The phylogeny of the hominoid primates, as indicated by DNA-DNA hybridization

Enhancer Recognition: A Transformer Encoder-Based Method with WGAN-GP for Data Augmentation

Enhancers are located upstream or downstream of key deoxyribonucleic acid (DNA) sequences in genes and can adjust the transcription activity of neighboring genes. Identifying enhancers and determining their functions are important for understanding gene regulatory networks and expression regulatory mechanisms. However, traditional enhancer recognition relies on manual feature engineering, which is time-consuming and labor-intensive, making it difficult to perform large-scale recognition analysis. In addition, if the original dataset is too small, there is a risk of overfitting. In recent years, emerging methods, such as deep learning, have provided new insights for enhancing identification. However, these methods also present certain challenges. Deep learning models typically require a large amount of high-quality data, and data acquisition demands considerable time and resources. To address these challenges, in this paper, we propose a data-augmentation method based on generative adversarial networks to solve the problem of small datasets. Moreover, we used regularization methods such as weight decay to improve the generalizability of the model and alleviate overfitting. The Transformer encoder was used as the main component to capture the complex relationships and dependencies in enhancer sequences. The encoding layer was designed based on the principle of k-mers to preserve more information from the original DNA sequence. Compared with existing methods, the proposed approach made significant progress in enhancing the accuracy and strength of enhancer identification and prediction, demonstrating the effectiveness of the proposed method. This paper provides valuable insights for enhancer analysis and is of great significance for understanding gene regulatory mechanisms and studying disease correlations.

Genome sequencing and application of Taiwanese macaque Macaca cyclopis

Formosan macaque (Macaca cyclopis) is the only non-human primate in Taiwan Island. We performed de novo hybrid assembly for M. cyclopis using Illumina paired-end short reads, mate-pair reads and Nanopore long reads and obtained 5065 contigs with a N50 of 2.66 megabases. M. cyclopis contigs >  = 10 kb were assigned to chromosomes using Indian rhesus macaque (Macaca mulatta mulatta) genome assembly Mmul_10 as reference, resulting in a draft of M. cyclopis genome of 2,846,042,475 bases, distributed in 21 chromosomes. The draft genome contains 23,462 transcriptional origins (genes), capable of expressing 716,231 exons in 59,484 transcripts. Genome-based phylogenetic study using the assembled M. cyclopis genome together with genomes of four other macaque species, human, orangutan and chimpanzee showed similar result as previously reported. However, the M. cyclopis species was found to diverge from Chinese M. mulatta lasiota about 1.8 million years ago. Fossil gene analysis detected the presence of gap and pol endogenous viral elements of simian retrovirus in all macaques tested, including M. fascicularis, M. m. mulatta and M. cyclopis. However, M. cyclopis showed ~ 2 times less in number and more uniform in chromosomal locations. The constrain in foreign genome disturbance, presumably due to geographical isolation, should be able to simplify genomics-related investigations, making M. cyclopis an ideal primate species for medical research.

Comparative physiological anthropogeny: exploring molecular underpinnings of distinctly human phenotypes

Anthropogeny is a classic term encompassing transdisciplinary investigations of the origins of the human species. Comparative anthropogeny is a systematic comparison of humans and other living nonhuman hominids (so-called "great apes"), aiming to identify distinctly human features in health and disease, with the overall goal of explaining human origins. We begin with a historical perspective, briefly describing how the field progressed from the earliest evolutionary insights to the current emphasis on in-depth molecular and genomic investigations of "human-specific" biology and an increased appreciation for cultural impacts on human biology. While many such genetic differences between humans and other hominids have been revealed over the last two decades, this information remains insufficient to explain the most distinctive phenotypic traits distinguishing humans from other living hominids. Here we undertake a complementary approach of "comparative physiological anthropogeny," along the lines of the preclinical medical curriculum, i.e., beginning with anatomy and considering each physiological system and in each case considering genetic and molecular components that are relevant. What is ultimately needed is a systematic comparative approach at all levels from molecular to physiological to sociocultural, building networks of related information, drawing inferences, and generating testable hypotheses. The concluding section will touch on distinctive considerations in the study of human evolution, including the importance of gene-culture interactions.

Systematics of Miocene apes: State of the art of a neverending controversy

Hominoids diverged from cercopithecoids during the Oligocene in Afro-Arabia, initially radiating in that continent and subsequently dispersing into Eurasia. From the Late Miocene onward, the geographic range of hominoids progressively shrank, except for hominins, which dispersed out of Africa during the Pleistocene. Although the overall picture of hominoid evolution is clear based on available fossil evidence, many uncertainties persist regarding the phylogeny and paleobiogeography of Miocene apes (nonhominin hominoids), owing to their sparse record, pervasive homoplasy, and the decimated current diversity of this group. We review Miocene ape systematics and evolution by focusing on the most parsimonious cladograms published during the last decade. First, we provide a historical account of the progress made in Miocene ape phylogeny and paleobiogeography, report an updated classification of Miocene apes, and provide a list of Miocene ape species-locality occurrences together with an analysis of their paleobiodiversity dynamics. Second, we discuss various critical issues of Miocene ape phylogeny and paleobiogeography (hylobatid and crown hominid origins, plus the relationships of Oreopithecus) in the light of the highly divergent results obtained from cladistic analyses of craniodental and postcranial characters separately. We conclude that cladistic efforts to disentangle Miocene ape phylogeny are potentially biased by a long-branch attraction problem caused by the numerous postcranial similarities shared between hylobatids and hominids-despite the increasingly held view that they are likely homoplastic to a large extent, as illustrated by Sivapithecus and Pierolapithecus-and further aggravated by abundant missing data owing to incomplete preservation. Finally, we argue that-besides the recovery of additional fossils, the retrieval of paleoproteomic data, and a better integration between cladistics and geometric morphometrics-Miocene ape phylogenetics should take advantage of total-evidence (tip-dating) Bayesian methods of phylogenetic inference combining morphologic, molecular, and chronostratigraphic data. This would hopefully help ascertain whether hylobatid divergence was more basal than currently supported.

