Chimpanzee chromosomes how many

Another gene connected with the brain size regulation, ASPM abnormal spindle-like microcephaly associated, MCPH5 , also evolved faster in hominids than in the other primates, having the highest rate of non-synonymous to synonymous substitutions in the human lineage [ 47 ]. Several sexual reproduction genes were also among the most rapidly evolving and positively selected hits [ 44 , 89 ], such as protamine genes PRM1 and PRM2 encoding histone analogs in sperm cells.

Remarkably, human protamines evolve oppositely to histones, whose structures are highly conservative [ 89 ]. Another group of highly diverged genes relates to immunity and cell recognition [ 8 ]. A point mutation in the variable domain of T-cell gamma-receptor TCRGV10 destroyed a donor splice-site, which prevented splicing of the leader intron.

Sialic acids, or N-acetyl neuraminic Neu5Ac and N-glycolyl neuraminic acid Neu5Gc , are common components of the carbohydrate cell surface complexes in mammals. It happened because of the loss of a nucleotide exon corresponding to the sixth ancestral exon, caused by insertion of an AluY element followed by recombination [ 20 , 91 ].

Moreover, the mechanism of sialic acids recognition was also affected in the human lineage. Another major affected group of genes is for the olfactory receptors. Humans and chimpanzees have a comparable number of olfactory receptor genes, around , and of them are orthologous in the two species [ 40 ].

However, in both species about half of them have lost their activities and became pseudogenes. This has led to an assumption that the most recent common ancestor had more active olfactory receptor genes than modern humans and chimpanzees [ 40 ].

Non-coding sequences play crucial roles in gene regulation [ 95 , 96 ]. The genes located near HARs are predominantly related to interaction with DNA, transcriptional regulation and neuronal development [ 48 , 97 ]. It codes for a transcription factor involved in brain development. The 14 HARs NPAS3 are located in non-coding regions and most of them may have regulatory functions, as confirmed by enhancer activities demonstrated in cell culture assay [ 98 ].

At the later gestation period and in adulthood HAR1F is expressed also in the other parts of the brain. This expression pattern is conserved in all higher primates, but human-specific nucleotide alterations affected the secondary structure of this RNA [ 48 , 99 ]. After human and chimpanzee ancestral divergence, their orthologous loci accumulated 10 and 6 nucleotide substitutions, respectively. FZD8 encodes a receptor protein in the WNT signaling pathway, which is involved in the regulation of brain development and size.

In transgenic mice with Fzd8 under control of either human or chimpanzee enhancer, both demonstrated their activities in the developing neocortex, but the human enhancer became active at the earlier stages of development and its effect was more pronounced. Embryos with the human HARE5, therefore, showed a marked acceleration of neural progenitor cell cycle and increased brain size [ 51 ].

There is also a particular fraction of non-coding sequences that was accelerated in humans but relatively conserved in the other species called HACNs human accelerated conserved noncoding sequences [ 49 ]. They can overlap with the abovementioned HARs [ 50 ]. HACNs are enriched near genes related to neuronal functioning, such as neuronal cell adhesion [ 49 ] and brain development [ ]. Based on structural analyses of HACNs, HARs and their genomic contexts, around one third of them was predicted to be developmental enhancers [ 50 ].

By functional role, they contribute in approximately equal proportions to brain and limb development and to a lesser extent - to heart development. Among 29 pairs of HARs and their chimpanzee orthologous regions tested in mouse embryos, 24 showed enhancer activity in vivo. Moreover, five of them demonstrated differential enhancer activities between human and chimpanzee sequences [ 50 ]. In another study, all human enhancers predicted by the FANTOM project [ ] were aligned with the primate genomes in order to obtain human-specific fraction [ 52 ].

Notably, the fastest evolving human enhancers predominantly regulated genes activated in neurons and neuronal stem cells. Totally, about human-specific neuronal enhancers were identified, and one of them located on the 8q It was assumed by the authors that recent human-specific enhancers, adaptive, on the one hand, may also impact age-related diseases [ 52 ]. It has been postulated few decades ago that differences between humans and chimpanzees are mostly caused by gene regulation changes rather than by alterations in their protein-coding sequences, and that these changes must affect embryo development [ 6 ].

For example, evolutional acquisitions such as enlarged brain or modified arm emerged as a result of developmental changes during embryogenesis [ , ]. Such changes include when, where and how genes are expressed.

A plethora of genes involved in embryogenesis have pleiotropic effects [ ] and mutations within their coding sequence may cause complex, mostly negative, consequences for an organism. On the other hand, changes in gene regulation could be limited to a certain tissue or time frame that can enable fine tuning of a gene activity [ ]. Indeed, the fast-evolving sequences HARs or HACNs are often found close to the genes active during embryo- and neurogenesis [ 48 , 49 , 50 , ].

