Subjective Reactions to First Coitus in Relation to Participant Sex, Partner Age, and Context in a German Nationally Representative Sample of Adolescents and Young Adults

Analysis of a Finnish nationally representative student sample found that subjective reactions to first intercourse (mostly heterosexual; usually in adolescence) were highly positive for boys and mostly positive for girls, whether involved with peers or adults (Rind, 2022). The present study examined the generality of these findings by examining subjective reactions to first coitus (heterosexual intercourse) in a German nationally representative sample of young people (data collected in 2014). Most first coitus was postpubertal. Males reacted mostly positively and uncommonly negatively in similar fashion in all age pairings: boy-girl (71% positive, 13% negative); boy-woman (73% positive; 17% negative); man-woman (73% positive, 15% negative). Females' reactions were more mixed, similar in the girl-boy (48% positive; 37% negative) and woman-man (46% positive, 36% negative) groups, but less favorable in the girl-man group (32% positive, 47% negative). In logistic regressions, adjusting for other factors, rates of positive reactions were unrelated to age groups. These rates did increase, in order of importance, when participants were male, their partners were close, they expected the coitus to happen, and they affirmatively wanted it. Reaction rates were computed from the Finnish sample, restricting cases to first coitus occurring in the 2000s, and then compared to minors' reactions in the German sample. The Finns reacted more favorably, similarly in both minor-peer and minor-adult coitus, with twice the odds of reacting positively. It was argued that this discrepancy was due to cultural differences (e.g., Finnish culture is more sex-positive). To account for the reaction patterns shown in the adolescent-adult coitus, sizably at odds with expectations from mainstream professional thinking, an evolutionary framework was employed.

Archimetrosis: the evolution of a disease and its extant presentation : Pathogenesis and pathophysiology of archimetrosis (uterine adenomyosis and endometriosis)

PURPOSE

This article presents a novel concept of the evolution and, thus, the pathogenesis of uterine adenomyosis as well as peritoneal and peripheral endometriosis. Presently, no unifying denomination of this nosological entity exists.

METHODS

An extensive search of the literature on primate evolution was performed. This included comparative functional morphology with special focus on the evolution of the birthing process that fundamentally differs between the haplorrhine primates and most of the other eutherian mammals. The data were correlated with the results of own research on the pathophysiology of human archimetrosis and with the extant presentation of the disease.

RESULTS

The term Archimetrosis is suggested as a denomination of the nosological entity. Archimetrosis occurs in human females and also in subhuman primates. There are common features in the reproductive process of haplorrhine primates such as spontaneous ovulation and corpus luteum formation, spontaneous decidualization and menstruation. These have fused Müllerian ducts resulting in a uterus simplex. Following a usually singleton pregnancy, the fetus is delivered in the skull position. Some of these features are shared by other mammals, but not in that simultaneous fashion. In haplorrhine primates, with the stratum vasculare, a new myometrial layer has evolved during the time of the Cretaceous-Terrestrial Revolution (KTR) that subserves expulsion of the conceptus and externalization of menstrual debris in non-conceptive cycles. Hypercontractility of this layer has evolved as an advantage with respect to the survival of the mother and the birth of a living child during delivery and may be experienced as primary dysmenorrhea during menstruation. It may result in tissue injury by the sheer power of the contractions and possibly by the associated uterine ischemia. Moreover, the lesions at extra-uterine sites appear to be maintained by biomechanical stress.

CONCLUSIONS

Since the pathogenesis of archimetrosis is connected with the evolution of the stratum vasculare, tissue injury and repair (TIAR) turns out to be the most parsimonious explanation for the development of the disease based on clinical, experimental and evolutionary evidence. Furthermore, a careful analysis of the published clinical data suggests that, in the risk population with uterine hypercontractility, the disease develops with a yet to be defined latency phase after the onset of the biomechanical injury. This opens a new avenue of prevention of the disease in potentially affected women that we consider to be primarily highly fertile.

