scholarly journals Homo sapiens, Homo neanderthalensis and the Denisova specimen: new insights on their evolutionary histories using whole-genome comparisons

2012 ◽  
Vol 35 (4 suppl 1) ◽  
pp. 904-911 ◽  
Author(s):  
Vanessa Rodrigues Paixão-Côrtes ◽  
Lucas Henrique Viscardi ◽  
Francisco Mauro Salzano ◽  
Tábita Hünemeier ◽  
Maria Cátira Bortolini
Author(s):  
Francisco J. Ayala ◽  
Camilo J. Cela-Conde

This chapter deals with the similarities and differences between Homo neanderthalensis and Homo sapiens, by considering genetic, brain, and cognitive evidence. The genetic differentiation emerges from fossil genetic evidence obtained first from mtDNA and later from nuclear DNA. With high throughput whole genome sequencing, sequences have been obtained from the Denisova Cave (Siberia) fossils. Nuclear DNA of a third species (“Denisovans”) has been obtained from the same cave and used to define the phylogenetic relationships among the three species during the Upper Palaeolithic. Archaeological comparisons make it possible to advance a four-mode model of the evolution of symbolism. Neanderthals and modern humans would share a “modern mind” as defined up to Symbolic Mode 3. Whether the Neanderthals reached symbolic Mode 4 remains unsettled.


Author(s):  
Francisco J. Ayala ◽  
Camilo J. Cela-Conde

This chapter analyzes the transition of the hominins from the Middle Pleistocene to the Late Pleistocene. Two alternative models are explored, the “Multiregional Hypothesis” (MH) and the “Replacement Hypothesis,” and how each model evaluates the existing relationships between the taxa Homo neanderthalensis and Homo sapiens. Next is the investigation of the transitional (or “archaic,” if this grade is taken into account) exemplars found in Europe, Africa, and Asia and their evolutionary significance. In particular, the comparison between H. erectus and H. sapiens in China and Java is investigated, as the main foundation of the MH. The chapter ends with the surprising discovery of Homo floresiensis and its description and interpretations concerning its taxonomic and phylogenetic significance. The correlation between brain development and technological progress is at odds with the attribution of perforators, microblades, and fishing hooks to a hominin with a small cranial volume, similar to that of Australopithecus afarensis.


2016 ◽  
Vol 83 (3) ◽  
Author(s):  
Jean F. Challacombe ◽  
Jeannine M. Petersen ◽  
La Verne Gallegos-Graves ◽  
David Hodge ◽  
Segaran Pillai ◽  
...  

ABSTRACT Francisella tularensis is a highly virulent zoonotic pathogen that causes tularemia and, because of weaponization efforts in past world wars, is considered a tier 1 biothreat agent. Detection and surveillance of F. tularensis may be confounded by the presence of uncharacterized, closely related organisms. Through DNA-based diagnostics and environmental surveys, novel clinical and environmental Francisella isolates have been obtained in recent years. Here we present 7 new Francisella genomes and a comparison of their characteristics to each other and to 24 publicly available genomes as well as a comparative analysis of 16S rRNA and sdhA genes from over 90 Francisella strains. Delineation of new species in bacteria is challenging, especially when isolates having very close genomic characteristics exhibit different physiological features—for example, when some are virulent pathogens in humans and animals while others are nonpathogenic or are opportunistic pathogens. Species resolution within Francisella varies with analyses of single genes, multiple gene or protein sets, or whole-genome comparisons of nucleic acid and amino acid sequences. Analyses focusing on single genes (16S rRNA, sdhA), multiple gene sets (virulence genes, lipopolysaccharide [LPS] biosynthesis genes, pathogenicity island), and whole-genome comparisons (nucleotide and protein) gave congruent results, but with different levels of discrimination confidence. We designate four new species within the genus; Francisella opportunistica sp. nov. (MA06-7296), Francisella salina sp. nov. (TX07-7308), Francisella uliginis sp. nov. (TX07-7310), and Francisella frigiditurris sp. nov. (CA97-1460). This study provides a robust comparative framework to discern species and virulence features of newly detected Francisella bacteria. IMPORTANCE DNA-based detection and sequencing methods have identified thousands of new bacteria in the human body and the environment. In most cases, there are no cultured isolates that correspond to these sequences. While DNA-based approaches are highly sensitive, accurately assigning species is difficult without known near relatives for comparison. This ambiguity poses challenges for clinical cases, disease epidemics, and environmental surveillance, for which response times must be short. Many new Francisella isolates have been identified globally. However, their species designations and potential for causing human disease remain ambiguous. Through detailed genome comparisons, we identified features that differentiate F. tularensis from clinical and environmental Francisella isolates and provide a knowledge base for future comparison of Francisella organisms identified in clinical samples or environmental surveys.


