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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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VI. Earth Life Emergence: A Development of Body, Brain, Selves and Societies

1. Paleogenomics, Gaiagenomics, Cosmogenomics: Natural Ancestry

This 2015 section is posted to gather novel advances of genetic research as human beings proceed to decipher, sequence and avail nature’s cosmos to children code. By this vista, a temporal “paleo” evolutionary retrospect, a current breadth of biospheric creatures from insects to sapiens, and a spatial “cosmo” milieu from universe to us can be perceived. As the entries describe, incipient attempts began in the 1980s and 1990s to recreate the DNA genomes of hominids and primates. After the 2001 Human Genome project, aided by sophisticated instruments and computer informatics, it became increasingly possible to sequence any present or past entity from Neanderthals and monkeys to dinosaurs and invertebrates. A revolutionary new method and window is thus opened for our whole scale evolutionary reconstruction.

A companion effort is the ENCODE: Encyclopedia of DNA Elements project, which began in 2003 and proceeds apace with extensive, advanced genome sequencing. In February 2015 a similar discernment of the multifaceted Human Epigenome was announced. Together with the molecular nucleotide substrate, this much expanded appreciation of genetic phenomena promises many benefits. If we might reflect upon and extrapolate these august abilities, scollaborative human beings over the Earth seem to be the universe’s way, billions of years on, to achieve a whole-scale self-sequence its own natural genetic code.

Alie, Alexandre, et al. The Ancestral Gene Repertoire of Animal Stem Cells. Procedings of the National Academy of Sciences. 112/E7093, 2015. As genomic retro-recovery proceeds apace, a team of Japanese and French researchers report on abilities to sequence a deeply conserved gene repertoire of these crucial cells from pre-metazoan sponges to mammalian species.

Stem cells are pivotal for development and tissue homeostasis of multicellular animals, and the quest for a gene toolkit associated with the emergence of stem cells in a common ancestor of all metazoans remains a major challenge for evolutionary biology. We reconstructed the conserved gene repertoire of animal stem cells by transcriptomic profiling of totipotent archeocytes in the demosponge Ephydatia fluviatilis and by tracing shared molecular signatures with flatworm and Hydra stem cells. Phylostratigraphy analyses indicated that most of these stem-cell genes predate animal origin, with only few metazoan innovations, notably including several partners of the Piwi machinery known to promote genome stability. (Abstract)

Allentoft, Morten, et al. Population Genomics of Bronze Age Eurasia. Nature. 552/167, 2015. With breakthrough 2010s instrumentation and collaboration capabilities, some 60 scientists from Denmark, Sweden, The Netherlands, Poland, Switzerland, Russia, Germany, Armenia, Italy, Hungary, Czech Republic, Estonia, Lithuania, the UK and USA, led by the University of Copenhagen Centre for GeoGenetics, open a whole new retrospective on this prehistoric age, circa 3000 – 500 BC, by way of genetic sequence analysis. Furthermore, in the same issue a parallel project to reconstruct languages is covered in Massive Migration from the Steppe was a Source for Indo-European Languages in Europe by Wolfgang Haak, et al (207). See also commentaries herein on this work by Ewen Callaway (140) and John Novembre (164).

The Bronze Age of Eurasia (around 3000–1000 BC) was a period of major cultural changes. However, there is debate about whether these changes resulted from the circulation of ideas or from human migrations, potentially also facilitating the spread of languages and certain phenotypic traits. We investigated this by using new, improved methods to sequence low-coverage genomes from 101 ancient humans from across Eurasia. We show that the Bronze Age was a highly dynamic period involving large-scale population migrations and replacements, responsible for shaping major parts of present-day demographic structure in both Europe and Asia. Our findings are consistent with the hypothesized spread of Indo-European languages during the Early Bronze Age. We also demonstrate that light skin pigmentation in Europeans was already present at high frequency in the Bronze Age, but not lactose tolerance, indicating a more recent onset of positive selection on lactose tolerance than previously thought. (Allentoft Abstract)