Molecular diversity and phenotypic pleiotropy of ancient genomic regulatory loci derived from human endogenous retrovirus type H (HERVH) promoter LTR7 and HERVK promoter LTR5_Hs and their contemporary impacts on pathophysiology of Modern Humans

Timelines of population-level effects of viruses on humans varied from the evolutionary scale of million years to contemporary spread of viral infections. Correspondingly, these events are exemplified by: (i) emergence of human endogenous retroviruses (HERVs) from ancient germline infections leading to stable integration of viral genomes into human chromosomes; and (ii) wide-spread viral infections reaching a global pandemic state such as the COVID-19 pandemic. Despite significant efforts, understanding of HERV’s roles in governance of genomic regulatory networks, their impacts on primate evolution and development of human-specific physiological and pathological phenotypic traits remains limited. Remarkably, present analyses revealed that expression of a dominant majority of genes (1696 of 1944 genes; 87%) constituting high-confidence down-steam regulatory targets of defined HERV loci was significantly altered in cells infected with the SARS-CoV-2 coronavirus, a pathogen causing the global COVID-19 pandemic. This study focused on defined sub-sets of DNA sequences derived from HERVs that are expressed at specific stages of human preimplantation embryogenesis and exert regulatory actions essential for self-renewal and pluripotency. Evolutionary histories of LTR7/HERVH and LTR5_Hs/HERVK were charted based on evidence of the earliest presence and expansion of highly conserved (HC) LTR sequences. Sequence conservation analyses of most recent releases 17 primate species’ genomes revealed that LTR7/HERVH have entered germlines of primates in Africa after the separation of the New World Monkey lineage, while LTR5_Hs/HERVK successfully colonized primates’ germlines after the segregation of Gibbons’ species. Subsequently, both LTR7 and LTR5_Hs undergo a marked ~ fourfold–fivefold expansion in genomes of Great Apes. Timelines of quantitative expansion of both LTR7 and LTR5_Hs loci during evolution of Great Apes appear to replicate the consensus evolutionary sequence of increasing cognitive and behavioral complexities of non-human primates, which seems particularly striking for LTR7 loci and 11 distinct LTR7 subfamilies. Consistent with previous reports, identified in this study, 351 human-specific (HS) insertions of LTR7 (175 loci) and LTR5_Hs (176 loci) regulatory sequences have been linked to genes implicated in establishment and maintenance of naïve and primed pluripotent states and preimplantation embryogenesis phenotypes. Unexpectedly, HS-LTRs manifest regulatory connectivity to genes encoding markers of 12 distinct cells’ populations of fetal gonads, as well as genes implicated in physiology and pathology of human spermatogenesis, including Y-linked spermatogenic failure, oligo- and azoospermia. Granular interrogations of genes linked with 11 distinct LTR7 subfamilies revealed that mammalian offspring survival (MOS) genes seem to remain one of consistent regulatory targets throughout ~ 30 MYA of the divergent evolution of LTR7 loci. Differential GSEA of MOS versus non-MOS genes identified clearly discernable dominant enrichment patterns of phenotypic traits affected by MOS genes linked with LTR7 (562 MOS genes) and LTR5_Hs (126 MOS genes) regulatory loci across the large panel of genomics and proteomics databases reflecting a broad spectrum of human physiological and pathological traits. GSEA of LTR7-linked MOS genes identified more than 2200 significantly enriched records of human common and rare diseases and gene signatures of 466 significantly enriched records of Human Phenotype Ontology traits, including Autosomal Dominant (92 genes) and Autosomal Recessive (93 genes) Inheritance. LTR7 regulatory elements appear linked with genes implicated in functional and morphological features of central nervous system, including synaptic transmission and protein–protein interactions at synapses, as well as gene signatures differentially regulated in cells of distinct neurodevelopmental stages and morphologically diverse cell types residing and functioning in human brain. These include Neural Stem/Precursor cells, Radial Glia cells, Bergman Glia cells, Pyramidal cells, Tanycytes, Immature neurons, Interneurons, Trigeminal neurons, GABAergic neurons, and Glutamatergic neurons. GSEA of LTR7-linked genes identified significantly enriched gene sets encoding markers of more than 80 specialized types of neurons and markers of 521 human brain regions, most prominently, subiculum and dentate gyrus. Identification and characterization of 1944 genes comprising high-confidence down-steam regulatory targets of LTR7 and/or LTR5_Hs loci validated and extended these observations by documenting marked enrichments for genes implicated in neoplasm metastasis, intellectual disability, autism, multiple cancer types, Alzheimer’s, schizophrenia, and other brain disorders. Overall, genes representing down-stream regulatory targets of ancient retroviral LTRs exert the apparently cooperative and exceedingly broad phenotypic impacts on human physiology and pathology. This is exemplified by altered expression of 93% high-confidence LTR targets in cells infected by contemporary viruses, revealing a convergence of virus-inflicted aberrations on genomic regulatory circuitry governed by ancient retroviral LTR elements and interference with human cells’ differentiation programs.

