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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

ENCODE, Project Consortium. A User's Guide to the Encyclopedia of DNA Elements ENCODE. PLoS Computational Biology. 9/4, 2011. A general introduction to this successful exemplar of worldwide scientific collaboration. See also in the Nature ENCODE issue “Lessons for Big-Data Projects” (489/49, 2012) by a lead bioinformatics organizer and director Ewan Birney.

The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. In the process, standards to ensure high-quality data have been implemented, and novel algorithms have been developed to facilitate analysis. Data and derived results are made available through a freely accessible database. Here we provide an overview of the project and the resources it is generating and illustrate the application of ENCODE data to interpret the human genome. (Abstract)

Ermini, Luca, et al. Major Transitions in Human Evolution Revisited: A Tribute to Ancient DNA. Journal of Human Evolution. Volume 79, 2015. In a special issue on this major advance, University of Copenhagen, Center for GeoGenetics, researchers survey much progress due to this novel ability to sequence past genomes so as to rearrange and clarify the temporal passage from primates and hominids to homo sapiens. Much future promise is then sketched as this method grows in veracity and application onto primordial creatures.

The origin and diversification of modern humans have been characterized by major evolutionary transitions and demographic changes. Patterns of genetic variation within modern populations can help with reconstructing this ∼200 thousand year-long population history. However, by combining this information with genomic data from ancient remains, one can now directly access our evolutionary past and reveal our population history in much greater detail. This review outlines the main recent achievements in ancient DNA research and illustrates how the field recently moved from the polymerase chain reaction (PCR) amplification of short mitochondrial fragments to whole-genome sequencing and thereby revisited our own history. Ancient DNA research has revealed the routes that our ancestors took when colonizing the planet, whom they admixed with, how they domesticated plant and animal species, how they genetically responded to changes in lifestyle, and also, which pathogens decimated their populations. (Abstract)

Frantz, Laurent, et al. Animal Domestication in the Era of Ancient Genomics. Nature Reviews Genetics. 21/8, 2020. Queen Mary University of London, Trinity College, Dublin, Oxford University, and University of Toulouse (Ludovic Orlando) paleogeneticists apply the latest advances in nucleotide recovery and sequencing ability to reconstruct, in this instance, the historic occasions by which many feral, native creatures were enjoined as beneficial hominid and human co-inhabitants. This long process, as readers know, led to much evolutionary modification, as cited and described in this paper.

The domestication of animals led to a major shift in human subsistence patterns from hunter–gatherers to a sedentary agricultural lifestyle. Over the past 15,000 years, the phenotype and genotype of multiple animal species, such as dogs, pigs, sheep, goats, cattle and horses, have been substantially altered during their adaptation to the human niche. Recent innovations such as improved ancient DNA extraction methods and next-generation sequencing, have enabled whole ancient genomes to be read. These genomes have helped reconstruct how animals entered into domestic relationships with humans and were subjected to selection pressures. Here, we discuss and update key concepts in animal domestication in light of these novel contributions. (Abstract)

Gerstein, Mark, et al. What is a Gene, post-ENCODE?: History and Updated Definition. Genome Research. 17/6, 2007. The National Human Genome Research Institute launched a public research consortium named ENCODE, the Encyclopedia Of DNA Elements, in September 2003 to carry out a project to identify all functional elements in this genome sequence. This article discusses recent results as they mandate a systems redefinition of the genetic code. A similar paper can be accessed in the journal Nature (447/799, 2007).

While sequencing of the human genome surprised us with how many protein-coding genes there are, it did not fundamentally change our perspective on what a gene is. In contrast, the complex patterns of dispersed regulation and pervasive transcription uncovered by the ENCODE project, together with non-genic conservation and the abundance of noncoding RNA genes, have challenged the notion of the gene. To illustrate this, we review the evolution of operational definitions of a gene over the past century—from the abstract elements of heredity of Mendel and Morgan to the present-day ORFs enumerated in the sequence databanks. We then summarize the current ENCODE findings and provide a computational metaphor for the complexity. Finally, we propose a tentative update to the definition of a gene: A gene is a union of genomic sequences encoding a coherent set of potentially overlapping functional products. (Abstract)

Gokeumen, Omer and Michael Frachetti. The Impact of Ancient Genome Studies in Archaeology. Annual Review of Anthropology. 49/277, 2020. SUNY Buffalo and Washington University, St. Louis researchers provide a latest, wide-ranging tutorial on these revolutionary collection and sequencing techniques as they result in a whole scale revision and expansion of past skeletal and artifact paleontological studies.

