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Reconstruction Era Research Paper



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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.

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Bioinformatics 34 , — Pucu, E. Hammerl, E. Agave chewing and dental wear: evidence from quids. Renaud, G. Bioinformatics 33 , — UniProt Consortium. UniProt: a worldwide hub of protein knowledge. Download references. We acknowledge and appreciate those individuals whose genetics and microorganisms were analysed for this research, as well as present-day individuals with associated genetic or cultural heritage. We thank members of the A. Chavkin and M. Tran for discussion and reading of the manuscript, and L. Pham for assistance with construction of sequencing libraries; J.

Fellows Yates and A. Rohrlach for discussion, advice on metagenomic analysis and reading of the manuscript; Y. Tseng for guidance and members of the Y. Tseng laboratory for discussions; M. Taylor and R. Wheeler from the Robert S. Peabody Institute of Archaeology for their roles in initiating and assisting with consultation with Native American communities. Support was also provided by NIH grant no. P30DK principal investigator, G. Marsha C. Wibowo, Zhen Yang, Braden T. Tierney, Samuel Zimmerman, Jacob M. You can also search for this author in PubMed Google Scholar. The other authors declare no competing interests.

Peer review information Nature thanks Marcus de Goffau, Ben Good, Philip Hugenholtz, Eske Willerslev and the other, anonymous, reviewer s for their contribution to the peer review of this work. Peer reviewer reports are available. Zape1, maize pollen grains more than , grains per gram top and agave phytoliths middle and bottom. Zape2, U. A complete description is provided in Supplementary Information section 2. Reproducibility and independently repeated experiments are described in the Methods. Species were identified by MetaPhlAn2 Archaeological sediment samples included three soil samples collected in this study, seven Holocene human-associated sediments from CoproID 71 and 40 Pleistocene sediment samples In f — h , data are presented as box plots middle line, median; lower hinge, first quartile; upper hinge, third quartile; upper whisker extends from the hinge to the largest value no further than 1.

New York, NY: St. Filip, V. Origins of American social policies: The progressive era. Universitatea Danubi Galati, 7 1 , George Washington University. The progressive era The Eleanor Roosevelt papers project. The Progressive Era. Social Welfare History Project. From your comment, it appears you want someone at the SWH Project to prepare a term paper or dissertation. Sorry to say, we have more to do than prepare your paper. Best wishes, Jack Hansan, Ph. I was wondering how the progressives promoted the general welfare of the people politically. The last person i asked said through referendum and reform but one cant typically write an essay in its entirety based on two words!

As I wrote on the entry you referenced: …Progressivism began as a social movement to cope with a variety of social needs and eventually evolved into a reform movement and greater political action. The early progressives rejected Social Darwinism. In other words, they were people who believed that the problems society faced poverty, poor health, violence, greed, racism, class warfare could best be addressed by providing good education, a safer environment, an efficient workplace and honest government. Progressives lived mainly in the cities, were college educated, and believed that government could be a tool for change….

I would recommend these for which there is a lot of content on the SWH Web site: child labor, woman suffrage, civil rights, mental health, corrections. You will have to do the work about how the results came about. Good luck, Jack Hansan. I enjoyed reading this. I am curious of who you believe best represented the progressive goals of the progressives. Personally, I have done some research, and I have chosen Jane Addams. Again, who would you choose? Thank you for the question. I never really thought about who was the most progressive of the Progressives. However, I did a little review and came up with a number of names you might want to consider instead of Woodrow Wilson. Clearly, Jane Addams qualifies; but there are others who contributed significantly.

Also, there are a number of labor leaders who might qualify:Rose Schneiderman,Robt. Upton Sinclair, Jr. Hansan, Ph. I was wondering what tactics exactly did the Progressive reformers use to promote reform? Which were the most effective? The answer to your question largely depends on which movement within Progressivism you are interested in. You may want to check out the linked articles about particular reformers that are contained in this article to get some ideas of where to start for your research. Thanks so much! I am doing a persuasive essay, after reading The Jungle, on how immigrants were treated and this helped me so much. I greatly appreciate it. Hello, I am participating in a national history competition and stumbled across this article in my research.

Thank you very much!

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