Evolution and molecular interactions of major histocompatibility complex (MHC)-G, -E and -F genes

Classical HLA (Human Leukocyte Antigen) is the Major Histocompatibility Complex (MHC) in man. HLA genes and disease association has been studied at least since 1967 and no firm pathogenic mechanisms have been established yet. HLA-G immune modulation gene (and also -E and -F) are starting the same arduous way: statistics and allele association are the trending subjects with the same few results obtained by HLA classical genes, i.e., no pathogenesis may be discovered after many years of a great amount of researchers’ effort. Thus, we believe that it is necessary to follow different research methodologies: (1) to approach this problem, based on how evolution has worked maintaining together a cluster of immune-related genes (the MHC) in a relatively short chromosome area since amniotes to human at least, i.e., immune regulatory genes (MHC-G, -E and -F), adaptive immune classical class I and II genes, non-adaptive immune genes like (C2, C4 and Bf) (2); in addition to using new in vitro models which explain pathogenetics of HLA and disease associations. In fact, this evolution may be quite reliably studied during about 40 million years by analyzing the evolution of MHC-G, -E, -F, and their receptors (KIR—killer-cell immunoglobulin-like receptor, NKG2—natural killer group 2-, or TCR-T-cell receptor—among others) in the primate evolutionary lineage, where orthology of these molecules is apparently established, although cladistic studies show that MHC-G and MHC-B genes are the ancestral class I genes, and that New World apes MHC-G is paralogous and not orthologous to all other apes and man MHC-G genes. In the present review, we outline past and possible future research topics: co-evolution of adaptive MHC classical (class I and II), non-adaptive (i.e., complement) and modulation (i.e., non-classical class I) immune genes may imply that the study of full or part of MHC haplotypes involving several loci/alleles instead of single alleles is important for uncovering HLA and disease pathogenesis. It would mainly apply to starting research on HLA-G extended haplotypes and disease association and not only using single HLA-G genetic markers.

Fossil apes and human evolution

Humans diverged from apes (chimpanzees, specifically) toward the end of the Miocene ~9.3 million to 6.5 million years ago. Understanding the origins of the human lineage (hominins) requires reconstructing the morphology, behavior, and environment of the chimpanzee-human last common ancestor. Modern hominoids (that is, humans and apes) share multiple features (for example, an orthograde body plan facilitating upright positional behaviors). However, the fossil record indicates that living hominoids constitute narrow representatives of an ancient radiation of more widely distributed, diverse species, none of which exhibit the entire suite of locomotor adaptations present in the extant relatives. Hence, some modern ape similarities might have evolved in parallel in response to similar selection pressures. Current evidence suggests that hominins originated in Africa from Miocene ape ancestors unlike any living species.

Functional Characterisation of Three Glycine N-Acyltransferase Variants and the Effect on Glycine Conjugation to Benzoyl-CoA

The glycine conjugation pathway in humans is involved in the metabolism of natural substrates and the detoxification of xenobiotics. The interactions between the various substrates in this pathway and their competition for the pathway enzymes are currently unknown. The pathway consists of a mitochondrial xenobiotic/medium-chain fatty acid: coenzyme A (CoA) ligase (ACSM2B) and glycine N-acyltransferase (GLYAT). The catalytic mechanism and substrate specificity of both of these enzymes have not been thoroughly characterised. In this study, the level of evolutionary conservation of GLYAT missense variants and haplotypes were analysed. From these data, haplotype variants were selected (156Asn > Ser, [17Ser > Thr,156Asn > Ser] and [156Asn > Ser,199Arg > Cys]) in order to characterise the kinetic mechanism of the enzyme over a wide range of substrate concentrations. The 156Asn > Ser haplotype has the highest frequency and the highest relative enzyme activity in all populations studied, and hence was used as the reference in this study. Cooperative substrate binding was observed, and the kinetic data were fitted to a two-substrate Hill equation. The coding region of the GLYAT gene was found to be highly conserved and the rare 156Asn > Ser,199Arg > Cys variant negatively affected the relative enzyme activity. Even though the 156Asn > Ser,199Arg > Cys variant had a higher affinity for benzoyl-CoA (s_0.5,benz = 61.2 µM), k_cat was reduced to 9.8% of the most abundant haplotype 156Asn > Ser (s_0.5,benz = 96.6 µM), while the activity of 17Ser > Thr,156Asn > Ser (s_0.5,benz = 118 µM) was 73% of 156Asn > Ser. The in vitro kinetic analyses of the effect of the 156Asn > Ser,199Arg > Cys variant on human GLYAT enzyme activity indicated that individuals with this haplotype might have a decreased ability to metabolise benzoate when compared to individuals with the 156Asn > Ser variant. Furthermore, the accumulation of acyl-CoA intermediates can inhibit ACSM2B leading to a reduction in mitochondrial energy production.

Insights into human evolution from 60 years of research on chimpanzees at Gombe

Sixty years of research on chimpanzees (Pan troglodytes) at Gombe National Park, Tanzania have revealed many similarities with human behaviour, including hunting, tool use, and coalitionary killing. The close phylogenetic relationship between chimpanzees and humans suggests that these traits were present in the last common ancestor of Pan and Homo (LCAPH). However, findings emerging from studies of our other closest living relative, the bonobo (Pan paniscus), indicate that either bonobos are derived in these respects, or the many similarities between chimpanzees and humans evolved convergently. In either case, field studies provide opportunities to test hypotheses for how and why our lineage has followed its peculiar path through the adaptive landscape. Evidence from primate field studies suggests that the hominin path depends on our heritage as apes: inefficient quadrupeds with grasping hands, orthograde posture, and digestive systems that require high quality foods. Key steps along this path include: (1) changes in diet; (2) increased use of tools; (3) bipedal gait; (4) multilevel societies; (5) collective foraging, including a sexual division of labor and extensive food transfers; and (6) language. Here I consider some possible explanations for these transitions, with an emphasis on contributions from Gombe.

