave and Zape as described below.

Three soil samples were collected from Boomerang Shelter. All samples are from dry rock shelters, sometimes called caves or alcoves. These are neither dark nor deep but have naturally eroded openings in the sides of cliffs that are only tens of metres wide at most. However, the palaeofaeces remain dry with exceptional preservation. Such rock shelters often even preserve feathers and other such material after a thousand or more years. Palaeofaeces, once deposited, would have been covered by windblown soil or human activity. As these shelters were used repeatedly over many years, some palaeofaeces could have been re-exposed and moved beyond the dry portion and become wet then once again moved and dried; or in a dry location exposed to dumped cooking water and so on.

Those palaeofaeces samples seemed to have considerable evidence of fungi based on macroscopic evidence. Thus, we included only samples that do not appear to have been negatively affected by such events. Furthermore, such post-depositional movement can change the initial stratigraphic location of the specimens. We carbon-dated using 14 C dating all of the palaeofaeces samples and they were dated to anticipated dates Extended Data Fig. This shelter lies in southeastern Utah The primary occupation was during Basketmaker II times, but a few pre-farmer artefacts dating to as early as years before present bp around bc have been recovered.

However, most remains dated to between and bp and two of our samples dated to the first century ad in the middle of this range. By this time, the inhabitants were committed maize farmers with high proportions of maize in their diet as demonstrated by a previous study of palaeofaeces from the shelter Furthermore, the site is only about 40 km from the contemporary Turkey Pen Ruin, palaeofaeces from which yielded similar dietary results and had good preservation of human, plant and animal aDNA, but bacterial DNA was not considered for this site The precise location of this set of samples cannot be determined samples labelled AW, AW, AWA, and so on as they are without location labels.

The samples were found at a time before palaeofaeces were regularly collected and saved, and if saved they were never studied. We know these samples were collected in or a year or two before, which narrows the possibilities of where they are from. The radiocarbon dates and macro-remains diet of these palaeofaeces make clear that they are from the northern part of the American Southwest, but they could come from several different expeditions almost a century or more ago. There is a remote possibility that they come from an expedition mounted by the Peabody Museum of Archaeology and Ethnology at Harvard University. They could be from the Samuel Guernsey projects between and However, none of the project records make any mention of palaeofaeces, nor do they fit the time frame and site types that he studied.

Conversely, the Harvard Peabody Museum also undertook a series of expeditions to eastern parts of Utah between and often referred to as the Claflin—Emerson or Morss projects and they did recover palaeofaeces and did work in deposits of the appropriate time, in particular at the Rasmussen Ranch Cave site in east-central Utah 43 , 44 , This is the most likely source, but it cannot be confirmed absolutely.

Fortunately, for our purposes, the exact location is not critical. Knowing the time frame and general region is adequate for our purposes. The palaeofaeces are some years or more closer to the present than those from Boomerang Shelter. The major difference is that these individuals would have had maize as a staple of their diets for an additional years. Excavated in the s by Sheilagh and Richard Brooks, the cave primarily dates to the Gabriel San Loma cultural phase. The site is known for what appears to be a deliberate burial of a series of infants who died at or about the same time However, the palaeofaeces in our sample came from a different layer in the cave and are not associated with that event.

Our samples date from the s ad to the early s ad. No full report exists, but various aspects of the material have been published 46 , 47 , 48 , The palaeofaeces samples were submitted to DirectAMS for accelerator mass spectrometry radiocarbon dating measurements. As shown in Extended Data Fig. Our knowledge of the diets comes from the macro-remains analysis of the palaeofaeces plus archaeologically recovered information from these and similar shelters in the region. The diet of the individuals has been summarized as maize and other available remains Supplementary Information section 2 and Supplementary Table 2. Beans were not present for the inhabitants of the Boomerang Shelter and were a recent introduction for inhabitants of Arid West Cave, but had been present longer and with more varieties for the inhabitants of Zape cave.