We generated genome-wide data from 69 Europeans who lived between 8,000–3,000 years ago by enriching ancient DNA libraries for a target set of almost 400,000 polymorphisms. Enrichment of these positions decreases the sequencing required for genome-wide ancient DNA analysis by a median of around 250-fold, allowing us to study an order of magnitude more individuals than previous studies and to obtain new insights about the past. We show that the populations of Western and Far Eastern Europe followed opposite trajectories between 8,000–5,000 years ago. At the beginning of the Neolithic period in Europe, ~8,000–7,000 years ago, closely related groups of early farmers appeared in Germany, Hungary and Spain, different from indigenous hunter-gatherers, whereas Russia was inhabited by a distinctive population of hunter-gatherers with high affinity to a ~24,000-year-old Siberian6. By ~6,000–5,000 years ago, farmers throughout much of Europe had more hunter-gatherer ancestry than their predecessors, but in Russia, the Yamnaya steppe herders of this time were descended not only from the preceding eastern European hunter-gatherers, but also from a population of Near Eastern ancestry. Western and Eastern Europe came into contact ~4,500 years ago, as the Late Neolithic Corded Ware people from Germany traced ~75% of their ancestry to the Yamnaya, documenting a massive migration into the heartland of Europe from its eastern periphery. This steppe ancestry persisted in all sampled central Europeans until at least ~3,000 years ago, and is ubiquitous in present-day Europeans. (Haak Abstract)

Baker, Jennifer, et al. Human Ancestry Correlates with Language and Reveals that Race is not an Objective Genomic Classifier. Nature Scientific Reports. 7/1572, 2017. Center for Research on Genomics and Global Health, National Human Genome Research Institute bioscientists Baker, Charles Rotimi, and David Shriner achieve a sophisticated tracery of prehistoric human migrations via genes and languages. The key contribution is a perception of how much genetic and linguistic endowments provide tandem, parallel markers to advise our late global reconstruction.

Genetic and archaeological studies have established a sub-Saharan African origin for anatomically modern humans with subsequent migrations out of Africa. Using the largest multi-locus data set known to date, we investigated genetic differentiation of early modern humans, human admixture and migration events, and relationships among ancestries and language groups. We compiled publicly available genome-wide genotype data on 5,966 individuals from 282 global samples, representing 30 primary language families. The best evidence supports 21 ancestries that delineate genetic structure of present-day human populations. Independent of self-identified ethno-linguistic labels, the vast majority (97.3%) of individuals have mixed ancestry, with evidence of multiple ancestries in 96.8% of samples and on all continents. The data indicate that continents, ethno-linguistic groups, races, ethnicities, and individuals all show substantial ancestral heterogeneity. Ancestry data yield insight into a deeper past than linguistic data can, while linguistic data provide clarity to ancestry data. (Abstract)

Benitez-Burraco, Antonio and Dan Dediu. Ancient DNA and Language. Journal of Language Evolution. 3/1, 2018. University of Seville linguists introduce a special section about how the latest genetic techniques can retrace, fill in and recover this parallel pathway to global literacy. Among entries are The Genomic Landscape of Language by Hayley Mountford and Dianne Newbury, and What aDNA can (and cannot) Tell us about the Emergence of Language and Speech by Rob DeSalle and Ian Tattersal.

Biscotti, Maria, et al. The Lungfish Transcriptome: A Glimpse into Molecular Evolution Events at the Transition from Water to Land. Nature Scientific Reports. 6/21571, 2016. A transcriptome is the full range of messenger RNA, or mRNA, molecules expressed by an organism. Marche Polytechnic University, University of Trieste, and University of Wurzburg researchers discuss the retrospective sequence of the genomes of these “living fossils” aquatic ancestors. Again by a natural philosophy view we wonder what kind of a reality evolves a global humanity whom may then proceed to convert all the present and prior creaturely codes from whom we altogether arose to be able to do this.