Analyses of the genetic diversity and protein expression variation of the acyl: CoA medium-chain ligases, ACSM2A and ACSM2B

Benzoate (found in milk and widely used as preservative), salicylate (present in fruits and the active component of aspirin), dietary polyphenols produced by gut microbiota, metabolites from organic acidemias, and medium-chain fatty acids (MCFAs) are all metabolised/detoxified by the glycine conjugation pathway. Xenobiotics are first activated to an acyl-CoA by the mitochondrial xenobiotic/medium-chain fatty acid: CoA ligases (ACSMs) and subsequently conjugated to glycine by glycine N-acyltransferase (GLYAT). The MCFAs are activated to acyl-CoA by the ACSMs before entering mitochondrial β-oxidation. This two-step enzymatic pathway has, however, not been thoroughly investigated and the biggest gap in the literature remains the fact that studies continuously characterise the pathway as a one-step reaction. There are no studies available on the interaction/competition of the various substrates involved in the pathway, whilst very little research has been done on the ACSM ligases. To identify variants/haplotypes that should be characterised in future detoxification association studies, this study assessed the naturally observed sequence diversity and protein expression variation of ACSM2A and ACSM2B. The allelic variation, haplotype diversity, Tajima's D values, and phylogenetic analyses indicated that ACSM2A and ACSM2B are highly conserved. This confirmed an earlier hypothesis that the glycine conjugation pathway is highly conserved and essential for life as it maintains the CoA and glycine homeostasis in the liver mitochondria. The protein expression analyses showed that ACSM2A is the predominant transcript in liver. Future studies should investigate the effect of the variants identified in this study on the substrate specificity of these proteins.

Biochemical, Cellular, Physiological, and Pathological Consequences of Human Loss of N-Glycolylneuraminic Acid

About 2-3 million years ago, Alu-mediated deletion of a critical exon in the CMAH gene became fixed in the hominin lineage ancestral to humans, possibly through a stepwise process of selection by pathogen targeting of the CMAH product (the sialic acid Neu5Gc), followed by reproductive isolation through female anti-Neu5Gc antibodies. Loss of CMAH has occurred independently in some other lineages, but is functionally intact in Old World primates, including our closest relatives, the chimpanzee. Although the biophysical and biochemical ramifications of losing tens of millions of Neu5Gc hydroxy groups at most cell surfaces remains poorly understood, we do know that there are multiscale effects functionally relevant to both sides of the host-pathogen interface. Hominin CMAH loss might also contribute to understanding human evolution, at the time when our ancestors were starting to use stone tools, increasing their consumption of meat, and possibly hunting. Comparisons with chimpanzees within ethical and practical limitations have revealed some consequences of human CMAH loss, but more has been learned by using a mouse model with a human-like Cmah inactivation. For example, such mice can develop antibodies against Neu5Gc that could affect inflammatory processes like cancer progression in the face of Neu5Gc metabolic incorporation from red meats, display a hyper-reactive immune system, a human-like tendency for delayed wound healing, late-onset hearing loss, insulin resistance, susceptibility to muscular dystrophy pathologies, and increased sensitivity to multiple human-adapted pathogens involving sialic acids. Further studies in such mice could provide a model for other human-specific processes and pathologies involving sialic acid biology that have yet to be explored.

DNA DIVERGENCE AMONG HOMINOIDS

We have determined the degree of single-copy DNA divergence among the extant members of the Hominoidea employing the technique of DNA-DNA hybridization. The species studied include humans, two species of chimpanzees, gorillas, two subspecies of orangutans, and two species of gibbons; as an outgroup we have used a member of the Old World monkeys (Cercopithecidae), the baboon. Our methods are different from those previously used and allow us to control for two factors other than base-pair mismatch that can affect the thermal stability of DNA duplexes: the base composition and duplex length. In addition, we have studied more than one individual for most species and thus are able to assess the effect of intraspecific variation on phylogenetic conclusions. The results indicate that the closest extant relatives of humans are the chimpanzees. Gorillas are the next closest, followed by orangutans and gibbons. This result is strongly supported statistically, as there is virtually no overlap in measurements between different taxa. Our conclusions are in agreement with a growing amount of molecular evidence supporting this pattern of relatedness. The data behave as a reasonably good molecular clock, and we do not see an indication of slowdown in molecular evolution in the clade containing humans and African apes, contrary to what has been documented for protein-coding regions. Because of the clocklike nature of the results, we have estimated that the divergence of humans and chimpanzees occurred about 6-8 million years ago. Results from orangutans indicate that the Borneo and Sumatra populations are genetically distinct, about as different as the named species of chimpanzees.

MOLECULAR EVOLUTIONARY DIVERGENCE AMONG NORTH AMERICAN CAVE CRICKETS. II. DNA-DNA HYBRIDIZATION

Single-copy DNA divergence among 23 populations of cave crickets belonging to two genera (Euhadenoecus and Hadenoecus) has been determined by DNA-DNA hybridization employing the TEACL method. These same populations have been studied for allozyme variation (Caccone and Sbordoni, 1987). In addition, a European relative (Dolichopoda laetitiae) has been included as an outgroup for rooting the phylogeny. One of the most remarkable findings is the large degree of DNA divergence among these species and populations. A ΔT_m of up to 5°C has been found between populations of the same species; even further divergence is indicated by a lowered normalized percentage of reassociation. A phylogeny was constructed and tested for synchrony of rates, i.e., a molecular clock. Statistically, we could not reject the clock hypothesis. Attempts to calibrate the clock led to the conclusion that these insects are among the fastest evolving (with respect to single-copy DNA) groups yet studied-at least as fast as Drosophila and sea urchins-where a ΔT_m of 1°C indicates 0.5 to 1.5 MY since the last common ancestor. In general, the phylogeny derived from the DNA data agrees with that derived from isozymes. Nei's D and ΔT_m are correlated; in this group a D of 0.1 corresponds to a ΔT_m of about 1.5°C. This indicates that, relative to total single-copy DNA, the protein-coding regions of the genome are slowly evolving.

