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Emerging evidence links genes within human-specific segmental duplications (HSDs) to traits and diseases unique to our species. Strikingly, despite being nearly identical by sequence (>98.5%), paralogous HSD genes are differentially expressed across human cell and tissue types, though the underlying mechanisms have not been examined. We compared cross-tissue mRNA levels of 75 HSD genes from 30 families between humans and chimpanzees and found expression patterns consistent with relaxed selection on or neofunctionalization of derived paralogs. In general, ancestral paralogs exhibited greatest expression conservation with chimpanzee orthologs, though exceptions suggest certain derived paralogs may retain or supplant ancestral functions. Concordantly, analysis of long-read isoform sequencing data sets from diverse human tissues and cell lines found that about half of derived paralogs exhibited globally lower expression. To understand mechanisms underlying these differences, we leveraged data from human lymphoblastoid cell lines (LCLs) and found no relationship between paralogous expression divergence and post-transcriptional regulation, sequence divergence, or copy-number variation. Considering cis-regulation, we reanalyzed ENCODE data and recovered hundreds of previously unidentified candidate CREs in HSDs. We also generated large-insert ChIP-sequencing data for active chromatin features in an LCL to better distinguish paralogous regions. Some duplicated CREs were sufficient to drive differential reporter activity, suggesting they may contribute to divergent cis-regulation of paralogous genes. This work provides evidence that cis-regulatory divergence contributes to novel expression patterns of recent gene duplicates in humans.

This review comes from a themed issue on Genetics of human origin. Edited by Sarah Tishkoff and Joshua Akey. https://doi.org/10.1016/j.gde.2020.06.006, The study of primate comparative genomics has long been a focus of research, particularly in the context of understanding human evolutionary history. Recently, high-throughput methods have become accessible that allow us to tackle these questions at scale by comparing genomes within and between species, or looking at gene regulatory and expression changes between species and tissues. This burst in large-scale genomic studies has drastically increased the resolution at which we are now able to understand the evolutionary forces acting upon our own species. Furthermore, the drop in sequencing costs has made it possible to go beyond generating datasets that focus purely on human biology, and to begin incorporating larger genomic studies of non-human primates. Here, we give an overview of recent advances in large-scale high-throughput studies across the whole primate radiation., L.F.K.K is supported by an FPI fellowship associated to BFU2014-55090-P (MINECO/FEDER, UE) and by an EMBO short-term fellowship STF-8286. P.E.-C. is supported by a Formació de Personal Investigador fellowship from Generalitat de Catalunya and European Social Fund (FI_B00122). T.M.-B. is supported by funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 864203), BFU2017-86471-P (MINECO/FEDER, UE), Howard Hughes International Early Career, Obra Social “La Caixa” and Secretaria d’Universitats i Recerca and CERCA Programme del Departament d’Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 880).

Germline mutations are the source of all heritable variation. In the past few years, whole genome sequencing has allowed direct and comprehensive surveys of mutation patterns in humans and other species. These studies have documented substantial variation in both mutation rates and spectra across primates, the causes of which remain unclear. Here, we review what is currently known about mutation rates in primates, highlight the factors proposed to explain the variation across species, and discuss some implications of these findings on our understanding of the chronology of primate evolution and the process of mutagenesis.

Many primate genes produce non-coding circular RNAs (circRNAs). However, the extent of circRNA conservation between closely related species remains unclear. By comparing tissue-specific transcriptomes across over 70 million years of primate evolution, we identify that within 3 million years circRNA expression profiles diverged such that they are more related to species identity than organ type. However, our analysis also revealed a subset of circRNAs with conserved neural expression across tens of millions of years of evolution. These circRNAs are defined by an extended downstream intron that has shown dramatic lengthening during evolution due to the insertion of novel retrotransposons. Our work provides comparative analyses of the mechanisms promoting circRNAs to generate increased transcriptomic complexity in primates.

Genes encoding glycosyltransferases can be under relatively high selection pressure, likely due to the involvement of the glycans synthesized in host-microbe interactions. Here, we used mice as an experimental model system to investigate whether loss of α−1,3-galactosyltransferase gene (GGTA1) function and Galα1-3Galβ1-4GlcNAcβ1-R (αGal) glycan expression affects host-microbiota interactions, as might have occurred during primate evolution. We found that Ggta1 deletion shaped the composition of the gut microbiota. This occurred via an immunoglobulin (Ig)-dependent mechanism, associated with targeting of αGal-expressing bacteria by IgA. Systemic infection with an Ig-shaped microbiota inoculum elicited a less severe form of sepsis compared to infection with non-Ig-shaped microbiota. This suggests that in the absence of host αGal, antibodies can shape the microbiota towards lower pathogenicity. Given the fitness cost imposed by bacterial sepsis, we infer that the observed reduction in microbiota pathogenicity upon Ggta1 deletion in mice may have contributed to increase the frequency of GGTA1 loss-of-function mutations in ancestral primates that gave rise to humans.