Narrative as co-regulation: A review of embodied narrative in infant development

We review evidence of non-verbal, embodied narratives in human infancy to better understand their form and function as generators of common experience, regulation, and learning. We examine their development prior to the onset of language, with a view to improve understanding of narrative as regular motifs or schemas of early experience in both solitary and social engagement. Embodied narratives are composed of regular patterns of interest, arousal, affect, and intention that yield a characteristic four-part structure of (i) introduction, (ii) development, (iii) climax, and (iv) resolution. Made with others these form co-created shared acts of meaning, and are parsed in time with discreet beginnings and endings that allow a regular pattern to frame and give predictive understanding for prospective regulation (especially important within social contexts) that safely returns to baseline again. This characteristic pattern, co-created between infant and adult from the beginning of life, allows the infant to contribute to, and learn, the patterns of its culture. We conclude with a view on commonalities and differences of co-created narrative in non-human primates, and discuss implications of disruption to narrative co-creation for developmental psychopathology.

Morphological integration and evolutionary potential of the primate shoulder: Variation among taxa and implications for genetic covariances with the basicranium, pelvis, and arm

Within the primate order, the morphology of the shoulder girdle is immensely variable and has been shown to reflect the functional demands of the upper limb. The observed morphological variation among extant primate taxa consequently has been hypothesized to be driven by selection for different functional demands. Evolutionary analyses of the shoulder girdle often assess this anatomical region, and its traits, individually, therefore implicitly assuming independent evolution of the shoulder girdle. However, the primate shoulder girdle has developmental and functional covariances with the basicranium and pelvic girdle that have been shown to potentially influence its evolution. It is unknown whether these relationships are similar or even present across primate taxa, and how they may affect morphological variation among primates. This study evaluates the strength of covariance and evolutionary potential across four anatomical regions: shoulder girdle, basicranium, pelvis, and distal humerus. Measures of morphological integration and evolutionary potential (conditioned covariance and evolutionary flexibility) are assessed across eight anthropoid primate taxa. Results demonstrate a consistent pattern of morphological constraint within paired anatomical regions across primates. Differences in evolutionary flexibility are observed among primate genera, with humans having the highest evolutionary potential overall. This pattern does not follow functional differences, but rather a separation between monkeys and apes. Therefore, evolutionary hypotheses of primate shoulder girdle morphological variation that evaluate functional demands alone may not account for the effect of these relationships. Collectively, our findings suggest differences in genetic covariance among anatomical regions may have contributed to the observable morphological variation among taxa.

Morphological affinities of a fossil ulna (KNM-WS 65401) from Buluk, Kenya

The morphological affinities of a primate proximal ulna (KNM-WS 65401) recovered from the late Early Miocene site Buluk, Kenya, are appraised. Nineteen three-dimensional landmarks on ulnae from 36 extant anthropoid species (n = 152 individuals) and KNM-WS 65401, as well as a subset of 14 landmarks on six ulnae belonging to other East African Miocene catarrhine taxa, were collected. To quantify ulnar shape, three-dimensional geometric morphometric techniques were used and linear dimensions commonly cited in the literature were derived from the landmark data. KNM-WS 65401 is situated between monkeys and hominoids in the principal components morphospace. KNM-WS 65401 shares features such as a short olecranon process, broad trochlear notch, and laterally oriented radial notch with extant hominoids, whereas features such as an anteriorly directed trochlear notch and flat, proximodistally elongated, and anteroposteriorly narrow radial notch are shared with extant monkeys. Principal component scores and linear metrics generally align KNM-WS 65401 with both suspensors and arboreal quadrupeds, but quadratic and linear discriminant analyses of principal component score data provide posterior probabilities of 80% and 83%, respectively, for assignment of KNM-WS 65401 to the suspensory group. Compared with fossil ulnae from other Miocene primates, KNM-WS 65401 is morphologically most distinct from KNM-LG 6, attributed to Dendropithecus macinnesi, and morphologically most similar to KNM-WK 16950R, attributed to Turkanapithecus kalakolensis. The KNM-WS 65401 individual likely possessed more enhanced capabilities for elbow joint extension, perhaps during suspensory behaviors, compared with other Miocene primates in the sample.