Author(s):  
Rainer Kühne

I argue that the evidence of the Out-of-Africa hypothesis and the evidence of multiregional evolution of prehistorical humans can be understood if there has been interbreeding between Homo erectus, Homo neanderthalensis, and Homo sapiens at least during the preceding 700,000 years. These interbreedings require descendants who are capable of reproduction and therefore parents who belong to the same species. I suggest that a number of prehistorical humans who are at present regarded as belonging to different species belong in fact to one single species.  


2006 ◽  
Vol 78 (1) ◽  
pp. 51-64
Author(s):  
John G. F. Wilks

This article explores the implications of personhood from artistic creativity. An investigation of the models of divine creative methods portrayed in Genesis 1 suggests that human creativity is comparable to that employed by God on days 5 and 6, where the waters and the earth are reshaped to produce something new. Consideration of Paleolithic rock art shows just how ancient artistic expression is, and that it is something unique to Homo sapiens, with no evidence that Homo neanderthalensis was artistically creative. The importance of artistic creativity within a community has further implications for our investigation of personhood. Even if the artistic merit of the art produced is far short of great, the desire to express oneself artistically is widespread.


Author(s):  
Jan Zalasiewicz ◽  
Mark Williams

It is just the latest of many climate phases of the Quaternary Period. The 103rd major shift in climate-driven global oxygen isotope values, to be precise, since the official-designated beginning of the Quaternary Period, 2.58 million years ago. And, many of those major phases, as we have seen, include dozens of climate oscillations far greater in scale than humans have witnessed since written records began. Nevertheless, it is our warm phase, that within which our civilization has grown, and hence it has been separated as a distinct epoch, the Holocene, a little over 0.01 of a million years long. Its counterpart is the Pleistocene Epoch, in which reside those other 2.57 million years of Quaternary time, and those other 102 major climate oscillations. Thus, we live—at least as far as formal geological nomenclature goes—in a privileged time. When this epoch began, Homo sapiens had already existed for some 150,000 years. As a species its prospects might not have seemed bright: this creature lacked anything terribly impressive in the way of claws or teeth or thick fur or armour. But by being ingenious at developing what one might describe as artificial claws and teeth—axes and spears and arrows—it could kill and eat mammals considerably larger than itself. In those early days, it might not have prospered, exactly, but it clung to existence, seemingly weathering at least one very bad patch, several tens of thousands of years ago, when its numbers dropped almost to extinction levels. It survived the climate oscillations of the late Pleistocene—the droughts and floods and episodes of bitter cold and killing heat—by adapting its behaviour or migrating as best it could. Its migrations from its place of origin, Africa, were on an epic scale. The many thousands of individual and collective stories of hope, fear, endurance, courage, tragedy, and (less commonly) triumph are all lost. What remains is the evidence that humans, by the beginning of the Holocene, had spread widely over Europe and Asia, ousting (it seems) their kindred hominin species, Homo neanderthalensis and Homo erectus.


Genes ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 197
Author(s):  
Ernesto Borrayo ◽  
Isaias May-Canche ◽  
Omar Paredes ◽  
J. Alejandro Morales ◽  
Rebeca Romo-Vázquez ◽  
...  

Alignment-free k-mer-based algorithms in whole genome sequence comparisons remain an ongoing challenge. Here, we explore the possibility to use Topic Modeling for organism whole-genome comparisons. We analyzed 30 complete genomes from three bacterial families by topic modeling. For this, each genome was considered as a document and 13-mer nucleotide representations as words. Latent Dirichlet allocation was used as the probabilistic modeling of the corpus. We where able to identify the topic distribution among analyzed genomes, which is highly consistent with traditional hierarchical classification. It is possible that topic modeling may be applied to establish relationships between genome’s composition and biological phenomena.


2020 ◽  
Vol 147 ◽  
pp. 102864
Author(s):  
S.E. Bailey ◽  
R. Sorrentino ◽  
G. Mancuso ◽  
J.-J. Hublin ◽  
S. Benazzi

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