Taste perception plays an essential role in food selection. Umami (savory) tastes are sensed by a taste receptor complex, T1R1/T1R3, that detects proteinogenic amino acids. High sensitivity to l-glutamate (l-Glu) is a characteristic of human T1R1/T1R3, but the T1R1/T1R3 of other vertebrates does not consistently show this l-Glu response. Here, we demonstrate that the l-Glu sensitivity of T1R1/T1R3 is a derived state that has evolved repeatedly in large primates that rely on leaves as protein sources, after their divergence from insectivorous ancestors. Receptor expression experiments show that common amino acid substitutions at ligand binding sites that render T1R1/T1R3 sensitive to l-Glu occur independently at least three times in primate evolution. Meanwhile T1R1/T1R3 senses 5′-ribonucleotides as opposed to l-Glu in several mammalian species, including insectivorous primates. Our chemical analysis reveal that l-Glu is one of the major free amino acids in primate diets and that insects, but not leaves, contain large amounts of free 5′-ribonucleotides. Altering the ligand-binding preference of T1R1/T1R3 from 5′-ribonucleotides to l-Glu might promote leaf consumption, overcoming bitter and aversive tastes. Altogether, our results provide insight into the foraging ecology of a diverse mammalian radiation and help reveal how evolution of sensory genes facilitates invasion of new ecological niches., 霊長類におけるグルタミン酸の旨味の起源 --体の大きな霊長類は旨味感覚で葉の苦さを克服--. 京都大学プレスリリース. 2021-08-30.

Development and speciation are directed by changes in gene expression programs, which are in turn controlled by regulatory elements such as enhancers, that act in a cell-type and temporal-specific manner. Recent whole genome sequencing of different primate species has identified genomic alterations that could account for the phenotypic differences between humans and other primate species. Moreover, as most of this variation resides in the non-coding part of the genome, they potentially affect the activity of these enhancer elements. Here, we charted active regulatory elements in the common marmoset and analyzed the regulatory rewiring that occurred during primate evolution. Comparison with other primates showed that a set of regulatory elements emerged upon the split of the great apes from the rest of the primate lineage. These elements emerged preferentially in oligodendrocytes and were found to be more often deregulated in autism spectrum disorder. This hints towards a link between oligodendrocytes, the evolution of a more complex brain and increased susceptibility to neurological disorders. Focusing more closely on evolutionary novel enhancers, we showed that these are mostly variable between individuals. They more often reside in inactive genomic compartments and seem to be devoid of functional contacts with other regulatory elements suggesting a lack of function. Instead, analysis of trait associated nucleotide variants showed that these are more often located in evolutionary conserved enhancers, providing valuable information on which variations can be modelled in non-human primates. Together these findings contribute to the understanding on the role of regulatory elements in evolution and disease.

International audience; Diet plays an incontrovertible role in primate evolution, affecting anatomy, growth and development, behavior, and social structure. It should come as no surprise that a myriad of methods for reconstructing diet have developed, mostly utilizing the element that is not only most common in the fossil record but also most pertinent to diet: teeth. Twenty years ago, the union of traditional, anatomical analyses with emerging scanning and imaging technologies led to the development of a new method for quantifying tooth shape and reconstructing the diets of extinct primates. This method became known as dental topography.

The neocortex, the seat of higher cognitive functions, exhibits a key feature across mammalian species-a highly variable degree of folding. Within the neocortex, two distinct subtypes of cortical areas can be distinguished, the isocortex and the proisocortex. Here, we have compared specific spatiotemporal aspects of folding between the proisocortex and the isocortex in 13 primates, including human, chimpanzee, and various Old World and New World monkeys. We find that folding at the boundaries of the dorsal isocortex and the proisocortex, which gives rise to the cingulate sulcus (CiS) and the lateral fissure (LF), is conserved across the primates studied and is therefore referred to as conserved folding. In contrast, the degree of folding within the dorsal isocortex exhibits huge variation across these primates, indicating that this folding, which gives rise to gyri and sulci, is subject to major changes during primate evolution. We therefore refer to the folding within the dorsal isocortex as evolved folding. Comparison of fetal neocortex development in long-tailed macaque and human reveals that the onset of conserved folding precedes the onset of evolved folding. Moreover, the analysis of infant human neocortex exhibiting lissencephaly, a developmental malformation thought to be mainly due to abnormal neuronal migration, shows that the evolved folding is perturbed more than the conserved folding. Taken together, our study presents a two-step model of folding that pertains to primate neocortex development and evolution. Specifically, our data imply that the conserved folding and the evolved folding constitute two distinct, sequential events.