A comprehensive analysis of gorilla-specific LINE-1 retrotransposons

BACKGROUND

Long interspersed element-1 (LINE-1 or L1) is the most abundant retrotransposons in the primate genome. They have approximately 520,000 copies and make up ~ 17% of the primate genome. Full-length L1s can mobilize to a new genomic location using their enzymatic machinery. Gorilla is the second closest species to humans after the chimpanzee, and human-gorilla split 7-12 million years ago. The gorilla genome provides an opportunity to explore primate origins and evolution.

OBJECTIVE

L1s have contributed to genome diversity and variations during primate evolution. This study aimed to identify gorilla-specific L1s using a more recent version of the gorilla reference genome (Mar. 2016 GSMRT3/gorGor5).

METHODS

We collected gorilla-specific L1 candidates through computational analysis and manual inspection. L1Xplorer was used to identify whether full-length gorilla-specific L1s were intact. In addition, to determine the level of sequence conservation between intact fulllength gorilla-specific L1s, two ORFs of intact L1s were aligned with the L1PA2 consensus sequence.

RESULTS

2002 gorilla-specific L1 candidates were identified through computational analysis. Among them, we manually inspected 1,883 gorilla-specific L1s, among which most of them belong to the L1PA2 subfamily and 12 were intact L1s that could influence genomic variations in the gorilla genome. Interestingly, the 12 intact full-length gorilla-specific L1s have 14 highly conserved nonsynonymous mutations, including 6 mutations and 8 mutations in ORF1 and ORF2, respectively. In comparison to the intact full-length chimpanzee-specific L1s and human-specific hot-L1s, two of these in ORF1 (L256F and E293G) were shown as gorilla-specific nonsynonymous mutations.

CONCLUSION

The gorilla-specific L1s may have had significantly affected the gorilla genome to compose a genome different form that of other primates during primate evolution.

Evidence for the loss and recovery of SLAMF9 during human evolution: implications on Dollo's law

Signaling lymphocyte activation molecule family member 9 (SLAMF9) is a cell surface protein of the CD2/SLAM family of leukocyte surface receptors. It is conserved throughout mammals and has roles in the initiation of inflammatory responses and regulation of plasmacytoid dendritic cell function. Through comparison of reference sequences encoding SLAMF9 in human, mouse, and primate sequences, we have determined that the SLAMF9 gene underwent successive mutation events, resulting in the loss of the protein and subsequent recovery of a less stable version. The mutations included a single base pair deletion in the second exon and a change in the splice acceptor site of that same exon. These changes would have had the effect of creating and later repairing a frameshift in the coding sequence. These events took place since the divergence of the human lineage from the chimpanzee-human last common ancestor and represent the first known case of the functional loss and recovery of a gene within the human lineage.

Identification and characterization of ERV-W-like sequences in Platyrrhini species provides new insights into the evolutionary history of ERV-W in primates

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.