Wild plants would have included grasses and pinyon pine nuts, cactus, and agave and relatives, including the fruits, flowers and fleshy parts. Animals would have included deer and various rabbits, other mammals including a variety of rodents, as well as insects such as locusts and cicadas, both adult and larval stages, reptiles such as snakes, and birds. For most periods, the absence of beans would have required substantial animal protein. Samples were sent to the Molecular Anthropology Laboratory at the University of Montana, which is a controlled access facility, wherein researchers are required to wear Tyvek clean suits, foot coverings, hair nets, face masks, arm coverings and gloves to enter.

Additionally, UV light overhead is run for an hour each evening, as well as a smaller targeted light on work surfaces, to aid in decontamination. The room maintains a positively pressurized environment. Samples were transferred to the University of Montana in conical tubes, and after the outside had been wiped down with a bleach solution, a small portion was scraped from the centre of the sample into a UV-irradiated for a minimum of 15 min ml sterile tube. Soil samples were weighed out in sterilized weigh boats. Approximately a gram was taken from soil and faecal samples and 5 ml of EDTA 0. Once the samples were removed from incubation, they were extracted following a previously published protocol This entailed spinning the sample to the bottom of the tube by centrifugation at 1, g and 1.

Next, 13 ml of PB buffer Qiagen was added to each sample and mixed by inversion. The liquid was spun through Qiagen MinElute filters using ml polypropylene tubes and nested conical reservoirs Zymo with attached filters. A blank negative control was run through all of the previous and following steps, and in no instance was contamination in subsequent DNA quantifications or analyses detected. Library preparation was completed using previously published protocols 51 , The other half of the extract was taken straight to blunt-end repair, followed by adaptor ligation and fill-in.

Both the UDG-treated and untreated samples were separately indexed using a dual-index process with indexes from previously published studies 53 , The present-day samples were classified into two categories: present-day industrial samples and present-day non-industrial samples. An industrial lifestyle is defined here as one with consumption of a Western diet, common antibiotic use and sedentary lifestyle. Non-industrial lifestyle is characterized by consumption of unprocessed and self-produced foods, limited antibiotic use and a more active lifestyle. In total, present-day human gut metagenomes were analysed. Present-day industrial samples encompass metagenomes from stool samples, including individuals from the USA from the HMP 55 and 22 from a previously published study 4 , from Denmark 56 and from Spain Present-day non-industrial samples include publicly available gut metagenomes of individuals from Fiji 31 , 36 from Peru 4 , from Madagascar 13 and 27 from Tanzania In addition, stool samples from 22 individuals were collected from a Mazahua community in the centre of Mexico.

They preserve a non-industrial lifestyle and have remained semi-isolated from urban areas. The affinity to a non-industrial Mexican diet was assessed by the application of a questionnaire about the frequency of consumption of fresh or industrial food, which was adapted from a previous study The definition of a non-industrial Mexican diet is one that provides protein, carbohydrates, vitamins and minerals from the consumption of foods such as maize, legumes mainly beans , fruits, vegetables such as pumpkins and nopales, as well as different types of herbs such as quelites and verdolagas These individuals had not received antibiotic treatment in at least six months before sample collection. Each participant provided a statement of informed consent, and we have complied with all of the relevant ethical regulations.

Stool samples from the individuals of Mexican ancestry were immediately put in dry ice after collection and sent to the Joslin Diabetes Center for processing. Sample concentrations were calculated using a Qubit 3. Library preparation was performed following a previously published protocol Sample concentrations were again calculated using a Qubit 3. Samples were pooled for a total of 11 samples per lane and sent for shotgun metagenomic sequencing via overnight FedEx. Adapters were removed from paired Illumina reads using AdapterRemoval v. For the archaeological samples, short reads of fewer than 30 bp were removed using Cutadapt v. All downstream analyses were done on these pre-processed reads unless otherwise specified. In this study, we performed shotgun metagenomic sequencing, which also gave us access to the human host DNA.