Significance Nucleosomal modifications have been implicated in fundamental epigenetic regulation, whereas the roles of nucleosome binding in shaping changes through evolution remain to be addressed. Here we performed a comparative study to clarify the roles of nucleosome occupancy in exon origination. By profiling a high-resolution, cross-species mononucleosome landscape for mammalian tissues, we found nucleosome occupancy profiles are conserved across tissues and species. Further, through a phylogenetic approach, we found that the feature of differential nucleosome occupancy appears prior to the origination of new exons and, presumably, facilitates the origin of new exons by increasing the splice strength of the ancestral nonexonic regions through driving a local difference in GC content, which suggests the function of nucleosome binding in exonization., Nucleosomal modifications have been implicated in fundamental epigenetic regulation, but the roles of nucleosome occupancy in shaping changes through evolution remain to be addressed. Here we present high-resolution nucleosome occupancy profiles for multiple tissues derived from human, macaque, tree shrew, mouse, and pig. Genome-wide comparison reveals conserved nucleosome occupancy profiles across both different species and tissue types. Notably, we found significantly higher levels of nucleosome occupancy in exons than in introns, a pattern correlated with the different exon–intron GC content. We then determined whether this biased occupancy may play roles in the origination of new exons through evolution, rather than being a downstream effect of exonization, through a comparative approach to sequentially trace the order of the exonization and biased nucleosome binding. By identifying recently evolved exons in human but not in macaque using matched RNA sequencing, we found that higher exonic nucleosome occupancy also existed in macaque regions orthologous to these exons. Presumably, such biased nucleosome occupancy facilitates the origination of new exons by increasing the splice strength of the ancestral nonexonic regions through driving a local difference in GC content. These data thus support a model that sites bound by nucleosomes are more likely to evolve into exons, which we term the “nucleosome-first” model.

Background Endogenous Retroviruses (ERVs) constitute approximately 8% of every human genome and are relics of ancestral infections that affected the germ line cells. The ERV-W group contributed to primate physiology by providing an envelope protein (Syncytin-1) that has been adopted for placenta development in hominoids. Expression of Human ERV-W (HERV-W) sequences is investigated for a pathological role in various human diseases. Results We previously characterized ERV-W group genomic sequences in human and non-human Catarrhini species. We now investigated ERV-W-like sequences in the parvorder Platyrrhini, especially regarding two species with complete genome assemblies, namely marmoset (Callithrix jacchus) and squirrel monkey (Saimiri boliviensis). We identified in both species proviral sequences, annotated as ERV1–1 in respective genome assemblies, sharing high sequence similarities with Catarrhini ERV-W. A total of 130 relatively intact proviruses from the genomes of marmoset and squirrel monkey were characterized regarding their structural and evolutionarily relationships with Catarrhini ERV-W elements. Platyrrhini ERV-W sequences share several structural features with Catarrhini ERV-W elements and are closely related phylogenetically with the latter as well as with other ERV-W-related gammaretrovirus-like ERVs. The ERV-W group colonized Platyrrhini primates of both Callitrichidae and Atelidae lineages, with provirus formations having occurred mostly between 25 and 15 mya. Two LTR subgroups were associated with monophyletic proviral bodies. A pre-gag region appears to be a sequence feature common to the ERV-W group: it harbors a putative intron sequence that is missing in some ERV-W loci, holding a putative ORF as well. The presence of a long pre-gag portion was confirmed among all gammaretroviral ERV analyzed, suggesting a role in the latter biology. It is noteworthy that, contrary to Catarrhini ERV-W, there was no evidence of L1-mediated mobilization for Platyrrhini ERV-W sequences. Conclusions Our data establish that ERV-W is not exclusive to Catarrhini primates but colonized both parvorders of Simiiformes, providing further insight into the evolution of ERV-W and the colonization of primate genomes.

