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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

Murat, Florent, et al. Understanding Brassicaceae Evolution Through Ancestral Genome Reconstruction. Genome Biology. 16/262, 2015. We note the ability of 2010s technologies to sequence not only fauna, but the genetic endowment of flora vegetation. The Abstract conveys one specific instance.

Brassicaceae is a family of green plants of high scientific and economic interest, including thale cress, cruciferous vegetables (cabbages) and rapeseed. We reconstruct an evolutionary framework composed of high-resolution ancestral karyotypes using the genomes. The ancestral Brassicaceae karyotype is composed of eight protochromosomes and 20,037 ordered and oriented protogenes. After speciation, it evolved into the ancestral Camelineae karyotype and the proto-Calepineae karyotype genomes. The three inferred ancestral karyotype genomes are shown here to be powerful tools to unravel the reticulated evolutionary history of extant Brassicaceae genomes regarding the fate of ancestral genes and genomic compartments, particularly centromeres and evolutionary breakpoints. (Abstract excerpts)

Orlando, Ludovic and Alan Cooper. Using Ancient DNA to Understand Evolutionary and Ecological Processes. Annual Review of Ecology, Evolution, and Systematics. 45/573, 2014. Centre for GeoGenetics, University of Copenhagen, and Australian Center for Ancient DNA, University of Adelaide researchers provide a synopsis to date of novel capabilities by which our collaborative humanity can retro-sequence the myriad animal genomes that we peoples have arisen from. A spate of companion papers likewise extol such as The Future of Ancient DNA by Michael Hofreiter, et al in BioEssays (Online November 2014), Human Paleogenetics of Europe by Guido Brandt, et al (online November 2014) and Major Transitions in Human Evolution Revisited by Luca Ermini, et al (online December 2014), both in the Journal of Human Evolution, and Ancient Humans and the Origin of Modern Humans by Janet Kelso and Kay Prufer in Current Opinion in Genetics & Development (29/133, 2014). A natural philosophy view would then wonder whom is this planetary progeny by which a certain cosmos seems trying to consciously reconstruct its genetic history. In some other words, are we seeing a creative process of Bit to It to Bit.

Ancient DNA provides a unique means to record genetic change through time and directly observe evolutionary and ecological processes. Although mostly based on mitochondrial DNA, the increasing availability of genomic sequences is leading to unprecedented levels of resolution. Temporal studies of population genetics have revealed dynamic patterns of change in many large vertebrates, featuring localized extinctions, migrations, and population bottlenecks. The pronounced climate cycles of the Late Pleistocene have played a key role, reducing the taxonomic and genetic diversity of many taxa and shaping modern populations. Importantly, the complex series of events revealed by ancient DNA data is seldom reflected in current biogeographic patterns. DNA preserved in ancient sediments and coprolites has been used to characterize a range of paleoenvironments and reconstruct functional relationships in paleoecological systems. In the near future, genome-level surveys of ancient populations will play an increasingly important role in revealing, calibrating, and testing evolutionary processes. (Orlando Abstract)

Paabo, Svante. Neanderthal Man: In Search of Lost Genomes. New York: Basic Books, 2011. The Swedish geneticist now at the Max Planck Institute for Evolutionary Anthropology is a leading pioneer in this field of sequencing past genomes of extinct species. Here he recounts how from bone fragments and the like, by means of 21st century techniques the genetic endowment of this main precursor hominid could be reconstructed. By virtue of this ability, much more information can be gained about Neanderthal habitations, culture, and interbreedings.

Neanderthal Man tells the story of geneticist Svante Pääbo’s mission to answer this question, and recounts his ultimately successful efforts to genetically define what makes us different from our Neanderthal cousins. Beginning with the study of DNA in Egyptian mummies in the early 1980s and culminating in the sequencing of the Neanderthal genome in 2010, Neanderthal Man describes the events, intrigues, failures, and triumphs of these scientifically rich years through the lens of the pioneer and inventor of the field of ancient DNA. We learn that Neanderthal genes offer a unique window into the lives of our hominin relatives and may hold the key to unlocking the mystery of why humans survived while Neanderthals went extinct. Drawing on genetic and fossil clues, Pääbo explores what is known about the origin of modern humans and their relationship to the Neanderthals and describes the fierce debate surrounding the nature of the two species’ interactions.

Paps, Jordi and Peter Holland. Reconstruction of the Ancestral Metazoan Genome Reveals an Increase in Genomic Novelty. Nature Communications. 9/1730, 2018. We enter this work by Oxford University biologists to report how deeply these novel abilities to sequence all manner of past creaturely genetic codes can now reach. A notable finding is that both environmental and internal genomic changes can be seen in effect. The whole endeavor, as the Abstract and quote alludes, then merits natural reflection. Whom are human peoples altogether, rising out of Metazoa kingdoms, so to re-read the phenotypes and genotypes we latecomers evolved from? What might the phenomenal identity and purpose of this collective genomic knowledge be?

