Neanderthal - Wikipedia
Despite this difference, Neanderthals and modern humans looked very similar as: What was the relationship between Neanderthals and anatomically modern Homo sapiens? Did Neanderthals and anatomically modern humans interbreed?. anatomically modern humans, who began to migrate out of Africa some 60, years ago. Lately, the relationship between Neanderthals and. The evidence we have of Neanderthal-modern human interbreeding sheds light in which anatomically modern humans replaced archaic hominins, like Neanderthals, However, even with some interbreeding between modern humans and.
Anatomically modern humans then, arrived in Eurasia much later than their evolutionary cousins.
Nevertheless, the two species lived alongside each other for several thousands of years, with the Neanderthals finally going extinct sometime between 40, and 30, years ago. Appearance Although similar in many ways, there are clear physical differences distinguishing Neanderthals and modern humans. Neanderthals were significantly shorter and stockier than modern humans, with much broader rib cages and pelvises.
To give some perspective, the average height for a man in the USA is 1. Conversely, based on the fossil records available, the average height for a Neanderthal was just 1. A study published late last year suggested that some of these anatomical differences could be the result of the Neanderthals being forced to adopt a much more high protein diet than modern humans.
Intelligence and Behaviour One of the hottest topics in scientific research right now involves determining just how intelligent Neanderthals were. For years, the prevailing view was that Neanderthals were primitive, poorly developed brutes when compared to modern humans, only capable of expressing themselves in grunts and groans. Discoveries in the last few years have really brought this assumption into question.
This is widely considered a signifier of cultural development. If true, any of these discoveries would point to Neanderthals being for more advanced than their typical depiction in popular culture would suggest.
The physical differences between Neanderthals and humans are quiet clear, especially in terms of anatomy. This article has been cited by other articles in PMC.
Abstract Many other human species appeared in evolution in the last 6 million years that have not been able to survive to modern times and are broadly known as archaic humans, as opposed to the extant modern humans. It has always been considered fascinating to compare the modern human genome with that of archaic humans to identify modern human-specific sequence variants and figure out those that made modern humans different from their predecessors or cousin species.
Neanderthals are the latest humans to become extinct, and many factors made them the best representatives of archaic humans. Even though a number of comparisons have been made sporadically between Neanderthals and modern humans, mostly following a candidate gene approach, the major breakthrough took place with the sequencing of the Neanderthal genome. The initial genome-wide comparison, based on the first draft of the Neanderthal genome, has generated some interesting inferences regarding variations in functional elements that are not shared by the two species and the debated admixture question.
However, there are certain other genetic elements that were not included or included at a smaller scale in those studies, and they should be compared comprehensively to better understand the molecular make-up of modern humans and their phenotypic characteristics. Besides briefly discussing the important outcomes of the comparative analyses made so far between modern humans and Neanderthals, we propose that future comparative studies may include retrotransposons, pseudogenes, and conserved non-coding regions, all of which might have played significant roles during the evolution of modern humans.
Fossils suggest that modern humans first emerged in East Africa and spread fairly quickly all over the world in the nextyears or so reviewed in Lu et al. After the divergence of humans and chimps, the major landmark in human history is the emergence of bipedals about 4 million years ago myawhich enabled them to use their two feet as hands. Many species evolved afterwards until the evolution of Homo erectus, who, for the first time, migrated out of Southern Africa and initiated the spread of humans all around the globe.
The migrated population of Homo erectus in East Africa eventually gave rise to modern humans aboutya and to Homo neanderthalensis, or Neanderthals, aboutya [ 34 ]. Neanderthals survived until 28, ya, while modern humans are still surviving [ 5 ].
During the latter part of their existence, Neanderthals lived in Europe, as well as in Western Asia and the Middle East [ 67 ].
Ancient DNA and Neanderthals | The Smithsonian Institution's Human Origins Program
Various lines of evidence suggest that modern humans started to migrate from East Africa to Europe and other parts of the worldya, and the fossil evidence of humans and Neanderthals indicated that these species might have come into contact as early as 80, ya and co-habited for up to 10, years at certain geographic locations [ 6 ]. In the field of evolutionary biology, one of the most sought after questions has been what made modern humans superior than other related species-i.
The whole-genome sequencing of chimps, rhesus macaque, and other primates has given considerable boosts in this field, as the sequences of these primates opened up the possibility to conduct comprehensive comparative studies to the single-nucleotide level [ 89 ]. Many attempts have been taken to identify the genetic reasons why modern humans developed such complex biological features than other primates, including the larger brain-to-body ratio, bipedalism, morphological changes, and significant development of communication skills and cognitive behavior.