Sleep influences cognitive performance in lemurs

Primates spend almost half their lives asleep, yet little is known about how sleep influences their waking cognition. We hypothesized that diurnal and cathemeral lemurs differ in their need for consistent, non-segmented sleep for next-day cognitive function-including long-term memory consolidation, self-control, foraging efficiency, and sociality. Specifically, we expected that strictly diurnal Propithecus is more reliant on uninterrupted sleep for cognitive performance, as compared to four other lemur species that are more flexibly active (i.e., cathemeral). We experimentally inhibited sleep and tested next-day performance in 30 individuals of 5 lemur species over 960 total nights at the Duke Lemur Center in Durham, North Carolina. Each set of pair-housed lemurs experienced a sleep restriction and/or deprivation protocol and was subsequently tested in a variety of fitness-relevant cognitive tasks. Within-subject comparisons of performance on these tasks were made by switching the pair from the experimental sleep inhibited condition to a normal sleep environment, thus ensuring cognitive equivalency among individuals. We validated effectiveness of the protocol via actigraphy and infrared videography. Our results suggest that 'normal' non-disrupted sleep improved memory consolidation for all lemurs. Additionally, on nights of normal sleep, diurnal lemurs performed better in foraging efficiency tasks than cathemeral lemurs. Social behaviors changed in species-specific ways after exposure to experimental conditions, and self-control was not significantly linked with sleep condition. Based on these findings, the links between sleep, learning, and memory consolidation appear to be evolutionarily conserved in primates.

Evolutionarily significant A-to-I RNA editing events originated through G-to-A mutations in primates

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.

Post-translational buffering leads to convergent protein expression levels between primates

BACKGROUND

Differences in gene regulation between human and closely related species influence phenotypes that are distinctly human. While gene regulation is a multi-step process, the majority of research concerning divergence in gene regulation among primates has focused on transcription.

RESULTS

To gain a comprehensive view of gene regulation, we surveyed genome-wide ribosome occupancy, which reflects levels of protein translation, in lymphoblastoid cell lines derived from human, chimpanzee, and rhesus macaque. We further integrated messenger RNA and protein level measurements collected from matching cell lines. We find that, in addition to transcriptional regulation, the major factor determining protein level divergence between human and closely related species is post-translational buffering. Inter-species divergence in transcription is generally propagated to the level of protein translation. In contrast, gene expression divergence is often attenuated post-translationally, potentially mediated through post-translational modifications.

CONCLUSIONS

Results from our analysis indicate that post-translational buffering is a conserved mechanism that led to relaxation of selective constraint on transcript levels in humans.

New cranium of the endemic Caribbean platyrrhine, Antillothrix bernensis, from La Altagracia Province, Dominican Republic

Recent paleontological collection in submerged caves in the eastern Dominican Republic has yielded new specimens of Antillothrix bernensis. Here we describe a complete cranium of an adult individual (MHD 20) and provide phenetic comparisons to other endemic Caribbean taxa and extant mainland platyrrhines using three-dimensional geometric morphometric methods (3DGM). Qualitative and quantitative comparisons support conclusions based on other recently described fossil material: Antillothrix has a dentition lacking clear dietary specialization, an elongated brain case with strong temporal lines, and a vertically oriented nuchal plane. MHD 20 shares a combination of traits with a previously published subadult specimen (MHD 01) including a deep depression at glabella, dorsoventrally elongated orbits, and a relatively large face. This shared morphology reinforces the taxonomic affinity of the two specimens, with differences between the two likely reflecting the younger ontogenetic age of MHD 01. Comparisons to the extant platyrrhines paint a complicated picture as the results of between-group principal components analyses (bgPCA) indicate that Antillothrix does not share a suite of morphological features exclusively with any one genus. Depending on which bgPC axes are visualized, and which subset of landmarks is included (i.e., only those describing the shape of the face/palate for inclusion of Xenothrix), MHD 20 is most similar in shape to the atelids, Alouatta, Lagothrix, and Brachyteles, or an otherwise "empty" region of shape space. It groups neither with Cebus nor Callicebus, two taxa that Antillothrix has been associated with in previous studies based on much less complete material. The Antillothrix cranium does not exhibit any of the derived characters classically used to diagnose or define any single clade; rather its morphology shares features with multiple platyrrhine groups. This is consistent with the interpretation that Antillothrix preserves a primitive morphology, which accords with the hypothesis positing an early arrival of platyrrhines in the Caribbean.