EVOLUTIONARY IMPLICATIONS OF DNA DIVERGENCE IN THE DROSOPHILA OBSCURA GROUP

Using DNA-DNA hybridization, we have determined the degree of single-copy DNA (scDNA) divergence among eight species of the Drosophila obscura group. These include Old World and New World species as well as members of two subgroups. Contrary to classical systematics, members of the affinis subgroup are more closely related to American members of the obscura subgroup than are Old World species. The Old World species are not a monophyletic group. The degree of scDNA divergence among species is not necessarily correlated with morphology, chromosomal divergence, or ability to form hybrids. A unique pattern of hybrid formation was found: species separated by a ΔT_m of 6.5°C can form hybrids whereas species separated by a ΔT_m of 2.5°C cannot. As with other groups of Drosophila, the obscura group has discrete parts of the genome evolving at very different rates. The slow evolving fraction of the nuclear genome is evolving at about the same rate as mitochondrial DNA. The additional scDNA divergence accompanying the step from partial reproductive isolation (between North American pseudoobscura and the isolated Bogotà population) to full isolation is very small. The resolution of the technique was challenged by five closely related taxa with a maximum ΔT_m of 2.5°C separating them; the taxa were unambiguously resolved and the "correct" phylogeny recovered. Finally, there is some indication that scDNA in the obscura group may be evolving considerably slower than in the melanogaster subgroup.

HALDANE'S RULE AND SEX BIASSED GENE FLOW BETWEEN TWO HYBRIDIZING FLYCATCHER SPECIES (FICEDULA ALBICOLLIS AND F. HYPOLEUCA, AVES: MUSCICAPIDAE)

The collared flycatcher (Ficedula albicollis) and the pied flycatcher (F. hypoleuca) hybridize where their geographic ranges overlap. Restriction fragment comparison of 5% of the mitochondrial genome showed a sequence divergence of 10% between these flycatcher species. This degree of sequence divergence between a closely related pair of bird species is unusually high and contrasts with the low level of divergence between F. albicollis and F. hypoleuca in nuclear genes (Nei's D = 0.0006) revealed by enzyme electrophoresis. The low nuclear differentiation is explained by sex biassed gene flow and introgression in nuclear genes (via fertile male hybrids), while the high mitochondrial DNA sequence divergence is preserved by sterility of female hybrids, which prevents mitochondrial introgression. This pattern is in accordance with Haldane's rule and is supported by field data on hybrid fertility. The high mtDNA differentiation could be explained by transfer of mitochondrial DNA from a third species during a past period of hybridization.

HISTORICAL EXAMINATION OF DELAYED PLUMAGE MATURATION IN THE SHOREBIRDS (AVES: CHARADRIIFORMES)

Delayed plumage maturation refers to the presence of nonadultlike immature plumages (juvenal plumage excluded). It is usually considered the result of selection for distinctive first-winter or first-summer appearance. In the present study, evolution of delayed plumage maturation is examined in the shorebirds: the sandpipers, plovers, gulls, and their allies. Nine plumage-maturation characters were identified, and their states were superimposed onto topologies generated during two recent investigations of shorebird relationships (Sibley and Ahlquist; revised Strauch). The characters were then optimized so as to assign character states to interior nodes of the trees in the most parsimonious way. Reconstructions of character evolution on six of the shortest revised Strauch trees were ambiguous with respect to delayed plumage maturation in the hypothetical ancestral shorebird. If plumage maturation was not delayed in the shorebird ancestor, optimization indicated that delay appeared when nonadultlike juvenal feathers were acquired. In contrast, on the single Sibley and Ahlquist tree, absence of delayed plumage maturation in the shorebird ancestor was indicated unambiguously, with three evolutionary novelties (nonadultlike juvenal feathers, seasonal plumage change, and a reduced first-spring molt) implicated in its acquisition. Optimization indicated that delayed plumage maturation in shorebirds can be explained plausibly without invoking selection for distinctive first-winter or first-summer appearance. Two of the novel conditions generating delayed plumage maturation (modified juvenal feathers and seasonal plumage change) did so only because they were acquired in a taxon possessing restricted first-year molts, which are primitive. Given these observations, it seems simplest to explain the delay in plumage maturation as an incidental consequence of the phylogenetic inertia of shorebird molts. The third novelty that generates delayed plumage maturation, a reduced first-spring molt, may have been acquired to reduce molt-associated energetic demands in young birds.

PHYLOGENIES FROM RESTRICTION SITES: A MAXIMUM-LIKELIHOOD APPROACH

Restriction sites data can be analyzed by maximum likelihood to obtain estimates of phylogenies. The likelihood methods of Smouse and Li, who were able to compute likelihoods for up to four species under a simplified model of base change, can be extended numerically to deal with any number of species. The computational methods for doing so are outlined. The resulting algorithms are slow but take multiple gains and losses of restriction sites fully into account, unlike parsimony methods. They allow for the failure to observe potential sites that are absent from all species. Analysis of the five-species hominoid data of Ferris and coworkers confirms the pattern found by Smouse and Li with four species-that a chimpanzee-gorilla clade is favored, but not statistically significantly over other tree topologies. A large data set produced by computer simulation has also been analyzed to confirm that the method works properly. The methods used here do not allow for different rates of transitions and transversions. They can be extended to do so, but only at a cost of considerably slower computations. The present method is available in a computer program.

Loss of CMAH during Human Evolution Primed the Monocyte-Macrophage Lineage toward a More Inflammatory and Phagocytic State

Humans and chimpanzees are more sensitive to endotoxin than are mice or monkeys, but any underlying differences in inflammatory physiology have not been fully described or understood. We studied innate immune responses in Cmah^-/- mice, emulating human loss of the gene encoding production of Neu5Gc, a major cell surface sialic acid. CMP-N-acetylneuraminic acid hydroxylase (CMAH) loss occurred ∼2-3 million years ago, after the common ancestor of humans and chimpanzees, perhaps contributing to speciation of the genus HomoCmah^-/- mice manifested a decreased survival in endotoxemia following bacterial LPS injection. Macrophages from Cmah^-/- mice secreted more inflammatory cytokines with LPS stimulation and showed more phagocytic activity. Macrophages and whole blood from Cmah^-/- mice also killed bacteria more effectively. Metabolic reintroduction of Neu5Gc into Cmah^-/- macrophages suppressed these differences. Cmah^-/- mice also showed enhanced bacterial clearance during sublethal lung infection. Although monocytes and monocyte-derived macrophages from humans and chimpanzees exhibited marginal differences in LPS responses, human monocyte-derived macrophages killed Escherichia coli and ingested E. coli BioParticles better. Metabolic reintroduction of Neu5Gc into human macrophages suppressed these differences. Although multiple mechanisms are likely involved, one cause is altered expression of C/EBPβ, a transcription factor affecting macrophage function. Loss of Neu5Gc in Homo likely had complex effects on immunity, providing greater capabilities to clear sublethal bacterial challenges, possibly at the cost of endotoxic shock risk. This trade-off may have provided a selective advantage when Homo transitioned to butchery using stone tools. The findings may also explain why the Cmah^-/- state alters severity in mouse models of human disease.

