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

Abstract

After a brief review of the most recent findings in the study of human evolution, an extensive comparison of the complete genomes of our nearest relative, the chimpanzee (Pan troglodytes), of extant Homo sapiens, archaic Homo neanderthalensis and the Denisova specimen were made. The focus was on non-synonymous mutations, which consequently had an impact on protein levels and these changes were classified according to degree of effect. A total of 10,447 non-synonymous substitutions were found in which the derived allele is fixed or nearly fixed in humans as compared to chimpanzee. Their most frequent location was on chromosome 21. Their presence was then searched in the two archaic genomes. Mutations in 381 genes would imply radical amino acid changes, with a fraction of these related to olfaction and other important physiological processes. Eight new alleles were identified in the Neanderthal and/or Denisova genetic pools. Four others, possibly affecting cognition, occured both in the sapiens and two other archaic genomes. The selective sweep that gave rise to Homo sapiens could, therefore, have initiated before the modern/archaic human divergence.

Comparative genomic analysis of a naturally born serpentized pig reveals putative mutations related to limb and bone development

“…However, the genome sequences of extinct species, if available, will be extremely helpful in the inference of adaptation and function, and this information could even calibrate the phylogeny. For instance, the sequences of extinct Neanderthals ( Homo neanderthalensis ) and Denisova help researchers define the mutations related to cognition that might cause the extinction of the ancient human species [ 29 ]. Intriguingly, the extinction process not only took place in ancient times, it takes place all the time.…”

Triangulating Neanderthal cognition: A tale of not seeing the forest for the trees

“…These physiological insights are complemented by stone tool analyses as well as experimental data evaluating the demands on cognition in tool production and assessing the role of communication in learning, concluding that even pre‐Neanderthal technologies likely necessitated active teaching and involved extensive planning (Lombao et al, 2017; Lycett, von Cramon‐Taubadel, & Eren, 2016; Morgan et al, 2015; Stout, Hecht, Khreisheh, Bradley, & Chaminade, 2015; but see Cataldo, Migliano, & Vinicius, 2018, on how speech alone was also a poor model). Adding to this picture, the modern variant of the FOXP2 gene, which is, among a multitude of other functions (Nudel & Newbury, 2013), linked to a normative development of language, has been shown to be present in both Neanderthals and Denisovans and therefore seems to date back to at least their last common ancestor with the lineage toward anatomically modern humans (Krause et al, 2007; Paixáo‐Côrtez, Vicardi, Salzano, Hunemeier, & Bortolini, 2012; Reich et al, 2010).…”

Conceptual issues in hominin taxonomy: Homo heidelbergensis and an ethnobiological reframing of species

“…The study of modern human variation has been the object of ongoing postcolonial critique ever since Washburn's New Physical Anthropology, but paleoanthropology as a sub‐discipline has not applied this self‐reflection to its use of typological and essentialist language for ancient humans (Wolpoff & Caspari, 2000). “Race” and “species” have long been co‐constituted (e.g., Dobzhansky, 1944) such that regional variation in both living and fossil groups—even minor differences at the molecular or cranio‐dental level—continue to be elevated to separate branches on the evolutionary tree (see Wolpoff, 2019), reflecting the fact that this ideology continues to shape how we name new hominin species (Harvati & Weaver, 2006; Marks, 2019; Paixão‐Côrtes et al, 2012; Reich et al, 2010). So despite the field's streamlining of taxonomic names in general (Cartmill, 2018; Jolly, 2009; Mikels‐Carrasco, 2012; Washburn, 1951; Washburn, 1963) it continues to perpetuate typological practices for hominins (Marks, 2007).…”