Copy number analysis of the low-copy repeats at the primate NPHP1 locus by array comparative genomic hybridization

Array comparative genomic hybridization (aCGH) has been widely used to detect copy number variants (CNVs) in both research and clinical settings. A customizable aCGH platform may greatly facilitate copy number analyses in genomic regions with higher-order complexity, such as low-copy repeats (LCRs). Here we present the aCGH analyses focusing on the 45 kb LCRs [1] at the NPHP1 region with diverse copy numbers in humans. Also, the interspecies aCGH analysis comparing human and nonhuman primates revealed dynamic copy number transitions of the human 45 kb LCR orthologues during primate evolution and therefore shed light on the origin of complexity at this locus. The original aCGH data are available at GEO under GSE73962.

Gene structure variation in segmental duplication block C of human chromosome 7q 11.23 during primate evolution

Segmental duplication, or low-copy repeat (LCR) event, occurs during primate evolution and is an important source of genomic diversity, including gain or loss of gene function. The human chromosome 7q 11.23 is related to the William-Beuren syndrome and contains large region-specific LCRs composed of blocks A, B, and C that have different copy numbers in humans and different primates. We analyzed the structure of POM121, NSUN5, FKBP6, and TRIM50 genes in the LCRs of block C. Based on computational analysis, POM121B created by a segmental duplication acquired a new exonic region, whereas NSUN5B (NSUN5C) showed structural variation by integration of HERV-K LTR after duplication from the original NSUN5 gene. The TRIM50 gene originally consists of seven exons, whereas the duplicated TRIM73 and TRIM74 genes present five exons because of homologous recombination-mediated deletion. In addition, independent duplication events of the FKBP6 gene generated two pseudogenes at different genomic locations. In summary, these clustered genes are created by segmental duplication, indicating that they show dynamic evolutionary events, leading to structure variation in the primate genome.

Evidence for a vestigial pinna-orienting system in humans

Although some people can voluntarily move their ears, overt reflexive control of the pinnae has been lost during the course of primate evolution. Humans and apes do not move their ears to express emotion, they do not defensively retract them when startled, and they do not point them at novel, salient, or task-relevant stimuli. Nevertheless, it is the thesis of this review that neural circuits for pinna orienting have survived in a purely vestigial state for over 25 million years. There are three lines of evidence: (1) Shifting the eyes hard to one side is accompanied by electromyographic (EMG) activity in certain ear muscles and by a barely visible (2-3 mm) curling of the dorsal edge of the pinna. (2) The capture of attention by a novel, unexpected sound emanating from behind and to one side has been found to trigger a weak EMG response in the muscle behind the corresponding ear. (3) Reflexive EMG bursts recorded during a selective attention task suggested that subjects were unconsciously attempting to orient their ears toward the relevant sounds. In addition to pinna orienting, the possibility that pinna startle might have survived in a vestigial state is also considered. It is suggested that the postauricular reflex to sudden, intense sounds constitutes a vestigial startle response, but that the reflex arc is dominated by a pathway that bypasses the main organizing center for startle.

Scaling of cerebral blood perfusion in primates and marsupials

The evolution of primates involved increasing body size, brain size and presumably cognitive ability. Cognition is related to neural activity, metabolic rate and rate of blood flow to the cerebral cortex. These parameters are difficult to quantify in living animals. This study shows that it is possible to determine the rate of cortical brain perfusion from the size of the internal carotid artery foramina in skulls of certain mammals, including haplorrhine primates and diprotodont marsupials. We quantify combined blood flow rate in both internal carotid arteries as a proxy of brain metabolism in 34 species of haplorrhine primates (0.116-145 kg body mass) and compare it to the same analysis for 19 species of diprotodont marsupials (0.014-46 kg). Brain volume is related to body mass by essentially the same exponent of 0.70 in both groups. Flow rate increases with haplorrhine brain volume to the 0.95 power, which is significantly higher than the exponent (0.75) expected for most organs according to 'Kleiber's Law'. By comparison, the exponent is 0.73 in marsupials. Thus, the brain perfusion rate increases with body size and brain size much faster in primates than in marsupials. The trajectory of cerebral perfusion in primates is set by the phylogenetically older groups (New and Old World monkeys, lesser apes) and the phylogenetically younger groups (great apes, including humans) fall near the line, with the highest perfusion. This may be associated with disproportionate increases in cortical surface area and mental capacity in the highly social, larger primates.