A Programmable DNA Double-Write Material: Synergy of Photolithography and Self-Assembly Nanofabrication

We demonstrate a DNA double-write process that uses UV to pattern a uniquely designed DNA write material, which produces two distinct binding identities for hybridizing two different complementary DNA sequences. The process requires no modification to the DNA by chemical reagents and allows programmed DNA self-assembly and further UV patterning in the UV exposed and nonexposed areas. Multilayered DNA patterning with hybridization of fluorescently labeled complementary DNA sequences, biotin probe/fluorescent streptavidin complexes, and DNA patterns with 500 nm line widths were all demonstrated.

Histories of molecules: Reconciling the past

Molecular data and methods have become centrally important to evolutionary analysis, largely because they have enabled global phylogenetic reconstructions of the relationships between organisms in the tree of life. Often, however, molecular stories conflict dramatically with morphology-based histories of lineages. The evolutionary origin of animal groups provides one such case. In other instances, different molecular analyses have so far proved irreconcilable. The ancient and major divergence of eukaryotes from prokaryotic ancestors is an example of this sort of problem. Efforts to overcome these conflicts highlight the role models play in phylogenetic reconstruction. One crucial model is the molecular clock; another is that of 'simple-to-complex' modification. I will examine animal and eukaryote evolution against a backdrop of increasing methodological sophistication in molecular phylogeny, and conclude with some reflections on the nature of historical science in the molecular era of phylogeny.

Antimicrobial potential of 27 plants consumed by chimpanzees (Pan troglodytes verus Blumenbach) in Ivory Coast

BACKGROUND

Due to their genetic proximity, chimpanzees share with human several diseases including bacterial, fungal and viral infections, such as candidiasis, acquired immune deficiency syndrome (AIDS), Ebola virus disease. However, in its natural environment, chimpanzees are tolerant to several pathogens including simian immunodeficiency virus (SIV), virus related to human immunodeficiency virus (HIV) that contribute to the emergence of opportunistic diseases such as microbial infections.

METHODS

Twenty seven species of plants consumed by chimpanzees were evaluated for their antimicrobial potential against Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, Candida albicans, Candida tropicalis and Candida glabrata using the agar diffusion technique and micro-dilution in 96-well plates. In total 132 extracts (33 dichloromethane, 33 methanol, 33 ethyl acetate and 33 aqueous) were tested.

RESULTS

The results showed that 24 extracts (18 %) showed activity against bacteria and 6 extracts (5 %) were active against yeasts. The minimal inhibitory concentrations (MICs) values of active extracts ranged between 23 and 750 μg/ml for bacteria and between 188 and 1500 μg/ml for yeasts.

CONCLUSION

Tristemma coronatum was the most promising on the studied microorganisms followed by Beilschmiedia mannii. The extracts of the two plants indicated by chimpanzees have potential for antimicrobial use in human.

Conservation of the coding regions of the glycine N-acyltransferase gene further suggests that glycine conjugation is an essential detoxification pathway

Thorough investigation of the glycine conjugation pathway has been neglected. No defect of the glycine conjugation pathway has been reported and this could reflect the essential role of glycine conjugation in hepatic metabolism. Therefore, we hypothesised that genetic variation in the open reading frame (ORF) of the GLYAT gene should be low and that deleterious alleles would be found at low frequencies. This hypothesis was investigated by analysing the genetic variation of the human GLYAT ORF using data available in public databases. We also sequenced the GLYAT ORF of a small cohort of South African Afrikaner Caucasian individuals. In total, data from 1537 individuals was analysed. The two most prominent GLYAT haplotypes in all populations analysed, were S156 (70%) and T17S156 (20%). The S156C199 and S156H131 haplotypes, which have a negative effect on the enzyme activity of a recombinant human GLYAT, were detected at very low frequencies. In the Afrikaner Caucasian cohort a novel Q61L SNP occurring at a high frequency (12%) was detected. The results of this study indicated that the GLYAT ORF is highly conserved and supported the hypothesis that the glycine conjugation pathway is an essential detoxification pathway. These findings emphasise the importance of future investigations to determine the in vivo capacity of the glycine conjugation pathway for the detoxification of benzoate and other xenobiotics.

Identification and functional comparison of seven-transmembrane G-protein-coupled BILF1 receptors in recently discovered nonhuman primate lymphocryptoviruses

Coevolution of herpesviruses with their respective host has resulted in a delicate balance between virus-encoded immune evasion mechanisms and host antiviral immunity. BILF1 encoded by human Epstein-Barr virus (EBV) is a 7-transmembrane (7TM) G-protein-coupled receptor (GPCR) with multiple immunomodulatory functions, including attenuation of PKR phosphorylation, activation of G-protein signaling, and downregulation of major histocompatibility complex (MHC) class I surface expression. In this study, we explored the evolutionary and functional relationships between BILF1 receptor family members from EBV and 12 previously uncharacterized nonhuman primate (NHP) lymphocryptoviruses (LCVs). Phylogenetic analysis defined 3 BILF1 clades, corresponding to LCVs of New World monkeys (clade A) or Old World monkeys and great apes (clades B and C). Common functional properties were suggested by a high degree of sequence conservation in functionally important regions of the BILF1 molecules. A subset of BILF1 receptors from EBV and LCVs from NHPs (chimpanzee, orangutan, marmoset, and siamang) were selected for multifunctional analysis. All receptors exhibited constitutive signaling activity via G protein Gαi and induced activation of the NF-κB transcription factor. In contrast, only 3 of 5 were able to activate NFAT (nuclear factor of activated T cells); chimpanzee and orangutan BILF1 molecules were unable to activate NFAT. Similarly, although all receptors were internalized, BILF1 from the chimpanzee and orangutan displayed an altered cellular localization pattern with predominant cell surface expression. This study shows how biochemical characterization of functionally important orthologous viral proteins can be used to complement phylogenetic analysis to provide further insight into diverse microbial evolutionary relationships and immune evasion function.