Primate Evolution There has been much focus on the evolution of primates and especially where and how humans diverged in this process. It has often been suggested that the last common ancestor between humans and other apes, especially our closest relative, the chimpanzee, was ape- or chimp-like. Almecija et al. review this area and conclude that the morphology of fossil apes was varied and that it is likely that the last shared ape ancestor had its own set of traits, different from those of modern humans and modern apes, both of which have been undergoing separate suites of selection pressures. Science , this issue p. [eabb4363][1] [1]: /lookup/doi/10.1126/science.abb4363

Background Recent studies have revealed thousands of A-to-I RNA editing events in primates, but the origination and general functions of these events are not well addressed. Results Here, we perform a comparative editome study in human and rhesus macaque and uncover a substantial proportion of macaque A-to-I editing sites that are genomically polymorphic in some animals or encoded as non-editable nucleotides in human. The occurrence of these recent gain and loss of RNA editing through DNA point mutation is significantly more prevalent than that expected for the nearby regions. Ancestral state analyses further demonstrate that an increase in recent gain of editing events contribute to the over-representation, with G-to-A mutation site as a favorable location for the origination of robust A-to-I editing events. Population genetics analyses of the focal editing sites further reveal that a portion of these young editing events are evolutionarily significant, indicating general functional relevance for at least a fraction of these sites. Conclusions Overall, we report a list of A-to-I editing events that recently originated through G-to-A mutations in primates, representing a valuable resource to investigate the features and evolutionary significance of A-to-I editing events at the population and species levels. The unique subset of primate editome also illuminates the general functions of RNA editing by connecting it to particular gene regulatory processes, based on the characterized outcome of a gene regulatory level in different individuals or primate species with or without these editing events. Electronic supplementary material The online version of this article (10.1186/s13059-019-1638-y) contains supplementary material, which is available to authorized users.

Trace amines (TAs) in the mammalian brain have been investigated for four decades. Trace amine‐associated receptors (TAARs) were discovered during the search for receptors activated by TAs. TAARs are considered a second class of vertebrate olfactory receptors and successfully proliferated in conjunction with adaptation to living on the ground to detect carnivore odors. Thus, therian mammals have a high number of TAAR genes due to rapid species‐specific gene duplications. In primate lineages, however, their genomes have significantly smaller numbers of TAAR genes than do other mammals. To elucidate the evolutionary force driving these patterns, exhaustive data mining of TAAR genes was performed for 13 primate genomes (covering all four infraorders) and two nonprimate euarchontan genomes. This study identified a large number of pseudogenes in many of these primate genomes and thus investigated the pseudogenization event process for the TAAR repertoires. The degeneration of TAARs is likely associated with arboreal inhabitants reducing their exposure to carnivores, and this was accelerated by the change in the nose shape of haplorhines after their divergence from strepsirrhines. Arboreal life may have decreased the reliance on the chemosensing of predators, suggestive of leading to the depauperation of TAAR subfamilies. The evolutionary deterioration of TAARs in primates has been reestablished in recently derived primates due to high selection pressure and probably functional diversity., The arboreal lifestyle derived from the Euarchonta ancestor may have reduced reliance on the chemosensing of predators, leading to the depauperation of TAAR subfamilies.

The divergence of crown catarrhines—i.e., the split of cercopithecoids (Old World monkeys) from hominoids (apes and humans)—is a poorly understood phase in our shared evolutionary history with other primates. The two groups differ in the anatomy of the hip joint, a pattern that has been linked to their locomotor strategies: relatively restricted motion in cercopithecoids vs. more eclectic movements in hominoids. Here we take advantage of the first well-preserved proximal femur of the early Oligocene stem catarrhine Aegyptopithecus to investigate the evolution of this anatomical region using 3D morphometric and phylogenetically-informed evolutionary analyses. Our analyses reveal that cercopithecoids and hominoids have undergone divergent evolutionary transformations of the proximal femur from a similar ancestral morphology that is not seen in any living anthropoid, but is preserved in Aegyptopithecus, stem platyrrhines, and stem cercopithecoids. These results highlight the relevance of fossil evidence for illuminating key adaptive shifts in primate evolution., The proximal femur is key for understanding locomotion in primates. Here, the authors analyze the evolution of the proximal femur in catarrhines, including a new Aegyptopithecus fossil, and suggest that Old World monkeys and hominoids diverged from an ancestral state similar to Aegyptopithecus.

