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IV. Ecosmomics: Independent, UniVersal, Complex Network Systems and a Genetic Code-Script Source

1. Paleogenomics, Archaeogenomics: Natural Ancestry

Shapiro, Beth and Michael Hofreiter. A Paleogenomic Perspective on Evolution and Gene Function: New Insights from Ancient DNA. Science. 343/6169, 2014. UC Santa Cruz and University of York scientists introduce this profound new capability via novel instrumentation and computation to sequence the genetic endowments of hominid precursors. This revolutionary new approach can then contribute to a much better reconstruction of how homo sapiens came to be and is able to do this.

The publication of partial and complete paleogenomes within the last few years has reinvigorated research in ancient DNA. No longer limited to short fragments of mitochondrial DNA, inference of evolutionary processes through time can now be investigated from genome-wide data sampled as far back as 700,000 years. Tremendous insights have been made, in particular regarding the hominin lineage. With rare exception, however, a paleogenomic perspective has been mired by the quality and quantity of recoverable DNA. Though conceptually simple, extracting ancient DNA remains challenging, and sequencing ancient genomes to high coverage remains prohibitively expensive for most laboratories. Still, with improvements in DNA isolation and declining sequencing costs, the taxonomic and geographic purview of paleogenomics is expanding at a rapid pace. With improved capacity to screen large numbers of samples for those with high proportions of endogenous ancient DNA, paleogenomics is poised to become a key technology to better understand recent evolutionary events. (Abstract)

Skoglund, Pontus and Iain Mathieson. Ancient Human Genomics: The First Decade. Annual Review of Genomics and Human Genetics. Vol. 19, 2018. The old procession and tree in schools and museums is gone. Here Francis Crick Institute, London and University of Pennsylvania geneticists well survey this 21st century revolution as it supplants a prior age of spare fossils with much more depth, expanse, and accuracy about the myriad, interbreeding primate and hominin predecessors to our worldwide reconstruction.. See also Tales of Human Migration, Admixture, and Selection in Africa by Carina Schlebusch and Mattias Jakobsson in this same volume, second Abstract.

The first decade of ancient genomics has revolutionized the study of human prehistory and evolution. We review new insights based on prehistoric human genomes, including greatly increased resolution of the timing and structure of the out-of-Africa event, the diversification of present-day non- African populations, and the earliest expansions of those populations into Eurasia and America. Despite these advances, much remains unknown, in particular about the genomic histories of Asia (the most populous continent) and Africa (the continent that contains the most genetic diversity). Ancient genomes from these and other regions, integrated with a growing understanding of the genomic basis of human phenotypic diversity, will be in focus during the next decade of research in the field. (Skoglund)

In the last three decades, genetic studies have helped to conclusively establish that anatomically modern humans first appeared in Africa roughly 250,000–350,000 years ago and subsequently migrated to other parts of the world. Through genetic studies, it has become evident that deep African population history is captured by relationships among African hunter–gatherers, as the world’s deepest population divergences occur among these groups, which dates to 300,000 years before present. However, the spread of pastoralism and agriculture in the last few thousand years has shaped the geographic distribution of present-day Africans and their genetic diversity. (Schlebusch)

Skoglund, Pontus and David Reich. A Genomic View of the Peopling of the Americas. Current Opinion in Genetics & Development. 41/27, 2016. In a special issue on the Genetics of Human Origin, Harvard Medical School researchers use the latest sequence techniques to recover and reconstruct how this continent originally became populated by the human phenomenon. See also for example herein Insights into Human Evolution from Ancient and Contemporary Microbiome Studies and Hunter-Gather Genomics.

Whole-genome studies have documented that most Native American ancestry stems from a single population that diversified within the continent more than twelve thousand years ago. However, this shared ancestry hides a more complex history whereby at least four distinct streams of Eurasian migration have contributed to present-day and prehistoric Native American populations. Whole genome studies enhanced by technological breakthroughs in ancient DNA now provide evidence of a sequence of events involving initial migrations from a structured Northeast Asian source population with differential relatedness to present-day Australasian populations, followed by a divergence into northern and southern Native American lineages. (Abstract excerpt)

Slatkin, Montgomery and Fernando Racimo. Ancient DNA and Human History. Proceedings of the National Academy of Sciences. 113/6380, 2016. UC Berkeley integrative biologists describe 21st century potentials by way of advanced genome sequence and computation techniques to reconstruct how primates and hominids evolved and emerged to a worldwide capability lately able to achieve this.

We review studies of genomic data obtained by sequencing hominin fossils with particular emphasis on the unique information that ancient DNA (aDNA) can provide about the demographic history of humans and our closest relatives. We concentrate on nuclear genomic sequences that have been published in the past few years. In many cases, particularly in the Arctic, the Americas, and Europe, aDNA has revealed historical demographic patterns in a way that could not be resolved by analyzing present-day genomes alone. Ancient DNA from archaic hominins has revealed a rich history of admixture between early modern humans, Neanderthals, and Denisovans, and has allowed us to disentangle complex selective processes. Information from aDNA studies is nowhere near saturation, and we believe that future aDNA sequences will continue to change our understanding of hominin history. (Abstract)

Vignieri, Sacha, ed.. The Zoonomia Project. Science. 380/356, 2023. This issue collects a papers on novel abilities to recover and sequence the past genetic basis of a diverse array of mammalian species. We note, e.g., Seeing Humans Through an Evolutionary Lens, Relating Enhancer Genetic variation Across Mammals to Complex Phenotypes, A Genetic Timescale for Placental Evolution, and Integrating Gene Annotation with Orthology Inference at Scale. These contributions were of such merit that two articles, What Cheetahs, Armadillos and Whales Revealed About Human DNA by Carl Zimmer and From Alpacas to Yaks, Mammal DNA Yields its Secrets by Emily Anthes, appeared in the New York Times on April 27, 2023. The international program itself can be reached at zoonomiaproject.org. So it seems that just as recent paleogenomic research, as noted herein, has been able to reconstruct many past histories, its compass can similarly include all manner a creaturely ancestors with a new heritage.

Mammals are diverse classes of animals, ranging in size across many orders of magnitude, and every possible shape. Understanding when, how, and under what selective pressures this variation has developed has long been of interest. But into the 21st century and 2020s, a robust science of paleogenomics can provide novel insights into the evolution of important genetic variation and morphological traits. Further, because we humans are also mammals, these understandings can help illume our own evolutionary history and health. Genes that are conserved across many species may indicate those that are essential for normal function and may lead to disease when altered. Here the genomes of 240 mammals inform studies to identify adaptive traits, morphologies and innovations all the way to homo sapiens. The Zoonomia project thus heralds a new era in which genomes recovered from hundreds of species will explain much about mammals, and ourselves. (VS, Issue Introduction)

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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