IMPORTANCE

Epstein-Barr virus (EBV), known as an oncovirus, is the only human herpesvirus in the genus Lymphocryptovirus (LCV). EBV uses multiple strategies to hijack infected host cells, establish persistent infection in B cells, and evade antiviral immune responses. As part of EBV's immune evasion strategy, the virus encodes a multifunctional 7-transmembrane (7TM) G-protein-coupled receptor (GPCR), EBV BILF1. In addition to multiple immune evasion-associated functions, EBV BILF1 has transforming properties, which are linked to its high constitutive activity. We identified BILF1 receptor orthologues in 12 previously uncharacterized LCVs from nonhuman primates (NHPs) of Old and New World origin. As 7TM receptors are excellent drug targets, our unique insight into the molecular mechanism of action of the BILF1 family and into the evolution of primate LCVs may enable validation of EBV BILF1 as a drug target for EBV-mediated diseases, as well as facilitating the design of drugs targeting EBV BILF1.

The long and winding road of molecular data in phylogenetic analysis

The use of molecules and reactions as evidence, markers and/or traits for evolutionary processes has a history more than a century long. Molecules have been used in studies of intra-specific variation and studies of similarity among species that do not necessarily result in the analysis of phylogenetic relations. Promoters of the use of molecular data have sustained the need for quantification as the main argument to make use of them. Moreover, quantification has allowed intensive statistical analysis, as a condition and a product of increasing automation. All of these analyses are subject to the methodological anxiety characteristic of a community in search of objectivity (Suárez-Díaz and Anaya-Muñoz, Stud Hist Philos Biol Biomed Sci 39:451-458, 2008). It is in this context that scientists compared and evaluated protein and nucleic acid sequence data with other types of molecular data - including immunological, electrophoretic and hybridization data. This paper argues that by looking at long-term historical processes, such as the use of molecular evidence in evolutionary biology, we gain valuable insights into the history of science. In that sense, it accompanies a growing concern among historians for big-pictures of science that incorporate the fruitful historical research on local cases of the last decades.

Reconstructing the demographic history of the human lineage using whole-genome sequences from human and three great apes

The demographic history of human would provide helpful information for identifying the evolutionary events that shaped the humanity but remains controversial even in the genomic era. To settle the controversies, we inferred the speciation times (T) and ancestral population sizes (N) in the lineage leading to human and great apes based on whole-genome alignment. A coalescence simulation determined the sizes of alignment blocks and intervals between them required to obtain recombination-free blocks with a high frequency. This simulation revealed that the size of the block strongly affects the parameter inference, indicating that recombination is an important factor for achieving optimum parameter inference. From the whole genome alignments (1.9 giga-bases) of human (H), chimpanzee (C), gorilla (G), and orangutan, 100-bp alignment blocks separated by ≥5-kb intervals were sampled and subjected to estimate τ = μT and θ = 4μgN using the Markov chain Monte Carlo method, where μ is the mutation rate and g is the generation time. Although the estimated τ_HC differed across chromosomes, τ_HC and τ_HCG were strongly correlated across chromosomes, indicating that variation in τ is subject to variation in μ, rather than T, and thus, all chromosomes share a single speciation time. Subsequently, we estimated Ts of the human lineage from chimpanzee, gorilla, and orangutan to be 6.0–7.6, 7.6–9.7, and 15–19 Ma, respectively, assuming variable μ across lineages and chromosomes. These speciation times were consistent with the fossil records. We conclude that the speciation times in our recombination-free analysis would be conclusive and the speciation between human and chimpanzee was a single event.

Molecular evidence for the presence of Rickettsia Felis in the feces of wild-living African apes

BACKGROUND

Rickettsia felis is a common emerging pathogen detected in mosquitoes in sub-Saharan Africa. We hypothesized that, as with malaria, great apes may be exposed to the infectious bite of infected mosquitoes and release R. felis DNA in their feces.

METHODS

We conducted a study of 17 forest sites in Central Africa, testing 1,028 fecal samples from 313 chimpanzees, 430 gorillas and 285 bonobos. The presence of rickettsial DNA was investigated by specific quantitative real-time PCR. Positive results were confirmed by a second PCR using primers and a probe targeting a specific gene for R. felis. All positive samples were sequenced.

RESULTS

Overall, 113 samples (11%) were positive for the Rickettsia-specific gltA gene, including 25 (22%) that were positive for R. felis. The citrate synthase (gltA) sequence and outer membrane protein A (ompA) sequence analysis indicated 99% identity at the nucleotide level to R. felis. The 88 other samples (78%) were negative using R. felis-specific qPCR and were compatible with R. felis-like organisms.

CONCLUSION

For the first time, we detected R. felis in wild-living ape feces. This non invasive detection of human pathogens in endangered species opens up new possibilities in the molecular epidemiology and evolutionary analysis of infectious diseases, beside HIV and malaria.