Recent studies have used various statistical methods to compare the sequence of these primates with humans in an attempt to find human-specific genes and gene regulatory sequences, eventually showing unexpectedly rapid evolution in the human lineage after the divergence from the ancestral primates [ 10 - 15 ]. The results from these analyses exhibit a good overview of the human-specific genomic elements, but these results are unable to distinguish which of these human-specific elements are specific to modern humans only.
Since there has been no complete genome sequence of any archaic humans until recently, such sequence comparisons have been made only between the modern human genome and other primates, bypassing archaic humans, resulting in an overwhelming number of differences and the inability to identify which sequences changes are unique to modern humans and which are shared by all Homo species.
In order to identify such sequence changes, the modern human genome sequence must be compared with that of archaic humans. Neanderthals have always been a desired target for this purpose for multiple reasons. They are the closest cousins of modern humans, both anatomically and based on intelligence. Their slightly larger brain and wider body structure are the primary anatomical differences from the modern humans [ 16 ].
Fossil evidence suggests that Neanderthals used stone tools, they were hunter gatherers, and they had a social life, indicating that they had similar intelligence as modern humans until about 50, ya, when a "Creative explosion" occurred in modern humans [ 1718 ].
Another critical reason to target Neanderthals is that they are the latest archaic humans to go extinct, and their remains have been found in sufficiently good condition for analyzing down to the molecular level [ 19 - 21 ]. To make a comprehensive genomic comparison between modern and archaic humans, the whole genome of archaic humans has to be sequenced. The availability and widespread use of massively parallel high-throughput sequencing have now made it possible to sequence archaic genomes, which seemed impossible even a decade ago.
The idea of sequencing an ancient genome was first implemented on cave bear [ 22 ] and, after its success, the mammoth genome [ 23 ]. The initial sequencing attempts on Neanderthals included sequencing of the mitochondrial genome, which was successful to a certain extent [ 24 - 26 ]. These successes eventually led paleogeneticists to attempt sequencing Neanderthal nuclear genomes.
Almost all of the attempts have been made by amplifying the genome fragments via PCR and parallel sequencing, while some involve the use of a metagenomic approach. The early success of such attempts eventually led to the establishment of the Neanderthal Genome Project inwhich first announced the complete genome sequence of Neanderthals in [ 27 ] and recently released a cleaner and higher-coverage version http: Comprehensive comparisons have been made by the group on certain genetic entities with some very interesting inferences, based on the initial low-coverage sequencing data, but improvements in many aspects can be made by utilizing the recent, better version of the sequence and considering more types of genetic variances in the study.
Here, we will discuss the inferences made from the comparison and what can be done next to answer some interesting questions regarding the evolution of modern humans. Why Whole Genome Sequence of Neanderthals?
Many lines of archaeological evidence indicate that humans and Neanderthals may have coexisted in certain geographic locations. This gives rise to the most debatable question regarding the recent history of humans: If they did, was it to an extent where meaningful exchange of genetic information may have occurred? Do we still carry any genetic elements of Neanderthals?
Comparing the genome sequences is probably the best way to answer all these questions. All other features, including the level of intelligence in Neanderthals, have been speculated from bones, settlements, or artifacts found, and there is no way to be certain about the practicality or validity of the inferences made from these remains. The hypothesis that Neanderthals were able to practice complex behavior has already been disputed [ 28 - 30 ].
There has also been a significant amount of debate about the admixture of humans and Neanderthals. Morphological analyses have provided strong arguments both for and against the genetic exchange between these two species [ 3132 ], as have the comparative analyses of DNA sequences of these species [ 33 - 35 ].
The genome sequence itself can not validate many of these inferences, either, but it can answer the question of admixture and articulate the genetic elements that are unique to Neanderthals or to humans or those that are shared by both.
Studies on the expression or protein functions in association with these unique elements, despite being plausible only for those found in the human genome, can eventually facilitate analysis of complex biological phenomena, such as reasoning, language, or other qualitative or behavioral traits, at the molecular level. In the past, a candidate gene approach has been successfully implemented to identify the presence or variance of certain genes that were believed to be modern human-specific.
Using this approach, a number of speculations about Neanderthals could be made, including their skin and hair color. It was also discovered that Neanderthals had the same FOXP2 gene as modern humans, which was previously linked to language ability [ 36 ].