The study of ancient genomes has proceeded at an incredible rate in the last decade. The result is a shift in archaeological narratives and a fierce debate on the place of genetics in anthropological research with regard to human origins, movement of ancient and modern populations, the role of social organization in shaping material culture, and the relationship between culture, language, and ancestry. Further concerns involve indigenous rights, ownership of ancient materials, inclusion in the scientific process, and even the meaning of what it is to be a human. (Abstract)

Gokhman, David, et al. Epigenetics: Its Getting Old: Past Meets Future in Paleoepigenetics. Trends in Ecology and Evolution. Online February, 2016. Hebrew University of Jerusalem researchers consider how novel abilities to reconstruct ancient genomes can also take on an epigenetic dimension, similar to its new significance in expansive human genetic repertoires.

Recent years have witnessed the rise of ancient DNA (aDNA) technology, allowing comparative genomics to be carried out at unprecedented time resolution. While it is relatively straightforward to use aDNA to identify recent genomic changes, it is much less clear how to utilize it to study changes in epigenetic regulation. Here we review recent works demonstrating that highly degraded aDNA still contains sufficient information to allow reconstruction of epigenetic signals, including DNA methylation and nucleosome positioning maps. We discuss challenges arising from the tissue specificity of epigenetics, and show how some of them might in fact turn into advantages. Finally, we introduce a method to infer methylation states in tissues that do not tend to be preserved over time. (Abstract)

Goldford, Joshua and Daniel Segre. Modern Views of Ancient Metabolic Networks. Current Opinion in Systems Biology. 8/117, 2018. Boston University bioinformatic researchers illustrate new abilities not only for paleogenetic sequences, but onto recoveries of physiological and cellular features of the long procession of evolutionary organisms.

Metabolism is a molecular, cellular, ecological and planetary phenomenon, whose fundamental principles are likely at the heart of what makes living matter different from inanimate. Systems biology approaches developed for the quantitative analysis of metabolism at multiple scales can help understand its ancient history. In this review, we highlight work that uses network-level approaches to shed light on key innovations in ancient life, including the emergence of proto-metabolic networks, collective autocatalysis and bioenergetics coupling. Recent experiments and computational analyses have revealed new aspects of this ancient history, paving the way for the use of large datasets to further improve our understanding of life's principles and abiogenesis. (Abstract)

Hagelberg, Erika, et al. Ancient DNA: The First Three Decades. Philosophical Transactions of the Royal Society B. 370/20130371, 2015. An introduction to an issue on advances in this retrospective reconstruction since Russell Higuchi, Allan Wilson and others were first able to sequence nucleotides from an extinct horse. The task remained daunting into the mid 1990s when DNA extraction and analysis methods improved. A premier achievement in 1997 was the sequencing of a Neanderthal genome by Svante Paabo. As automated computational techniques became common in past years, it is now possible to analyze and recreate any prior creaturely genome. With such present capacities, this field of paleogenomics is on a mission to retro-sequence as many evolutionary organisms as possible. A main article is Ancient Genomics by Clio Der Sarkissian, Clio, et al, a 28 member team from the Center for GeoGenetics at the University of Copenhagen, the leading research institute, see also Ancient Population Genomics and the Study of Evolution by Matthew Parks, et al.

The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field's focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequence throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when testing specific hypotheses related to the past. (Der Sarkissian Abstract)

Recently, the study of ancient DNA (aDNA) has been greatly enhanced by the development of second-generation DNA sequencing technologies and targeted enrichment strategies. These developments have allowed the recovery of several complete ancient genomes, a result that would have been considered virtually impossible only a decade ago. Prior to these developments, aDNA research was largely focused on the recovery of short DNA sequences and their use in the study of phylogenetic relationships, molecular rates, species identification and population structure. However, it is now possible to sequence a large number of modern and ancient complete genomes from a single species and thereby study the genomic patterns of evolutionary change over time. Such a study would herald the beginnings of ancient population genomics and its use in the study of evolution. Species that are amenable to such large-scale studies warrant increased research effort. We report here progress on a population genomic study of the Adélie penguin (Pygoscelis adeliae). This species is ideally suited to ancient population genomic research because both modern and ancient samples are abundant in the permafrost conditions of Antarctica. This species will enable us to directly address many of the fundamental questions in ecology and evolution. (Parks Abstract)

Harris, Eugene. Ancestors in Our Genome: The New Science of Human Evolution. Oxford: Oxford University Press, 2014. A CCNY geneticist and anthropologist writes one of the first books on this new field of paleogenetics, the retrospective sequencing of hominid and primate genetic endowments. By means of sophisticated instruments and informatics techniques, it is possible to recover and decipher not only present species, but past genomes across the whole span of creaturely evolution. A consequence and advance described in this book is a recast family tree from Australopithecus to Neanderthal, as nucleotide molecules complement and supplant fossil bones alone.