The lemur revolution starts now: the genomic coming of age for a non-model organism

Morris Goodman was a revolutionary. Together with a mere handful of like-minded scientists, Morris established himself as a leader in the molecular phylogenetic revolution of the 1960s. The effects of this revolution are most evident in this journal, which he founded in 1992. Happily for lemur biologists, one of Morris Goodman's primary interests was in reconstructing the phylogeny of the primates, including the tooth-combed Lorisifomes of Africa and Asia, and the Lemuriformes of Madagascar (collectively referred to as the suborder Strepsirrhini). This paper traces the development of molecular phylogenetic and evolutionary genetic trends and methods over the 50-year expanse of Morris Goodman's career, particularly as they apply to our understanding of lemuriform phylogeny, biogeography, and biology. Notably, this perspective reveals that the lemuriform genome is sufficiently rich in phylogenetic signal such that the very earliest molecular phylogenetic studies - many of which were conducted by Goodman himself - have been validated by contemporary studies that have exploited advanced computational methods applied to phylogenomic scale data; studies that were beyond imagining in the earliest days of phylogeny reconstruction. Nonetheless, the frontier still beckons. New technologies for gathering and analyzing genomic data will allow investigators to build upon what can now be considered a nearly-known phylogeny of the Lemuriformes in order to ask innovative questions about the evolutionary mechanisms that generate and maintain the extraordinary breadth and depth of biological diversity within this remarkable clade of primates.

Molecular phylogenetics by direct comparison of tandem mass spectra

RATIONALE

Molecular phylogenetics is the study of evolution and relatedness of organisms or genes. Mass spectrometry is used routinely for bacterial identification and has also been used for phylogenetic analysis, for instance from bone material. Unfortunately, only a small fraction of the acquired tandem mass spectra allow direct interpretation.

METHODS

We describe a new algorithm and software for molecular phylogenetics using pairwise comparisons of tandem mass spectra from enzymatically digested proteins. The spectra need not be annotated and all acquired data is used in the analysis. To demonstrate the method, we analyzed tryptic digests of sera from four great apes and two other primates.

RESULTS

The distribution of spectra dot products for thousands of tandem mass spectra collected from two samples provides a measure on the fraction of shared peptides between the two samples. When inverted, this becomes a distance metric. By pairwise comparison between species and averaging over four individuals per species, it was possible to reconstruct the unique correct phylogenetic tree for the great apes and other primates.

CONCLUSIONS

The new method described here has several attractive features compared with existing methods, among them simplicity, the unbiased use of all acquired data rather than a small subset of spectra, and the potential use of heavily degraded proteins or proteins with a priori unknown modifications.

Lessons from chimpanzee-based research on human disease: the implications of genetic differences

Assertions that the use of chimpanzees to investigate human diseases is valid scientifically are frequently based on a reported 98-99% genetic similarity between the species. Critical analyses of the relevance of chimpanzee studies to human biology, however, indicate that this genetic similarity does not result in sufficient physiological similarity for the chimpanzee to constitute a good model for research, and furthermore, that chimpanzee data do not translate well to progress in clinical practice for humans. Leading examples include the minimal citations of chimpanzee research that is relevant to human medicine, the highly different pathology of HIV/AIDS and hepatitis C virus infection in the two species, the lack of correlation in the efficacy of vaccines and treatments between chimpanzees and humans, and the fact that chimpanzees are not useful for research on human cancer. The major molecular differences underlying these inter-species phenotypic disparities have been revealed by comparative genomics and molecular biology - there are key differences in all aspects of gene expression and protein function, from chromosome and chromatin structure to post-translational modification. The collective effects of these differences are striking, extensive and widespread, and they show that the superficial similarity between human and chimpanzee genetic sequences is of little consequence for biomedical research. The extrapolation of biomedical data from the chimpanzee to the human is therefore highly unreliable, and the use of the chimpanzee must be considered of little value, particularly given the breadth and potential of alternative methods of enquiry that are currently available to science.

Defining pathogenic bacterial species in the genomic era

Actual definitions of bacterial species are limited due to the current criteria of definition and the use of restrictive genetic tools. The 16S ribosomal RNA sequence, for example, has been widely used as a marker for phylogenetic analyses; however, its use often leads to misleading species definitions. According to the first genetic studies, removing a certain number of genes from pathogenic bacteria removes their capacity to infect hosts. However, more recent studies have demonstrated that the specialization of bacteria in eukaryotic cells is associated with massive gene loss, especially for allopatric endosymbionts that have been isolated for a long time in an intracellular niche. Indeed, sympatric free-living bacteria often have bigger genomes and exhibit greater resistance and plasticity and constitute species complexes rather than true species. Specialists, such as pathogenic bacteria, escape these bacterial complexes and colonize a niche, thereby gaining a species name. Their specialization allows them to become allopatric, and their gene losses eventually favor reductive genome evolution. A pathogenic species is characterized by a gene repertoire that is defined not only by genes that are present but also by those that are lacking. It is likely that current bacterial pathogens will disappear soon and be replaced by new ones that will emerge from bacterial complexes that are already in contact with humans.

Neotropical mammals and the myth of amazonian biodiversity

Data were compiled on the distribution of mammal taxa (883 species, 242 genera, 45 families, and 10 orders) among South America's six major macrohabitats: lowland Amazon forest, western montane forests, Atlantic rain forest, upland semideciduous forest, southern mesophytic forest, and drylands. The drylands are the richest area in numbers of species supported and are more diverse than the other habitats, including the lowland Amazon rain forest, when endemics are considered. An analysis of number of endemic and nonendemic taxa versus size of area found a simple positive linear relationship: the drylands, almost twice as extensive as the Amazon lowlands, support more endemic taxa. Conservation plans that emphasize the wet tropics and fail to consider the drylands as special repositories of mammal diversity will be unable to preserve a significant number of novel taxa.

Extensive genetic divergence associated with speciation in filamentous fungi

Little is known about genetic differentiation during speciation in fungi. The Collybia dryophila complex (Basidiomycetes: Tricholomataceae) contains several closely related groups of fungi at various levels of evolutionary divergence. Mating compatibility studies show there are several intersterile groups within the complex, three of which are distributed over two or more continents. Genetic relationships among five intersterility groups were compared by the method of DNA.DNA hybridization. Clustering techniques were used to reconstruct phylogenetic relationships of these fungi. Genic identity based on DNA.DNA hybridization corresponds well with mating compatibility. Reduced genic identity was observed between geographically isolated populations of a single mating group. This evidence suggests an allopatric mode of evolution for the C. dryophila group. These results indicate extensive genic divergence is associated with the appearance of intersterility barriers in basidiomycetous fungi. The levels of divergence observed in these and in other fungi are significantly higher than that observed in many other eukaryotes, and this suggests that the rate of molecular or morphological evolution in fungi may differ from that found in other organisms.