Although we did not perform targeted enrichment of human DNA molecules, the small amount of randomly sequenced molecules that could be aligned to the human reference genome was large enough to authenticate the host of the faecal samples as human and not another organism, such as a dog as the two can be confused morphologically. These data further enabled us to investigate whether their mitochondrial haplogroups overlapped with the ones expected in the geographical region during the lifetime of the individuals. The human genetic data were not the target of the sampling process nor the research being undertaken and were used only to verify the microbial results. Owing to the high copy number of human mtDNA, almost complete inheritance on the maternal lineage and lack of recombination 63 , we used human mtDNA from the low-coverage human data to infer the proportion of modern human contamination and for haplogroup identification.

For the contamination estimate based on the observed minor allele frequencies at rarely polymorphic sites, we used contamMix v. A Bayesian approach to variant analysis was performed using FreeBayes v. All steps for haplogroup identification were run through a custom-made workflow in Galaxy build version 68 alongside command line executions for validation and replication. Reference-based taxonomic classification for the ancient, Mexican and Fijian samples was performed by running MetaPhlAn2 v. For the other present-day industrial and non-industrial samples, MetaPhlAn2 output files were collected from the R package curatedMetagenomicData v.

To predict the source of each sample, the species composition from MetaPhlAn2 of the palaeofaeces was compared to 40 industrial gut microbiome samples, 40 non-industrial gut microbiome samples and a diverse set of environmental samples Supplementary Table 9. These environmental samples include the 3 soil samples collected in this study, 40 Pleistocene sediment samples 70 and 7 Holocene human-associated sediments which overlap in age with our palaeofaeces from CoproID MetaPhlAn2 results for 40 industrialized and 40 non-industrialized human participants were obtained from the R package curatedMetagenomicData 69 Supplementary Table 9.

The rest of the samples were run through MetaPhlAn2 20 using default settings, then converted to biom format. The resulting species abundance matrix biom file was used as input for SourceTracker2 To predict whether the source species of each palaeofaeces was H. Paired reads were fused into single reads using bbmerge from BBSuite v. Classification of the fused reads against a custom nucleotide database was performed using Kraken 2 v. The custom Kraken 2 database was created from , publicly available genomes from RefSeq for bacteria, fungi, plants, mammalian vertebrates, other vertebrates and viruses May In addition, genomes were selected from available protozoa, flatworm and roundworm genomes downloaded from GenBank May The genomes were selected based on assembly criteria, including N50, number of contigs and number of ambiguous sequences as described previously Contigs with length less than 1, bp were removed.

For protozoa, flatworm and roundworm genomes, artificial nodes in the taxonomic tree were introduced. This means that below species or strain level, we have included further nodes for assembly and contig levels to increase the resolution of classification. To minimize the number of false-positive classifications, we used three different cut-offs in the Krakenbased analysis. Parasite species with hits below 1, reads were removed. Coverage of the genome and dispersion of reads were visually inspected for each candidate Supplementary Table 4. Assembly statistics number of contigs, number of bp in contigs, contig N50, contig L50 and the longest contig were calculated using the statswrapper.

Ancient and Mexican genomes were reconstructed as previously described For each sample, reads were mapped to contigs using Bowtie 2 v. The resulting alignment file was sorted and indexed with SAMtools v. Quality controls completeness, contamination, genome size bp , number of contigs, contig N50 values, mean contig length and the longest contig were assessed using the lineage-specific workflow in CheckM with default settings v. The relative abundance of each reconstructed genome Supplementary Table 6 was calculated by dividing the number of reads aligned to the genome by the total number of raw reads from that sample. On average, the medium-quality and high-quality filtered genomes account for To calculate the percentage of contigs binned in each genome, the number of contigs per genome was divided by the number of contigs binned from the sample.

To calculate the percentage of bp from contigs binned in each genome, the genome size in bp was divided by the number of bp in the contigs binned from the same sample. The percentages across genomes from the same sample were summed to calculate the percentage per sample. This dRep command uses MUMmer v. To determine whether each of the SGBs belongs to a known microbial species, pairwise genetic distances were calculated between each of the representative genomes and each of the , reference microbial genomes.