Molecular phylogenetic analysis of the Papionina using concatenation and species tree methods

The Papionina is a geographically widespread subtribe of African cercopithecid monkeys whose evolutionary history is of particular interest to anthropologists. The phylogenetic relationships among arboreal mangabeys (Lophocebus), baboons (Papio), and geladas (Theropithecus) remain unresolved. Molecular phylogenetic analyses have revealed marked gene tree incongruence for these taxa, and several recent concatenated phylogenetic analyses of multilocus datasets have supported different phylogenetic hypotheses. To address this issue, we investigated the phylogeny of the Lophocebus + Papio + Theropithecus group using concatenation methods, as well as alternative methods that incorporate gene tree heterogeneity to estimate a 'species tree.' Our compiled DNA sequence dataset was ∼56 kb pairs long and included 57 independent partitions. All analyses of concatenated alignments strongly supported a Lophocebus + Papio clade and a basal position for Theropithecus. The Bayesian concordance analysis supported the same phylogeny. A coalescent-based Bayesian method resulted in a very poorly resolved species tree. The topological agreement between concatenation and the Bayesian concordance analysis offers considerable support for a Lophocebus + Papio clade as the dominant relationship across the genome. However, the results of the Bayesian concordance analysis indicate that almost half the genome has an alternative history. As such, our results offer a well-supported phylogenetic hypothesis for the Papio/Lophocebus/Theropithecus trichotomy, while at the same time providing evidence for a complex evolutionary history that likely includes hybridization among lineages.

Olfactory receptor multigene family in vertebrates: from the viewpoint of evolutionary genomics

Olfaction is essential for the survival of animals. Diverse odor molecules in the environment are detected by the olfactory receptors (ORs) in the olfactory epithelium of the nasal cavity. There are ~400 and ~1,000 OR genes in the human and mouse genomes, respectively, forming the largest multigene family in mammals. The relationships between ORs and odorants are multiple-to-multiple, which allows for discriminating almost unlimited number of different odorants by a combination of ORs. However, the OR-ligand relationships are still largely unknown, and predicting the quality of odor from its molecular structure is unsuccessful.Extensive bioinformatic analyses using the whole genomes of various organisms revealed a great variation in number of OR genes among species, reflecting the diversity of their living environments. For example, higher primates equipped with a well-developed vision system and dolphins that are secondarily adapted to the aquatic life have considerably smaller numbers of OR genes than most of other mammals do. OR genes are characterized by extremely frequent gene duplications and losses. The OR gene repertories are also diverse among human individuals, explaining the diversity of odor perception such as the specific anosmia.OR genes are present in all vertebrates. The number of OR genes is smaller in teleost fishes than in mammals, while the diversity is higher in the former than the latter. Because the genome of amphioxus, the most basal chordate species, harbors vertebrate-like OR genes, the origin of OR genes can be traced back to the common ancestor of the phylum Chordata.

The blind men ‘see’ the elephant-the many faces of fatty liver disease

Nonalcoholic fatty liver disease (NAFLD) is a group of diseases with excess fat in liver in the absence of a poorly defined limit of alcohol consumption. Most common variety, a universal public health problem, is associated with insulin resistance caused by a host of genetic and epigenetic defects modulated by life style and environmental factors. In fact the term NAFLD is loose to incorporate so many etiologies except alcoholism and few other etiologies, presenting as fat in liver. However as a sign fatty liver is very important in predicting the risk of diabetes, cardiovascular disease, stroke, cirrhosis and cancer. Abnormal fat accumulation can result from several defects in nuclear receptors associated with lipid sensing, synthesis and oxidation like LXR, FXR, SREBP, ChREBP and PPAR; defects in the lipid influx-efflux channels, insulin signaling, proteins involved in fatty acid catabolism, defects in adipose tissue development and function, inappropriate nutrition and finally defects in neural regulatory mechanisms. The progress of the disease is determined by the basic defects which results in fat accumulation, an individual’s immunological response to the accumulated fat and its derivatives and the oxidant stress response. Congregation of unrelated genetic defects under same diagnosis ‘NAFLD’ can result in inefficient patient management. Further studies are required to understand the molecular basis of fatty liver to enable a personalized management of diseases presenting as fatty liver in the absence of alcohol abuse.