For example, HACNS1 HAR2 demonstrates greater enhancer activity in limb buds of transgenic mice compared to orthologous sequences from chimpanzee or rhesus macaque [ ]. Many studies were focused on finding differences between humans, chimpanzees and other mammals at the level of gene transcription [ , , ]. Importantly, tissue-specific differences within the same species significantly exceeded in amplitude all species-specific differences in any tissue.

The most transcriptionally divergent organs between humans and chimpanzees were liver and testis, and to a lesser extent — kidney and heart [ , ]. A transcriptional distinction of liver may be a consequence of different nutritional adaptations in the two species. The major differences in testes are largely unexplained but may be related to predominantly monogamous behavior in humans.

Surprisingly, the brain was the least divergent organ between humans and chimpanzees at the transcriptional level.

In this regard, it is suggested that tighter regulation of signaling pathways in the brain underlies behavioral and cognitive differences [ , ]. However, it was found that during evolution in the human cerebral cortex there were more transcriptional changes than in the chimpanzee [ ]. Among them, the prevailed difference was increased transcriptional activity [ , ].

Another study of transcriptional activity in the forebrain evidenced the higher difference between human and chimpanzee in the frontal lobe [ ]. The functions of frontal lobe-specific groups of co-expressed genes dealt mostly with neurogenesis and cell adhesion [ ]. Furthermore, the analysis of genes associated with communication showed that about a quarter of them was differentially expressed in the brains of humans and other primates [ ]. Remarkably, the KRAB-ZNF gene family is known for its rapid evolution in primates, especially for its human- or chimpanzee-specific members [ ].

The studies of transcriptional timing in the postnatal brain development also revealed a number of human-specific features. A specific set of genes was found whose expression was delayed in humans compared to the other primates. It is congruent with the prolonged brain development period in humans relative to other primates [ , ].

The results recently published by Pollen and colleagues allowed to look deeper into the developing human and chimpanzee brains by applying the organoid model [ ].

Cerebral organoids were generated from induced pluripotent stem cells iPSCs of humans and chimpanzees. Transcriptome analyses revealed genes deferentially expressed in human versus chimpanzee cerebral organoids and macaque cortex. Epigenetic regulation is another factor that should be considered when looking at interspecies differences in gene expression.

High throughput analysis of differentially methylated DNA in human and chimpanzee brains showed that human promoters had lower degree of methylation. The analysis of H3K4me3 trimethylated histone H3 is a marker of transcriptionally active chromatin distribution in the neurons of prefrontal lobe revealed human-specific regions, 33 of them were neuron-specific. Another active chromatin biomarker is the distribution of DNase I hypersensitivity sites DHSs , that often indicate gene regulatory elements.

Using chromatin immunoprecipitation assay, a number of haDHSs interacting genes were identified, many of which were connected with early development and neurogenesis [ 3 , ]. In a later study [ ], about 3,5 thousand haDHSs were found, that were enriched near the genes related to neuronal functioning [ ]. It is now generally accepted that both changes in gene regulation and alterations of protein coding sequences might have played a major role in shaping the phenotypic differences between humans and chimpanzees.

In this context, complex bioinformatic approaches combining various OMICS data analyses, are becoming the key for finding genetic elements that contributed to human evolution. It is also extremely important to have relevant experimental models to validate the candidate species-specific genomic alterations.

However, at least for now using these experimental approaches for millions of species specific potentially impactful features reviewed here is impossible due to high costs and labor intensity. In turn, an alternative approach could be combining the refined data in a realistic model of human-specific development using a new generation systems biology approach trained on a functional genomic Big Data of humans and other primates.

Such an approach could integrate knowledge of protein-protein interactions, biochemical pathways, spatio-temporal epigenetic, transcriptomic and proteomic patterns as well as high throughput simulation of functional changes caused by altered protein structures. The differences revealed could be also analyzed in the context of mammalian and primate-specific evolutionary trends, e.

Apart from the single-gene level of data analysis, this information could be aggregated to look at the whole organismic, developmental or intracellular processes e. And finally, most of the results described here were obtained for the human and chimpanzee reference genomes, which were built each using DNAs of several individuals.

Nowadays the greater availability of whole-genome sequencing highlighted the next challenge in human and chimpanzee comparison — populational genome diversity. For example, the recent study [ ] of native African genomes was focused on the fraction of sequences absent from the reference Hg38 genome assembly. Furthermore, it also reflects the high degree of genome heterogeneity of the African population [ ]. Similar studies were performed for other populations as well.

The chimpanzees also demonstrate substantial genome diversity with many population-specific traits: the central chimpanzees retain the highest diversity in the chimpanzee lineage, whereas the other subspecies show multiple signs of population bottlenecks [ ]. So far there were not so many studies published on the topic of non-reference human and chimpanzee genome comparison. However, some estimates can be made. As expected, NSs were enriched in simple repeats and satellites and varied greatly among the individuals.