Long interspersed element-1 (LINE-1 or L1) is one of the most abundant retrotransposons in the primate genomes and has contributed to their genome diversity and variations during the primate evolution. Among primate L1 subfamilies, L1Pt subfamilies include Pan troglodytes-specific L1s. L1Pt elements have been successfully expanded in the chimpanzee genome since the divergence of human and chimpanzee lineages. However, only a few full-length L1Pt copies were previously detected in the chimpanzee genome due to incomplete chimpanzee reference genome sequences at the time. In the present study, we aimed to identify chimpanzee-specific L1s using the most recent version of the chimpanzee reference genome (May 2016, panTro5). We identified a total of 3731 chimpanzee-specific L1s. This is much more than previously reported chimpanzee-specific L1 copies. Among these, 223 are full-length (>6 kb), and we annotated their subfamilies and examined their retrotransposition-competency. The result showed that there are two L1Pt subfamilies in the chimpanzee genome, and the nine structurally intact elements belong to L1Pt-1, L1Pt-2, and L1PA2 subfamilies. In addition, we found that the intact full-length L1 group showed significantly higher L1 expression level than the non-intact full-length L1 group using limited RNA-seq data. It is interesting to notice that the number of retrotransposition-competent elements is much less in the chimpanzee genome than that in the human genome. In conclusion, there is increasing evidence to indicate that chimpanzee-specific L1s have changed the chimpanzee genome, causing genomic difference from other primate genomes.

Studies that measured mutation rates in human populations using pedigrees have reported values that differ significantly from rates estimated from the phylogenetic comparison of humans and chimpanzees. Consequently, exchanges between mutation rate values across different timescales lead to conflicting divergence time estimates. It has been argued that this variation of mutation rate estimates across hominoid evolution is in part caused by incorrect assignment of calibration information to the mean coalescent time among loci, instead of the true genetic isolation (speciation) time between humans and chimpanzees. In this study, we investigated the feasibility of estimating the human pedigree mutation rate using phylogenetic data from the genomes of great apes. We found that, when calibration information was correctly assigned to the human–chimpanzee speciation time (and not to the coalescent time), estimates of phylogenetic mutation rates were statistically equivalent to the estimates previously reported using studies of human pedigrees. We conclude that, within the range of biologically realistic ancestral generation times, part of the difference between whole-genome phylogenetic and pedigree mutation rates is due to inappropriate assignment of fossil calibration information to the mean coalescent time instead of the speciation time. Although our results focus on the human–chimpanzee divergence, our findings are general, and relevant to the inference of the timescale of the tree of life.

Comparative variation in brain size is arguably one of the most dominant features of primate evolution. Enduring questions in this context comprise whether evolutionary changes in certain brain regions outpace changes in other regions, and to what extent such regional variation between species explains comparative variation in overall brain size. To answer this question, we investigate the tempo and mode of evolution of brain organization using the largest combination of brain regions and species analyzed to date (36 brain regions, together representing over 90% of overall brain size, across 17 anthropoid primates, including humans). Following studies suggesting that the expansion of the major constituent regions of the cortico-cerebellar system (CCS) predominantly explain human brain size expansion, we test whether the link between variation in the CCS and brain size is consistent across primates. Results indicate that the constituent brain regions of the CCS show the highest rates of evolution, demonstrate a significant modular pattern of evolution, and closely align with changes in overall brain size. This phenotypic structure is consistent across different taxonomic scales, suggesting that the evolution of anthropoid brain organization is underpinned by a stable genetic structure and is characterized by a conserved evolutionary trajectory towards the CCS. Results hereby suggest that the expansion of the CCS is the primary driver of brain expansion in anthropoid primates. These findings have fundamental implications for our understanding of the nature of primate and human cognition, and the genetic and developmental structure that underpins brain evolution.

Many genera of terrestrial vertebrates diversified exclusively on one or the other side of Wallace’s Line, which lies between Borneo and Sulawesi islands in Southeast Asia, and demarcates one of the sharpest biogeographic transition zones in the world. Macaque monkeys are unusual among vertebrate genera in that they are distributed on both sides of Wallace‘s Line, raising the question of whether dispersal across this barrier was an evolutionary one-off or a more protracted exchange—and if the latter, what were the genomic consequences. To explore the nature of speciation over the edge of this biogeographic divide, we used genomic data to test for evidence of gene flow between macaque species across Wallace’s Line after macaques colonized Sulawesi. We recovered evidence of post-colonization gene flow, most prominently on the X chromosome. These results are consistent with the proposal that gene flow is a pervasive component of speciation—even when barriers to gene flow seem almost insurmountable.

Although population genetics studies have significantly accelerated the evolutionary and functional interrogations of genes and regulations, limited polymorphism data are available for rhesus macaque, the model animal closely related to human. Here, we report the first genome-wide effort to identify and visualize the population genetics profile in rhesus macaque. On the basis of the whole-genome sequencing of 31 independent macaque animals, we profiled a comprehensive polymorphism map with 46,146,548 sites. The allele frequency for each polymorphism site, the haplotype structure, as well as multiple population genetics parameters were then calculated on a genome-wide scale. We further developed a specific interface, the RhesusBase PopGateway, to facilitate the visualization of these annotations, and highlighted the applications of this highly integrative platform in clarifying the selection signatures of genes and regulations in the context of the primate evolution. Overall, the updated RhesusBase provides a comprehensive monkey population genetics framework for in-depth evolutionary studies of human biology.