Lungfish and coelacanths are the only living sarcopterygian fish. The phylogenetic relationship of lungfish to the last common ancestor of tetrapods and their close morphological similarity to their fossil ancestors make this species uniquely interesting. However their genome size, the largest among vertebrates, is hampering the generation of a whole genome sequence. To provide a partial solution to the problem, a high-coverage lungfish reference transcriptome was generated and assembled. The present findings indicate that lungfish, not coelacanths, are the closest relatives to land-adapted vertebrates. Whereas protein-coding genes evolve at a very slow rate, possibly reflecting a “living fossil” status, transposable elements appear to be active and show high diversity, suggesting a role for them in the remarkable expansion of the lungfish genome. Analyses of single genes and gene families documented changes connected to the water to land transition and demonstrated the value of the lungfish reference transcriptome for comparative studies of vertebrate evolution. (Abstract)

Booth, David and Nicole King. Gene Regulation in Transition. Nature. 534/482, 2016. We cite this paper by UC Berkeley biologists to record how novel capabilities of a collaborative humanity, as if a personal Anthropo Sapiens, are proceeding apace to retrospectively sequence creaturely genomes from primates to protozoa. The specific candidate here is Capsaspora owczarzaki, a single-celled eukaryote seen as an iconic entity by which to reconstruct the evolutionary emergence of multi-cellularity.

Bortolini, Eugenio, et al. Inferring Patterns of Folktale Diffusion Using Genomic Data. Proceedings of the National Academy of Sciences. 114/9140, 2017. We cite this contribution by a 13 member team from Spain, Estonia, Italy, the UK, Germany, and Portugal including Jamshid Tehrani to convey the degree that global scientific faculties, by way of genetic evidence as a cultural measure, are proceeding to reconstruct how we peoples began on the way to this sapient personsphere.

This paper presents unprecedented evidence on the transmission mechanism underlying the spread of a broad cross-cultural assemblage of folktales in Eurasia and Africa. State-of-the-art genomic evidence is used to directly assess the relevance of demic diffusion processes, in particular on the distribution of Old World folktales at intermediate geographic scales, and identify individual stories that are more likely to be transmitted through population movement and replacement. The results provide an empirical solution to operate with linguistic barriers and highlight the impossibility of disentangling genetic from geographic relationships at a cross-continental scale, warning against the direct use of extant genetic variability to infer processes of long-range cultural transmission. (Significance)

Brandao, Marcelo, et al. Ancient DNA Sequence Revealed by Error-Correcting Codes. Nature Scientific Reports. 5/12051, 2015. University of Campinas, Brazil, geneticists describe another innovative and incisive way that this retrospective capability can recover and sequence the prior evolutionary of nucleotide genome endowments.

A previously described DNA sequence generator algorithm (DNA-SGA) using error-correcting codes has been employed as a computational tool to address the evolutionary pathway of the genetic code. The code-generated sequence alignment demonstrated that a residue mutation revealed by the code can be found in the same position in sequences of distantly related taxa. Furthermore, the code-generated sequences do not promote amino acid changes in the deviant genomes through codon reassignment. A Bayesian evolutionary analysis of both code-generated and homologous sequences of the Arabidopsis thaliana malate dehydrogenase gene indicates an approximately 1 MYA divergence time from the MDH code-generated sequence node to its paralogous sequences. The DNA-SGA helps to determine the plesiomorphic state of DNA sequences because a single nucleotide alteration often occurs in distantly related taxa and can be found in the alternative codon patterns of noncanonical genetic codes. As a consequence, the algorithm may reveal an earlier stage of the evolution of the standard code. (Abstract)

Brucato, Nicolas, et al. Genomic Admixture Tracks Pulses of Economic Activity over 2,000 Years in the Indian Ocean Trading Network. Nature Scientific Reports. 7/2919, 2017. We enter this entry by a team of Université de Toulouse, Institut des Mondes Africains, University of Indonesia, Jakarta, and Massey University, New Zealand, bioanthropologists, among many kindred papers, to show how novel genetic curations can serve our late collaborative reconstruction of the long trek by whence homo to anthropo sapiens came to cover the round Earth.

