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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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IV. Ecosmomics: An Independent Source Script of Generative, Self-Similar, Complex Network Systems

1. Paleogenomics, Archaeogenomics: Natural Ancestry

Warinner, Christina, et al. Ancient Human Microbiomes. Journal of Human Evolution. 79/2, 2015. In this special issue, University of Oklahoma and University of York archeologists describe how it is even possible by rapidly advancing techniques to recover this pervasive symbiont realm that graces every creature. Why can a late composite worldwide sapiens then achieve this “paleomicrobiology,” ought we ask for what purpose?

Very recently, we discovered a vast new microbial self: the human microbiome. Our native microbiota interface with our biology and culture to influence our health, behavior, and quality of life, and yet we know very little about their origin, evolution, or ecology. With the advent of industrialization, globalization, and modern sanitation, it is intuitive that we have changed our relationship with microbes, but we have little information about the ancestral state of our microbiome, and we therefore lack a foundation for characterizing this change. High-throughput sequencing has opened up new opportunities in the field of paleomicrobiology, allowing us to investigate the evolution of the complex microbial ecologies that inhabit our bodies. By focusing on recent coprolite and dental calculus research, we explore how emerging research on ancient human microbiomes is changing the way we think about ancient disease and how archaeological studies can contribute to a medical understanding of health and nutrition today. (Abstract)

Weiss, Madeline, et al. The Physiology and Habitat of the Last Universal Common Ancestor. Nature Microbiology. 1/16116, 2016. Heinrich Heine University molecular biologists reconstruct our evolutionary heritage all the way back to its primal cellular origin. And again, how amazing that we peoples can lately do this, whatever kind of creative organic universe needs to know, and for what reason?

The concept of a last universal common ancestor of all cells (LUCA, or the progenote) is central to the study of early evolution and life's origin, yet information about how and where LUCA lived is lacking. We investigated all clusters and phylogenetic trees for 6.1 million protein coding genes from sequenced prokaryotic genomes in order to reconstruct the microbial ecology of LUCA. Among 286,514 protein clusters, we identified 355 protein families (∼0.1%) that trace to LUCA by phylogenetic criteria. Because these proteins are not universally distributed, they can shed light on LUCA's physiology. The 355 phylogenies identify clostridia and methanogens, whose modern lifestyles resemble that of LUCA, as basal among their respective domains. LUCA inhabited a geochemically active environment rich in H2, CO2 and iron. The data support the theory of an autotrophic origin of life involving the Wood–Ljungdahl pathway in a hydrothermal setting. (Abstract excerpts)

Yang, Melinda and Qiaomei Fu. Insights into Modern Human Prehistory using Ancient Genomes. Trends in Genetics. 34/3, 2018. Chinese Academy of Sciences, Beijing vertebrate paleoanthropologists provide a tutorial as our global humankinder proceeds to reconstruct via recovered genetic sequence how our hominid to homo to anthropo sapiens came to evolve out of diverse, interbreeding lineages. From China, studies are seen to range widely to Russia, Romania, Belgium, Italy, Georgia, Iran Malawi, and around the world. Novel mappings of Eurasia and the Americas can also plot migratory routes and populations. In addition, a good degree of admixtures and introgressed DNA between modern humans and Neanderthals has been found.

The genetic relationship of past modern humans to today’s populations and each other was largely unknown until recently, when advances in ancient DNA sequencing allowed for unprecedented analysis of the genomes of these early people. These ancient genomes reveal new insights into human prehistory not always observed studying present-day populations, including greater details on the genetic diversity, population structure, and gene flow that characterized past human populations, particularly in early Eurasia, as well as increased insight on the relationship between archaic and modern humans. Here, we review genetic studies on ∼45 000- to 7500-year-old individuals associated with mainly preagricultural cultures found in Eurasia, the Americas, and Africa. (Abstract)

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