Allomaternal care (AMC) (i.e., infant care that is provided by group members other than an infant's mother) is a rare, although phylogenetically widespread, mammalian infant care strategy. In primates, however, AMC occurs at unusually high frequencies, particularly among several haplorhine (monkey and ape) taxa. In fact, AMC is present in every major primate radiation and has been described in 74% of 154 species for which data are available. Its widespread presence in the Order Primates suggests that there may have been strong selective pressure for AMC early in primate evolution, but it is currently unknown why these behaviors are so common in primates. Research focused on captive callitrichids (tamarins and marmosets) has contributed greatly to our understanding of the potential causes and consequences of highly derived forms of AMC (i.e., cooperative breeding). Recent efforts have shifted focus to understand the selective pressures leading to the expansion and diversification of AMC throughout the Primate Order, thus expanding research to investigate the causes and consequences of less derived forms of AMC. Here we review the broad-scale patterns observed in primates and outline innovative and exciting avenues of research moving forward. Keywords: infant care; allomother; helper; hormones; behavioral genetics

The basicranium and facial skeleton are two integrated structures displaying great morphological diversity across primates. Previous studies focusing on limited taxonomic samples have demonstrated that morphological integration has a significant impact on the evolution of these structures. However, this influence is still poorly understood. A more complete understanding of craniofacial integration across primates has important implications for functional hypotheses of primate evolution. In the present study, we analyzed a large sample of primate species to assess how integration affects the relationship between basicranial and facial evolutionary pathways across the order. First, we quantified integration and modularity between basicranium and face using phylogenetically-informed partial least squares analyses. Then, we defined the influence of morphological integration between these structures on rates of evolution, using a time-calibrated phylogenetic tree, and on disparity through time, comparing the morphological disparity across the tree with that expected under a pure Brownian process. Finally, we assessed the correlation between the basicranium and face, and three factors purported to have an important role in shaping these structures during evolution: endocranial volume, positional behavior (i.e., locomotion and posture), and diet. Our findings show that the face and basicranium, despite being highly integrated, display significantly different evolutionary rates. However, our results demonstrate that morphological integration impacted shape disparity through time. We also found that endocranial volume and positional behavior are important drivers of cranial shape evolution, partly affected by morphological integration.

Researchers have long sought to understand the genetic basis of the cognitive differences between primates, with particular focus on the human brain. Although all mutational types have worked in concert with evolutionary forces to generate the current human brain, in this review we will explore the impact of mobile elements, specifically non-LTR retrotransposons. Non-LTR retrotransposons have contributed coding and regulatory sequences to the genome throughout evolution. During primate evolution there have been multiple waves of LINE retrotransposition as well as the birth of new mobile elements such as the SINEs Alu and SVA and we will explore what kinds of impacts these may have had on the evolving human brain.

Transposable elements (TEs) have skill of altering the position inside the genome and these TEs are widespread in both of plants and animals. They are separated into class I called retrotransposons, and class II called DNA transposons. According to the previous studies, not only TEs are related with disease, they are key factor of human and primate evolution. From this review, we discussed about the impact of transposable element, its role in the genome of human and primates and how TE distribution is differ from them. Additionally, we described how TEs contributed on primate evolution by its unique role. This review could be great use for further studies in relation to evolution mechanism and various diseases.

Early primate evolution is connected to the efficient exploitation of the terminal branch habitat. Mammals that forage in this habitat constantly encounter flexible thin branches that bend under the weight of the animals and thus form steeply inclined and declined supports. This study was aimed to gain insight into how cotton-top tamarins – a previously proposed modern analogue for a hypothetical stage in early primate evolution with prehensile autopodia – meet the specific functional demands when navigating thin, branch-like supports of different orientation. X-ray motion analysis was combined with synchronous single limb substrate reaction force measurements to discern limb mechanical adjustments. Previously reported gait parameter adjustments were confirmed for moderate support orientations, but on the steepest inclines and declines kinematic discontinuities were observed. These are interpreted to emphasize the functional roles of the forelimbs (net-braking role) and hind limbs (net-propulsive role) already established for level and moderately inclined supports. Tensile forces were exerted by the forelimbs on the steepest inclines and by the hind limbs on the steepest declines (head-first descents). Even though non-specialized small mammals have also been shown to successfully negotiate similar supports, prehensility offers advantages for foraging on thin, steeply inclined and declined terminal branches. Thus, the evolution of prehensile autopodia in small early primates likely has enhanced the exploitation of the terminal branch habitat.