Henn, Brenna and Lluis Quintana-Murci. The History, Geography and Adaptation of Human Genes: A Tribute to Luca Cavalli-Sforza. Current Opinion in Genetics & Development. 53/iii, 2018. An introduction to this special issue by a UC Davis anthropologist and a Pasteur Institute, Paris evolutionary geneticist about the lifetime contributions (1922-2018) of the University of Parma, Pavia and Stanford population geneticist, who first realized and pursued historic parallels between genomes and languages. Among the 26 entries, e.g., are Admixture and Adaptation in Human Evolution by Michael Dannemann and Fernando Racimo, Insights from Epigenetic Studies on Human Health by Connie Mulligan, Clarify Distince Models of Modern Human Origins in Africa by B. Henn, et al, and Fine-Tuning of Approximate Bayesian Computation for Human Population Genomics by Niall Cooke and Shigeki Nakagome.

This special issue on the Genetics of Human Origins is dedicated to Luigi Luca Cavalli-Sforza who passed away last August 2018. Luca — “please, call me Luca” he always said whoever he was talking to — was the grandfather of the field of human population genetics , and influenced many of the perspectives we review here in foundational ways. His interests in human prehistory cut across several disciplines, as he worked to compare patterns from linguistic, cultural and archaeological data with emerging protein polymorphism, mitochondrial and Y-chromosomal data. His cross-disciplinary thinking opened new avenues of research, including that of how cultural evolution may impact biological evolution: “If there's any interaction between genes and languages, it is often languages that influence genes, since linguistic differences between populations lessen the chance of genetic exchange between them”.

Hofreiter, Michael, et al. The Future of Ancient DNA: Technical Advances and Conceptual Shifts. BioEssays. 37/3, 2015. By means of hybridization capture, multi-locus data, next generation sequencing, and more, University of York, University of Potsdam, and Institute for Zoo and Wildlife Research, Berlin, evolutionary archaeologists press the frontiers of this new method and vista for the collaborative reconstruction of past animal genomes onto the earliest rudiments.

Technological innovations such as next generation sequencing and DNA hybridisation enrichment have resulted in multi-fold increases in both the quantity of ancient DNA sequence data and the time depth for DNA retrieval. To date, over 30 ancient genomes have been sequenced, moving from 0.7× coverage (mammoth) in 2008 to more than 50× coverage (Neanderthal) in 2014. Studies of rapid evolutionary changes, such as the evolution and spread of pathogens and the genetic responses of hosts, or the genetics of domestication and climatic adaptation, are developing swiftly and the importance of palaeogenomics for investigating evolutionary processes during the last million years is likely to increase considerably. However, these new datasets require new methods of data processing and analysis, as well as conceptual changes in interpreting the results. In this review we highlight important areas of future technical and conceptual progress and discuss research topics in the rapidly growing field of palaeogenomics. (Abstract)

Joy, Jeffrey, et al. Ancestral Reconstruction. PLoS Computational Biology. Online July, 2016. As the quote cites, University of British Columbia research physicians give a good overview of novel capabilities by Anthropo sapiens to retrospectively learn and describe how our personsphere came to be. As this endeavor takes off, a table of two dozen software programs is posted. See also, e.g., Buds of the Tree: The Highway to the Last Universal Common Ancestor by Savio Torres de Farias and Francisco Prosdocimi in the International Journal of Astrobiology (Online July 2016). And again, we just wonder what kind of a procreative universe attains a worldwise faculty by which to look back and recreate how it came to be. Why can we altogether do this, for what great discovery and purpose?

Ancestral reconstruction is the extrapolation back in time from measured characteristics of individuals (or populations) to their common ancestors. It is an important application of phylogenetics, the reconstruction and study of the evolutionary relationships among individuals, populations, or species to their ancestors. In the context of biology, ancestral reconstruction can be used to recover different kinds of ancestral character states, including the genetic sequence (ancestral sequence reconstruction), the amino acid sequence of a protein, the composition of a genome (e.g., gene order), a measurable characteristic of an organism (phenotype), and the geographic range of an ancestral population or species (ancestral range reconstruction). Nonbiological applications include the reconstruction of the vocabulary or phonemes of ancient languages [and cultural characteristics of ancient societies such as oral traditions or marriage practices. (1)

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