The Indian Ocean has long been a hub of interacting human populations. Following land- and sea-based routes, trade drove cultural contacts between far-distant ethnic groups in Asia, India, the Middle East and Africa, creating one of the world’s first proto-globalized environments. However, the extent to which population mixing was mediated by trade is poorly understood. Reconstructing admixture times from genomic data in 3,006 individuals from 187 regional populations reveals a close association between bouts of human migration and trade volumes during the last 2,000 years across the Indian Ocean trading system. Temporal oscillations in trading activity match phases of contraction and expansion in migration, with high water marks following the expansion of the Silk Roads in the 5th century AD, the rise of maritime routes in the 11th century and a drastic restructuring of the trade network following the arrival of Europeans in the 16th century. The economic fluxes of the Indian Ocean trade network therefore directly shaped exchanges of genes, in addition to goods and concepts. (Abstract)

Burki, Fabien. The Eukaryotic Tree of Life from a Global Phylogenomic Perspective. Cold Spring Harbor Perspectives in Biology. 6/5, 2014. Phylogenomics blends evolutionary studies and genomic analysis to designate endeavors to reconstruct the long genetic heritage from invertebrates to homo sapiens. A University of British Columbia systems botanist here extols the latest superkingdom expansions from original animal and vegetable to Rhizaria, Amoebozoa, Stramenopiles, Opisthokonts where we bilateria mammals reside, and more classes because of novel capabilities to sequence and quantify. See also a Science News (August 8, 2015) report Strange Relations on these advances. And it is ever amazing that a genesis cosmos billions of years on, in which we find our local and global selves, can reconstruct the nucleotide program that brought this sapient ability into existence, witness, and continuance.

Molecular phylogenetics has revolutionized our knowledge of the eukaryotic tree of life. With the advent of genomics, a new discipline of phylogenetics has emerged: phylogenomics. This method uses large alignments of tens to hundreds of genes to reconstruct evolutionary histories. This approach has led to the resolution of ancient and contentious relationships, notably between the building blocks of the tree (the supergroups), and allowed to place in the tree enigmatic yet important protist lineages for understanding eukaryote evolution. Here, I discuss the pros and cons of phylogenomics and review the eukaryotic supergroups in light of earlier work that laid the foundation for the current view of the tree, including the position of the root. I conclude by presenting a picture of eukaryote evolution, summarizing the most recent progress in assembling the global tree. (Abstract)

Creanza, Nicole, et al. A Comparison of Worldwide Phonemic and Genetic Variation in Human Populations. Proceedings of the National Academy of Sciences. 112/1265, 2015. Ever since Charles Darwin, and in the 1980s since Luigi Cavalli-Sforza, it has become evident that human population genetic endowments and language families are deeply related. Here Stanford University, University of Manitoba, and Brown University biologists, anthropologists, and linguists including Merritt Ruhlen and Marcus Feldman, confirm that genomes and phonemes (meaningful linguistic units) track a similar geographic and historic course. Across continents and centuries, genetic and dialect trees proceed in parallel ways, which then provide a retrospective chronicle. Circa 2015, a singular biomolecular to grammatical milieu, as if cosmome to languagome, is being revealed as it rises to its own self-cognizance.

Worldwide patterns of genetic variation are driven by human demographic history. Here, we test whether this demographic history has left similar signatures on phonemes—sound units that distinguish meaning between words in languages—to those it has left on genes. We analyze, jointly and in parallel, phoneme inventories from 2,082 worldwide languages and microsatellite polymorphisms from 246 worldwide populations. On a global scale, both genetic distance and phonemic distance between populations are significantly correlated with geographic distance. (Abstract)

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)

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