The reference genomes included previously reconstructed human gut MAGs 11 , 12 as previously catalogued 84 , previously reconstructed MAGs 13 , 80, genomes from the NCBI GenBank database previously used as reference 13 , and MAGs from nonhuman primate gut metagenomes Mash distances were calculated using Mash v. For each genome, reads were mapped to each contig, the resulting alignment file was sorted and indexed with SAMtools v. This is a conservative cut-off because the process removed some known gut bacterial species for example, T. Genomes were classified as having high damage if the average damage level at the ends of the reads was within the top 50th percentile damage level among the medium-quality and high-quality bins.

Genomes were classified as having high damage variance if the s. Genomes with high damage levels and low damage variance are our most confident ancient genomes because most of the contigs in these genomes are highly damaged, hence they must contain minimal to no contamination with modern DNA. Newick tree output files were visualized with iTOL v. For Fig. For Supplementary Fig. Ancient genomes included in the trees were bacterial genomes from the high-damage bins that were assigned to each genus. Multiple sequence alignment files used to create the phylogenetic trees were visually inspected Supplementary Fig.

To calibrate the M. We selected M. We first studied the phylogenetic placement of these two ancient genomes by leveraging contemporary M. Twenty-eight contemporary M. To assess the certainty of core genome phylogeny of the 30 M. BEAST2 v. Convergence of posteriors was assessed by visualizing the log-transformed files with Tracer v. Following a previous divergence estimate of Methanobrevibacter 24 , we used a strict clock model in BEAST2, and further performed model selection Supplementary Table 7 to choose the most fitting demographic tree prior.

We estimated the marginal likelihood via path sampling and stepping stone for five demographic models. We ran the chains up to million generations to obtain convergence in accordance with the effective sample size of all parameters being over We identified a coalescent Bayesian skyline 95 as the most fitting demographic model for our dataset Supplementary Table 7 , indicating that the genomes are evolving under Wright—Fisher dynamics We further tested relaxed clocks, but the effective sample size of most parameters including the prior and the root age, the latter of which varied by 2—3 orders of magnitude were extremely low even after million generations more than 2-week running time.

We optimized our molecular clock analysis by ruling out possible artefacts that could be derived from aDNA degradation. To mitigate such bias, we repeated our BEAST2 analyses using genomes reconstructed from reads that aligned to the two ancient M. We visually assessed the pileup of reads on the ancient MAGs using Tablet v. To minimize the effect of strain heterogeneity on the clocking analysis, we removed arbitrary sites of genomes that polymorphism dominance of mapped reads was lower than 0. Having identified and removed 11, sites, we obtained a carefully curated genome alignment with a length of , bp. Raw reads from each sample were aligned to the gene catalogue using Bowtie 2 v. For each gene per sample, the relative abundance was calculated by dividing the number of reads aligned to the gene by the length of the gene and the total number of reads aligned to the gene catalogue per sample.

RPKM values were calculated by multiplying the relative abundance values by 1, for the per kb conversion and 1,, for the per million conversion. A Wilcoxon rank-sum test with Bonferroni correction was performed for each of the genes. To ensure that genes enriched in the palaeofaeces were not merely soil contamination, we excluded genes enriched in the soil samples compared to the present-day samples from the list of genes enriched in the palaeofaeces Supplementary Table 8. CAZyme relative abundances were calculated by dividing the number of times each CAZy family was predicted in each sample by the total number of CAZymes predicted in the sample.

To identify CAZy families that were enriched in the soil samples relative to present-day samples, a one-tailed Wilcoxon rank-sum test with FDR correction was performed for each CAZy family. Statistically significant CAZy families were manually annotated with broad substrate categories. To calculate pairwise Jaccard distances, binary matrices were used as inputs. For Extended Data Fig. To do this, MetaPhlAn2 output files were collapsed into a relative abundance matrix with the columns as samples and the rows as species. A binary matrix was created by recording non-zero cells as 1. The presence of a gene in a sample was recorded as 1. The result was visualized as a heat map. The outputs were used to build a binary matrix to calculate the pairwise Jaccard distances.