This approach of fishing for particular genes proved efficient, but there is a lot more than known genes in the whole genome that may play a critical regulatory role in gene expression and thus development. For instance, almost half of the human genome consists of transposable elements; these elements can affect gene expression by activating or deactivation functional genetic elements and by altering the protein coding by creating alternative splicing or creating new chimeric genes [ 37 - 39 ], reviewed in [ 4041 ].
Transposable elements are also polymorphic among different populations of modern humans, and their association with phenotypic traits, including diseases, has been extensively studied, albeit with a lot more to be learned [ 42 - 44 ]. The whole-genome sequence is necessary for identifying transposable element insertions that may have taken place only in modern humans and subsequently assessing their functional impact.
Comparative analysis The only part of the Neanderthal genome that was sequenced completely from multiple specimens until recently was the mitochondrial DNA mtDNA. The major analysis that was made with the mtDNA sequence was to seek an answer to the question of interbreeding. The Neanderthal mtDNA sequence consistently falls outside the spectrum of variations observed in the modern human mtDNA sequence, indicating no interbreeding between the species [ 24 - 264546 ]. Previously, besides detecting specific mutations in MCPH1 and FOXP2, the candidate gene approach also detected the presence of fragments of the MC1R gene that may indicate the red hair and pale skin of Neanderthals [ 47 ], segments of the ABO blood group locus [ 48 ], and a taste receptor gene [ 49 ].
Despite many critical technical challenges in sequencing ancient genomes [ 26 ]; reviewed in [ 50 ]the whole genome of Neanderthals has been sequenced recently by Green et al.
Substitutions and indels Green et al. The vast majority of these occurred before Neanderthals and modern humans diverged. However, 78 non-synonymous nucleotide substitutions that are fixed for a derived state in modern humans are different in the Neanderthal counterpart, as Neanderthals carry the ancestral state of these polymorphic nucleotides.
Only five genes were identified that have more than one fixed substitution in their coding regions, and one of them has an altered start or stop codon. This might be indicative of a change in selection of skin physiology in the modern human lineage.
When looking into differences in regulatory elements, a total of substitutions and 36 indels were identified in the untranslated regions. One microRNA of unknown function, hsa-mir, which was identified by parallel sequencing of human embryonic stem cells [ 51 ], was found to have one fixed substitution and one single nucleotide insertion.
Since the substitution occurs in the seed region, it is not unlikely that this microRNA has different targets between these two species. Selective sweeps in modern humans There are positively selected regions identified in modern humans that occurred early during the history in conjunction with or shortly after their divergence from Neanderthals.
This change may have affected the energy metabolism of early modern humans. A number of other genes that lie on these selectively swept regions have been associated with other genetic disorders, such as autism, schizophrenia, and Down syndrome. Since both autism and schizophrenia are related to cognitive development, it could be assumed that multiple genes involved in cognitive development in humans were positively selected early in the history of modern humans.
Admixture Even though previous studies with Neanderthal mtDNA [ 2633 ] and initial sequencing of nuclear DNA showed no evidence of interbreeding between Neanderthals and humans [ 2153 ], the most striking revelation after the comparative analyses between the whole-genome sequence of Neanderthals and multiple modern human individual genomic sequences was the demonstration of admixture between these two species.
Surprisingly, the Neanderthal genome appeared more similar to all non-African genomes than to African ones. They share significantly more derived alleles alleles that are different from in chimp with non-African populations than with the African, and when compared with European and Asian individual genomes, Neanderthals are found equally close to both populations.
This and some other analyses made by the group only indicate an exchange of DNA between Neanderthals and the non-African population. With further comparative analysis, the same group also identified that gene flow occurred unidirectionally from Neanderthals to the modern non-African human population. A couple of other findings from different experiments, along with a genome-wide comparison, provide strong evidence for exchange of genetic information.
H1 is abundant in almost all populations of modern humans, while H2 is found only among Europeans and found to have entered into the Homo lineage approximately only 10, to 30, ya. However, a comparison between H1 and H2 in chimp suggests that the common founder of H1 and H2 is far older than 30, years. Even though the Neanderthal genome sequence has been found to carry the H1 haplotype, coinhabitation of the H2 chromosome carriers during the time period when modern humans coexisted with archaic humans can not be ruled out because of the scarcity of archaic genome data.
Thus, one can still argue that the H2 haplotype found in modern humans could possibly be a result of horizontal gene transfer between modern humans and Neanderthals and remained in modern humans under selective pressure, possibly because the H1 haplotype has a role in neurodegenerative diseases [ 54 ]. In a similar scenario, haplotype D of the microcephalin gene is found to have originated 1.