Human genome diversity: frequently asked questions

Despite our relatively large population size, humans are genetically less variable than other primates. Many allele frequencies and statistical descriptors of genome diversity form broad gradients, tracing the main expansion from Africa, local migrations, and sometimes adaptation. However, this continuous variation is discordant across loci, and principally seems to reflect different blends of common and often cosmopolitan alleles rather than the presence of distinct gene pools in different regions of the world. The elusive structure of human populations could lead to spurious associations if the effects of shared ancestry are not properly dealt with; indeed, this is among the causes (although not the only one) of the difficulties encountered in discovering the loci responsible for quantitative traits and complex diseases. However, the rapidly growing body of data on our genomic diversity has already cast new light on human population history and is now revealing intricate biological relationships among individuals and populations of our species.

Colloquium paper: phylogenomic evidence of adaptive evolution in the ancestry of humans

In Charles Darwin's tree model for life's evolution, natural selection adaptively modifies newly arisen species as they branch apart from their common ancestor. In accord with this Darwinian concept, the phylogenomic approach to elucidating adaptive evolution in genes and genomes in the ancestry of modern humans requires a well supported and well sampled phylogeny that accurately places humans and other primates and mammals with respect to one another. For more than a century, first from the comparative immunological work of Nuttall on blood sera and now from comparative genomic studies, molecular findings have demonstrated the close kinship of humans to chimpanzees. The close genetic correspondence of chimpanzees to humans and the relative shortness of our evolutionary separation suggest that most distinctive features of the modern human phenotype had already evolved during our ancestry with chimpanzees. Thus, a phylogenomic assessment of being human should examine earlier stages of human ancestry as well as later stages. In addition, with the availability of a number of mammalian genomes, similarities in phenotype between distantly related taxa should be explored for evidence of convergent or parallel adaptive evolution. As an example, recent phylogenomic evidence has shown that adaptive evolution of aerobic energy metabolism genes may have helped shape such distinctive modern human features as long life spans and enlarged brains in the ancestries of both humans and elephants.

Using comparative genomic hybridization to survey genomic sequence divergence across species: a proof-of-concept from Drosophila

Background

Genome-wide analysis of sequence divergence among species offers profound insights into the evolutionary processes that shape lineages. When full-genome sequencing is not feasible for a broad comparative study, we propose the use of array-based comparative genomic hybridization (aCGH) in order to identify orthologous genes with high sequence divergence. Here we discuss experimental design, statistical power, success rate, sources of variation and potential confounding factors. We used a spotted PCR product microarray platform from Drosophila melanogaster to assess sequence divergence on a gene-by-gene basis in three fully sequenced heterologous species (D. sechellia, D. simulans, and D. yakuba). Because complete genome assemblies are available for these species this study presents a powerful test for the use of aCGH as a tool to measure sequence divergence.

Results

We found a consistent and linear relationship between hybridization ratio and sequence divergence of the sample to the platform species. At higher levels of sequence divergence (< 92% sequence identity to D. melanogaster) ~84% of features had significantly less hybridization to the array in the heterologous species than the platform species, and thus could be identified as "diverged". At lower levels of divergence (≥ 97% identity), only 13% of genes were identified as diverged. While ~40% of the variation in hybridization ratio can be accounted for by variation in sequence identity of the heterologous sample relative to D. melanogaster, other individual characteristics of the DNA sequences, such as GC content, also contribute to variation in hybridization ratio, as does technical variation.

Conclusions

Here we demonstrate that aCGH can accurately be used as a proxy to estimate genome-wide divergence, thus providing an efficient way to evaluate how evolutionary processes and genomic architecture can shape species diversity in non-model systems. Given the increased number of species for which microarray platforms are available, comparative studies can be conducted for many interesting lineages in order to identify highly diverged genes that may be the target of natural selection.

Life history influences rates of climatic niche evolution in flowering plants

Across angiosperms, variable rates of molecular substitution are linked with life-history attributes associated with woody and herbaceous growth forms. As the number of generations per unit time is correlated with molecular substitution rates, it is expected that rates of phenotypic evolution would also be influenced by differences in generation times. Here, we make the first broad-scale comparison of growth-form-dependent rates of niche evolution. We examined the climatic niches of species on large time-calibrated phylogenies of five angiosperm clades and found that woody lineages have accumulated fewer changes per million years in climatic niche space than related herbaceous lineages. Also, climate space explored by woody lineages is consistently smaller than sister lineages composed mainly of herbaceous taxa. This pattern is probably linked to differences in the rate of climatic niche evolution. These results have implications for niche conservatism; in particular, the role of niche conservatism in the distribution of plant biodiversity. The consistent differences in the rate of climatic niche evolution also emphasize the need to incorporate models of phenotypic evolution that allow for rate heterogeneity when examining large datasets.

Chimpanzee nest distribution and site reuse in a dry habitat: implications for early hominin ranging

This paper reports on a 20-month study of chimpanzee nesting patterns in Issa, Ugalla, western Tanzania. Ugalla is one of the driest, most open, and seasonal habitats where chimpanzees are found. The methods used were ethoarchaeological, as the chimpanzees were not habituated and behavioural observations were rare. Systematic data on the spatial and temporal distribution of nests are presented. Places with no nests at the beginning of the study, despite being suitable for nesting, were used as controls. Similar to other chimpanzee study sites, nests were highly concentrated in some parts of the landscape. Issa chimpanzees preferred to nest on slopes. They extensively used the woodland vegetation type of their habitat for nesting throughout the annual cycle. Ninety percent of nest sites were used repeatedly throughout the study period, but none of the control places had nests during this period. The results indicate that chimpanzees ranged more widely during the dry season, when food abundance was lowest, food was available mainly in open vegetation types, and when drinking water was restricted to a few sources. Early hominins in similar habitats may have followed the ranging strategy of Issa chimpanzees. As with a previous study, the distribution of nests was spatially similar to archaeological distributions in early hominin sites. Hominin topography and vegetation type preferences may be misrepresented in the archaeological record. Nest sites may have been the antecedents of carcass processing sites.