Scientific study of lemurs, a group of primates found only on Madagascar, is crucial for understanding primate evolution. Unfortunately, lemurs are among the most endangered animals in the world, so there is a strong impetus to maximize as much scientific data as possible from available physical specimens. MicroCT scanning efforts at Duke University have resulted in scans of more than 100 strepsirrhine cadavers representing 18 species from the Duke Lemur Center. An error study of the microCT scanner recovered less than 0.3% error at multiple resolution levels. Scans include specimen overviews and focused, high-resolution selections of complex anatomical regions (e.g., cranium, hands, feet). Scans have been uploaded to MorphoSource, an online digital repository for 3D data. As captive (but free ranging) individuals, these specimens have a wealth of associated information that is largely unavailable for wild populations, including detailed life history data. This digital collection maximizes the information obtained from rare and endangered animals with minimal degradation of the original specimens.

Retroviruses, a form of mobile genetic elements, have important roles in disease and primate evolution. Exogenous retroviruses, such as human immunodeficiency virus (HIV), have significant pathological implications that have created a massive public health challenge in recent years. Endogenous retroviruses (ERVs), which are the primary focus of this review, can also be pathogenic, as well as being beneficial to a host in some cases. Furthermore, retroviruses may have played a key role in primate evolution that resulted in the incorporation of these elements into the human genome. Retroviruses are mobile genetic elements that have important roles in disease and primate evolution. We will further discuss the pathogenic potential of retroviruses, including their role in cancer biology, and will briefly summarize their evolutionary implications.

The first primates evolved special features that paved the way for human evolution – and to discover why we have to go out on a limb

The long-term human evolution is first explained. Starting from the origin of life, emergence of mammals and evolution of primates and hominoids are outlined, followed by classification of family Hominidae. We then move to the human genome. Its structure in terms of chromosomes and dichotomy of coding and noncoding regions are discussed, followed with general description on various types of mutations such as nucleotide substitutions, insertions and deletions, repeat number changes, and gene duplications.

Events in primate evolution are often dated by assuming a "molecular clock", i.e., a constant rate of substitution per unit time, but the validity of this assumption remains unclear. Among mammals, it is well known that there exists substantial variation in yearly substitution rates. Such variation is to be expected from differences in life-history traits, suggesting that it should also be found among primates. Motivated by these considerations, we analyze whole genomes from ten primate species, including Old World Monkeys (OWMs), New World Monkeys (NWMs) and apes, focusing on putatively neutral autosomal sites and controlling for possible effects of biased gene conversion and methylation at CpG sites. We find that substitution rates are ~65% higher in lineages leading from the hominoid-NWM ancestor to NWMs than to apes. Within apes, rates are ~2% higher in chimpanzees and ~7% higher in the gorilla than in humans. Substitution types subject to biased gene conversion show no more variation among species than those not subject to it. Not all mutation types behave similarly, however: in particular, transitions at CpG sites exhibit a more clock-like behavior than do other types, presumably due to their non-replicative origin. Thus, not only the total rate, but also the mutational spectrum varies among primates. This finding suggests that events in primate evolution are most reliably dated using CpG transitions. Taking this approach, we estimate that the average time to the most recent common ancestor of human and chimpanzee is 12.1 million years and their split time 7.9 million years.

The conditions under which early euprimates (adapids and omomyids) originated and evolved is an area of longstanding debate. The leading hypotheses of euprimate origins promulgate diet as a core component of the early evolution of this group, despite the role of dietary competition in euprimate originations never being tested directly. This study compared three competition models (non-competition, competitive displacement, competitive coexistence) with observed patterns of dietary niche overlap, reconstructed from three-dimensional molar morphology, at the time of the euprimate radiation in North America (at the Paleocene–Eocene boundary). Overlap of reconstructed multidimensional dietary niches between euprimates and members of their guild were analysed using a modified MANOVA to establish the nature of the competitive environment surrounding euprimate origins in North America (an immigration event). Results indicated that adapids entered the mammalian guild in the absence of competition, suggesting dietary adaptations that were unique within the community. Conversely, omomyids experienced strong, but transitory, competition with nyctitheriids, suggesting that omomyids possessed the ability to out-compete this group. These results show that adapids and omomyids experienced different competitive scenarios upon their arrival (origination) in North America and confirm the significance of diet (and dietary adaptations) in euprimate origination and early diversification in mammalian communities.