Understanding the emergence of the Animal Kingdom is one of the major challenges of modern evolutionary biology. Many genomic changes took place along the evolutionary lineage that gave rise to the Metazoa. Recent research has revealed the role that co-option of old genes played during this transition, but the contribution of genomic novelty has not been fully assessed. Here, using extensive genome comparisons between metazoans and multiple outgroups, we infer the minimal protein-coding genome of the first animal (how incredible to do this), in addition to other eukaryotic ancestors, and estimate the proportion of novelties in these ancient genomes. Contrary to the prevailing view, this uncovers an unprecedented increase in the extent of genomic novelty during the origin of metazoans, and identifies 25 groups of metazoan-specific genes that are essential across the Animal Kingdom. We argue that internal genomic changes were as important as external factors in the emergence of animals. (Abstract)

Metazoa are the multicellular eukaryotic group with the largest number of described species, over 1.6 million. They evolved within the eukaryotic supergroup Opisthokonta, most closely related to choanoflagellates, filastereans, and ichthyosporeans. In addition to environmental and ecological triggers, biological functions encoded in the genome were crucial in this transition, including genes involved in differential gene regulation (e.g., several transcription factors, signaling pathways), cell adhesion (e.g., cadherins), cell type specification, cell cycle, and immunity. Recent studies show that many genes typically associated with metazoan functions actually pre-date animals themselves, supporting functional co-option of ‘unicellular genes’ during the genesis of metazoans. (2)

Racimo, Fernando, et al. Beyond Broad Strokes: Sociocultural Insights from the Study of Ancient Genomes. Nature Reviews Genetics. June, 2020. With prior hominids, migrations, primates, animal creatures and more now sequenced, and as techniques ever improve, University of Copenhagen and Universitat Pompeu Fabra, Barcelona researchers discuss a new phase which can reconstruct intangible behavioral, artifactual, and tribal features. So we wonder, what kind of temporal reality is this whereof a global species finally appears and becomes capable to recover, learn about and convert to knowledge all of whom and what went before. Why can we peoples do this, what is the great revelation and purpose?

In the field of human history, ancient DNA has provided answers to long-standing debates about major movements of people and has begun to inform on other important facets of the human experience. The field is now moving from large-scale supraregional studies to local perspectives of socioeconomic processes, inheritance rules, marriage practices and technological diffusion. In this Review, we summarize recent studies, insights and methods to infer sociocultural aspects of human behaviour. This approach often involves working across disciplines — such as anthropology, archaeology, linguistics and genetics — that have until recently evolved in separation. (Abstract)

Reich, David. Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past. New York: Pantheon, 2018. The Harvard Medical School and Howard Hughes Medical Institute senior geneticist writes a comprehensive edition about this incredible ability just becoming possible to sequence and reconstruct, way beyond fossil shards, how our worldwide humanity capable of doing this actually arrived. For one example from Reich’s Lab see The Evolutionary History of Human Populations in Europe by Iosif Lazaridis.

Building an Ancient DNA Atlas of Humanity: We know next to nothing about how the people of the world got to be how they are today. The reason for this ignorance is that studies of the DNA of diverse populations have mostly depended on samples taken from present-day people. But now a technological revolution has made it possible to sequence whole genomes from ancient bones, giving us an unanticipated opportunity to understand how humans are changing. Ancient DNA allows us to go beyond the two-dimensional map of genetic variation based on the coordinates of latitude and longitude. The rapid increase in the number of ancient genomes makes it entirely feasible that the world's combined ancient DNA data set will reach 10,000 ancient genomes within a few years. We work alongside other laboratories to generate ancient DNA from every archaeological culture from all parts of the world over the last 50,000 years. (Reich Lab Research Web Page)

Rokas, Antonis and Pamela Soltis. Genomes and Evolution: Seq-ing Answers in Life’s Genomes. Current Opinion in Genetics & Development. 35/1, 2015. An introduction to a special title issue with papers such as The Evolution of Animal Genomes, The Evolution of the Human Genome, and The Language of the Protein Universe (search Levitt).

Schuster, Astrid, et al. Deceptive Desmas: Molecular Phylogenetics Suggests a New Classification and Uncovers Convergent Evolution of Lithistid Demosponges. PLoS One. Online January, 2015. While many ancient DNA studies have been on hominids, in the mid 2010s it is now possible to re-sequence almost any prior entity. Here German, Polish and Australian paleontologists apply these methods to the diverse Porifera phylum of invertebrate sponges.

Reconciling the fossil record with molecular phylogenies to enhance the understanding of animal evolution is a challenging task, especially for taxa with a mostly poor fossil record, such as sponges (Porifera). ‘Lithistida’, a polyphyletic group of recent and fossil sponges, are an exception as they provide the richest fossil record among demosponges. Lithistids, currently encompassing 13 families, 41 genera and >300 recent species, are defined by the common possession of peculiar siliceous spicules (desmas) that characteristically form rigid articulated skeletons. Their phylogenetic relationships are to a large extent unresolved and there has been no (taxonomically) comprehensive analysis to formally reallocate lithistid taxa to their closest relatives. (Abstract excerpt)

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)

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