It has thus been speculated that this haplotype was horizontally transferred into modern humans from archaic humans, most likely Neanderthals [ 34 ]. However, in a more recent study, the microcephalin locus from a Neanderthal individual in Italy was sequenced and found to be homozygous for the ancestral non-D haplotype [ 55 ].
The whole-genome study by Green et al. One striking revelation from the whole-genome comparison by Green et al.
Neanderthals and Humans – What Are the Differences?
The group explained this anomaly by arguing that the interbreeding between the species occurred earlier than previously expected, before the divergence of Europeans, East Asians, and Papuans. Archaeological evidence suggests that modern humans appeared in the Middle East beforeya, where Neanderthals were already present, and probably remained until 50, ya [ 56 ]; this makes the prediction by Green et al. Future Directions Increasing coverage, sequencing more Neanderthals, and the Y chromosome For a more comprehensive comparison of whole-genome sequences between Neanderthals and modern humans, the sequence coverage of Neanderthals has to be increased.
The three approaches made so far to sequence the Neanderthal genome have resulted in the sequencing of only 65, bases [ 21 ], 1 million bases [ 19 ], and finally, the draft genome sequenced recently [ 27 ], consisting of only two-thirds of the whole genome with a mere 1. With such low coverage, it is hard to form meaningful contigs, and a number of important genetic entities will remain unnoticed.
Even though it was beyond imagination to sequence a Pleistocene specimen a decade ago, the progress that has been made in the last 5 years is good enough to expect that more such specimens be sequenced in coming years. The more specimens from various geographic locations that are sequenced, the more likely it will be to construct a reference genome sequence for Neanderthals.
As the human genome sequence varies considerably among different populations, it is expected that Neanderthals also have variation in their genomic sequences among different populations from different locations. Such variations can only be identified by sequencing a wide range of specimens, and these variations may again change insights into the Neanderthal-modern human relationship.
The sequencing of Neanderthals first started with its mitochondrial DNA in [ 25 ]. Comparisons between Neanderthal and modern human mitochondrial DNA have been made extensively, but these comparisons only reveal the maternally inherited difference between the species, as mitochondria DNA is transmitted maternally.
The complete genomic sequence of Neanderthals published recently is also from a female specimen. Thus, the Y-chromosome of Neanderthals or paternal inheritance has yet to be examined.
Comparisons of the Y chromosome sequence of Neanderthals with currently established Y-haplogroups for modern humans should provide some insights into the admixture hypothesis.
With respect to the recent finding of admixture of Neanderthals with non-African populations, the Neanderthal Y chromosome should not match the Y haplogroups A or B, as these haplogroups are the oldest of the clades and almost restricted to Africans and their descendants [ 5758 ].
Retrotransposon insertion polymorphism Almost half of the human genome comprises retrotransposons. Although they were overlooked for a significant period of time in our genetic study, their importance in chromosome structure, gene regulation, and disease predisposition has now been well established.
Retroelements are widely divided into two categories-one with long terminal repeats LTRs and another without the LTRs. Among all Alus found in the entire human genome, only about 0.
This 'young' group of Alus is composed of only about 5, Alu elements that are believed to have integrated in the human genome after the divergence of humans and great apes [ 64 - 68 ]. Studying the retrotransposon insertion loci in Neanderthals will identify truly modern human-specific retrotransposon insertion polymorphisms.
A similar comparative analysis would reveal other transposable elements, such as L1, SVAs, and HERVs, that are specific to modern humans only, as well as those that are specific to Neanderthals. Retroelements are particularly important in population genetics. It is extremely rare that a newly inserted transposable element is completely excised; thus, they act as a genetic fossil that is homoplasy-free.
This identical-by-descent nature of retroelements makes them better markers for population and evolutionary studies than SNPs, in the sense that SNPs can, though rarely, be mutated back to the previous state. SNPs are also very hard to detect while handling ancient genomes due to transformation and deamination [ 69 ], while retrotransposon insertion polymorphisms RIPs refer to the presence or absence of a retrotransposon. Once a retrotransposon is inserted at a new location in an individual, it is subject to genetic drift.
Over a short period, it starts spreading in to the population. Depending on when a retroelement has integrated at a certain locus, it will be shared by different species or, if recently enough, by different populations of the same species. Thus, RIPs occurring before the divergence of chimps and humans are shared by humans and chimps, but those occurring after are present only in humans. RIPs that are even more recent are specific to certain human populations only [ 7071 ].