A key feature in primate evolution is a foot with a divergent opposable hallucal metatarsal bearing a large peroneal process. Extant primates are characterized by a powerful hallucal grasp-an either "euprimate" or "plesiadapoid-euprimate" ancestor acquisition-that facilitates the exploitation of fine branches, an ability that increased the fitness of ancestral euprimates. In this context, the didelphid marsupial Caluromys has been used as the extant analog to this primate morphotype stage due to some morphological, ecological, and behavioral features. However, the extent to which and the positional and support contexts in which Caluromys uses powerful hallucal grasping are not known. This renders analogies to any mode of "euprimate" or "stem primate" grasping poorly substantiated. The present paper quantifies locomotor and postural behavior, support use, and associated frequencies of hallucal grasping in captive Caluromys philander via analysis of video recordings. During locomotion, Caluromys primarily used diagonal sequence walk, clamber, and climb, whereas stand, foot-hang, and bipedal stand were the dominant postures. Small, fine, horizontal, and moderately inclined branches were frequently used. Overall rates of "apparently powerful hallucal grasps" were high, but were exceptionally high during clamber, climb, foot-hang, and bipedal stand. Additionally, an "apparently powerful hallucal grasp" was very common upon fine, small, steep, and vertical branches. The extensive use of such powerful hallucal grasping provided stability and safety that enabled Caluromys to proficiently utilize fine branches of various orientations. The ability to negotiate such unstable supports, further reflected in foot anatomy, provides evidence that the morphobehavioral complex of Caluromys can serve as an extant analog to the plesiadapoid-euprimate ancestor, represented as a terminal branch feeder with effective hallucal grasping.

The molecular clock has become an increasingly important tool in evolutionary biology and biological anthropology. Nevertheless, a source of contention with respect to this method is the frequent discordance with fossil-based estimates of divergence times. The primate radiation is a case in point: Numerous studies have dated the major primate nodes (reviewed in Steiper and Young,1, 2) and there are many instances where molecular and fossil-based estimates of divergence times differ (Fig. 1). Some investigators have recently focused on phenomena such as stratigraphic dating, the stochastic nature of molecular time estimates, and other sources as potential biases in molecular clock estimates.3, 4 In this paper we do not focus on accuracy or statistical error; rather, we argue that discordance is a predictable phenomenon that provides valuable information about the tempo and mode of primate molecular and morphological evolution. Using this perspective, we reexamine the principal theoretical and methodological factors that lead to discordance between molecular and fossil estimates of the origins of taxa and discuss how a better understanding of these factors can help to improve our understanding of primate evolution.

Lineage-specific microRNA (miRNA) families may contribute to developmental novelties during evolution. However, little is known about the origin and evolution of new miRNA families. We report evidence of an Alu-mediated rapid expansion of miRNA genes in a previously identified primate-specific miRNA family, drawn from sequencing and comparative analysis of 9 diverse primate species. Evolutionary analysis reveals similar divergence among miRNA copies whether they are within or between species, lineage-specific gain and loss of miRNAs, and gene pseudolization in multiple species. These observations support a birth-and-death process of miRNA genes in this family, implicating functional diversification during primate evolution. In addition, both secondary structure conservation and reduced single nucleotide polymorphisms density attest to functional constraint of this family in primates. Finally, we observed preferential expression of miRNAs in human placenta and fetal brain, suggesting a functional importance of this family for primate development.

The contribution from selective sweeps to variation in genetic diversity has proven notoriously difficult to assess, in part because polymorphism data only allows detection of sweeps in the most recent few hundred thousand years. Here we show how linked selection in ancestral species can be quantified across evolutionary timescales by analyzing patterns of incomplete lineage sorting (ILS) along the genomes of closely related species. We show that sweeps in the human-chimpanzee and human-orangutan ancestors can be identified as depletions of ILS in regions in excess of 100 kb in length. Sweeps predicted in each ancestral species, as well as recurrent sweeps predicted in both species, often overlap sweeps predicted in humans. This suggests that many genomic regions experience recurrent selective sweeps. By comparing the ILS patterns along the genomes of the closely related human-chimpanzee and human-orangutan ancestors, we are further able to quantify the impact of selective sweeps relative to that of background selection. Compared to the human-orangutan ancestor, the human-chimpanzee ancestor shows a strong excess of regions depleted of ILS as well as a stronger reduction in ILS around genes. We conclude that sweeps play a strong role in reducing diversity along the genome and that sweeps have reduced diversity in the human-chimpanzee ancestor much more than in the human-orangutan ancestor.

The study of primate evolution opens a fascinating window onto the varied adaptations, behaviors, and origins of our closest relatives and therefore ourselves. Four books reviewed give different pe...