The most part of NSs 32, aligned confidently to the non-reference sequences from the aforementioned study of African genomes [ ].

Finally, as many as 18, NSs were present also in the chimpanzee PT4 genome assembly. Positioning of NS insertions in the human genome revealed that of them located within genes, where 85 NS insertion events were found within the exons of 82 genes [ ].

Another research consortium studied non-repetitive non-reference sequences NRNR in the genomes of 15, Icelanders [ ]. Thus, the lack of information on genome populational diversity could impact the total extent of human and chimpanzee interspecies divergence by misinterpretation of polymorphic sequences. Still, these findings inevitably lead to the idea of the need, firstly, to create, and secondly, to compare human and chimpanzee pan-genomes.

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Mamedov I, et al. If you come to these facts cold, you might think this represented an existential crisis for evolutionary biologists. If we do indeed descend from a common ancestor with great apes, then our ancestors must have lost a pair after our lineage branched off, some six million years ago.

How on Earth could we just give up an entire chromosome. We just combined a couple of them. Every now and then, chromosomes fuse. This fusion occurs as sperm and eggs develop, as pairs of chromosomes fold over each other and swap chunks of DNA.

Sometimes two different chromosomes grab onto each other and then fail to separate. Scientists have observed both humans and mammals with fused chromosomes. Chromosomes typically have distinctive stretches of DNA in their center and at their ends. This might seem like a fantastic mutation—something like a human and a horse being joined into a centaur.

Remarkably, however, fused chromosomes are real, and there are surprising number of normal, healthy people carrying them. If humans and apes did indeed share a common ancestor, then it would make sense that two chromosomes fused in our ancestors.

The rise of genome sequencing allowed them to test that hypothesis. They found that human chromosome two bears the hallmarks of an ancient chromosome fusion , with remnants of chromosome ends nestled at its core.

In , it became possible to test the hypothesis again, when a team of scientists sequenced the chimpanzee genome and could compare it to the human genome. The chimp genome team were able to match human chromosome two to two unfused chromosomes in the chimpanzee genome.

Ken Miller, a biologist at Brown who was an expert witness in the Dover creationism trial , includes this research in his lectures on evolution. What makes evolutionary biology such a fun subject to write about is that it does not stay still. Last month, Evan Eichler at the University of Washington and his colleagues published a study in the journal Genome Research in which they deeper into the history of our missing chromosome.

They were able to do so thanks to the publication earlier this year of the gorilla genome. A comparison of the human, chimpanzee, and gorilla genomes confirms that the ancestors of gorillas branched off from the ancestors of chimpanzees and humans about ten million years ago.

Humans and chimpanzees then branched apart later. By comparing human chromosome two to the unfused versions in the chimpanzees and gorillas, Eichler and his colleagues reconstructed the chromosomes in the common ancestor of all three species:. The bands correspond to segments of each chromosome. The hash marks represent regions of very unstable DNA. These areas, which are full of repeating sequences, are prone to accidentally getting duplicated, expanding the chromosome. It had picked up part of the green chromosome earlier than the common ancestor of us, chimpanzees, and gorillas.

Three key events are illustrated here. First, the top of the green chromosome flipped another common type of mutation, called an inversion.

Then a chunk of yet another chromosome got stuck to the end of the green chromosome, marked here in pink. And then a new piece of DNA got stuck at the end of the green chromosome, known as StSat, and marked here as a yellow dot. The ancestors of gorillas then diverged from the ancestors of chimpanzees and humans.

They underwent some ten million years of independent evolution, during which time a lot happened. For one thing, the cap on the green chromosome got duplicated and pasted onto other chromosomes, including the red one, and even on the other end of the green one itself.

Based on fossil evidence and comparative anatomy, Charles Darwin proposed that humans and great apes—which include chimpanzees, gorillas, and orangutans—share a common ancestor that lived several million years ago. More recent research has propped up Darwin's theory of common descent also called common ancestry : genome analysis reveals the genetic difference between humans and chimps to be less than 2 percent. In other words, humans and chimps have DNA sequences that are greater than 98 percent similar.

While the genetic similarity between human and ape strengthened Darwin's theory, a significant, unexplained discrepancy remained. While great apes all have 48 chromosomes 24 pairs , humans have only 46 23 pairs. If humans and apes shared a common ancestor, shouldn't both have the same number of chromosomes in their cells? The phases through which chromosomes replicate, divide, shuffle, and recombine are imperfect, as DNA is subject to random mutations.

Mutations do not always produce harmful outcomes. In fact, many mutations are thought to be neutral, and some even give rise to beneficial traits. To corroborate Darwin's theory, scientists would need to find a valid explanation for why a chromosome pair is missing in humans that is present in apes. A fundamental part of the process by which science is done involves developing a testable prediction, also known as a hypothesis.