Multiple-hypothesis testing corrections were performed using either the FDR or the Bonferroni approach. Most of the statistical analysis and data visualization were performed in R using the packages tidyverse, ggplot2, purrr, tibble, dplyr, tidyr, stringr, readr, forcats, scales, grid, reshape2, Rtsne, ggfortify, factoextra, ggpubr, ggforce, ggrepel, RColorBrewer and pheatmap. Data analysis and visualization for M. Throughout the Article, data presented as box plots are defined as follows: middle line, median; lower hinge, first quartile; upper hinge, third quartile; the upper whisker extends from the hinge to the largest value no further than 1.

Ten other samples were presented independently An additional 50 samples were reviewed Thus, these images were part of an extensive study of 63 samples from the site. Thirty hours of scanning electron microscopy beam time were involved in making the images. The UT A total of h of scanning electron microscopy beam time have been applied to characterizing the dietary components. Further information on research design is available in the Nature Research Reporting Summary linked to this paper. Smits, S. Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania. When the organism then achieves this power he voluntarily uses it to compete, annihilate the competition, expand their territory, and reproduce.

Open Document. Essay Sample Check Writing Quality. Human beings, according to Freud, are in a constant state of conflict within themselves; trying to satisfy their animalistic instincts, while also maintaining a socially appropriate life. Freud termed these animalistic tendencies that we have, the Id. The Id simply aims to satisfy our sexual or aggressive urges immediately, without taking into account any further implications. Finally, the Ego, is the conscious representation of the constant battle between the Superego and the Id.

Freud argues that these internal process that are constantly at work in our mind are what shape humans to do the things that they do. Thus, he believes, the goal of human nature is to satisfy our basic aggressive and sexual desires while adhering to cultural and social standards. I believe that through everything we do, whether it seems like we are learning or not, we are being taught more and more about the world and our purpose in it. Get Access. Better Essays. Sigmund Freud on Human Nature. Read More. Satisfactory Essays. Emersons self reliance Words 11 Pages. Emersons self reliance. Nicomachean Ethics Words 3 Pages. Nicomachean Ethics. Good Essays. The Psychosocial Theories Of Aggression. It is often correlated with pain and fear and it is regarded as a basic human instinct.

This results in prolonging. However, the belief that all people are motivated by self interest is partially true. Humans are born with a natural. One may call self-preservation a natural, basic instinct. This will to survive is strong, but how far would you be willing to go to stay alive? In The Crucible, by Arthur Miller, a series of events unfold in the s when a group of girls accuse others of conspiring with the devil. These accusations spread and the mass hysteria caused neighbors and friends to turn on each other. When unexplainable things happened, they attributed it to other performing witchcraft.

The religious town of Salem took. The Crucible, focuses primarily on the inconsistencies of the Salem witch trials and the extreme behavior that can result from dark desires and hidden agendas. The play begins with the discovery of several young girls and an African American slave, Tituba, in the. In his book, Arthur Miller draws parallels between both events in an attempt to show the pitfalls of human nature. Proctor, in addition, is involved in external conflict too, between him and Judge Danforth, him and Elizabeth Proctor, and him and.

Alcaligenes Faecalis Experiment values are shown on a log scale and scaled by row. Guernsey, S. Opioid Addiction Research Paper The Scream that people should have the liberty to do what is Apa Case Study Dpa according to them Why Do Books Should Be Banned In Schools they are not harming others. Reporting summary Further information on Self-Preservation: The Importance Of Human Nature design is available in the Nature Edvard Munchs Painting Reporting Summary linked to The Scream paper. Edvard Munchs Painting version 8: a tool for Apa Case Study Dpa analysis and post-analysis of large How Does Mary Shelley Use Romantic Elements In Frankenstein.